H-InvDB - Topic Annotation

	H-InvDB_8.3 released on March 26, 2013.
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H-InvDB topic annotation

UM: Annotation for unmapped transcripts (UM transcripts) [Download]

Description: There are many mRNA sequences which can not be aligned correctly onto the human reference genome due to several reasons. We annotated these UM mRNA sequences and categorized them according to the reason for the failure of mapping. Here, we provide the annotated set of UM genes which are predicted to be transcribed from the gap region or from the unsequenced region of the reference genome. These UM genes are supported by at least one line of evidence other than the alignment on the human reference genome. In addition, we also provide the annotation information for the chimera transcripts which may contain trans-splicing candidates or fusion transcripts transcribed from a rearranged genome.

This topc includes three sub-topics:

1. Annotated UM genes supported by evidences other than alignment on the NCBI reference genome. Download

[Download (1)-1] Annotated UM genes supported by evidences other than alignment on the NCBI reference genome

File name: um_dlfile1.txt
Format:
1: HIX
2: Representative HIT
3: Similarity category
4: Definition
5: Supporting evidences (comma separated)
     5-1 Watson genome
     5-2 Venter genome
     5-3 Celera alternative genome (alternative b.36.3)
     5-4 Experimental evidence for translation
     5-5 Supported by two or more transcripts (reproductive)
     5-6 Conserved on the other mammal’s genome
         5-6-1 chimpanzee
         5-6-2 macaque
         5-6-3 mouse
         5-6-4 rat
6: Position
7: Annotation status (auto or manual)

HIX	Representative HIT	Similarity category	Definition	Supporting evidences (comma separated)	Position	Annotation status (auto or manual)
HIX0060313	HIT000323848	3	von Willebrand factor, type D domain containing protein.	5-1,5-2,5-3,5-5	-	manual
HIX0041649	HIT000243877	3	Homeobox domain containing protein.	5-1,5-5	-	manual
HIX0060423	HIT000192492	3	von Willebrand factor, type D domain containing protein.	5-5	-	manual
HIX0159179	HIT000326960	2	Mucin (Fragment).	5-5	-	auto
HIX0060216	HIT000026013	3	Plectin repeat containing protein.	5-2,5-3,5-5	-	manual
HIX0080310	HIT000339687	3	Coatomer, gamma subunit family protein.	5-2,5-3,5-5,5-6-1,5-6-2,5-6-3	-	auto
HIX0060229	HIT000048686	4	Conserved hypothetical protein.	5-2,5-5	-	auto
HIX0044052	HIT000067464	3	Aconitase, mitochondrial-like family protein.	5-5,5-6-3,5-6-4	-	auto
HIX0027940	HIT000043513	5	Hypothetical protein.	5-1,5-2,5-5,5-6-1	-	manual
HIX0055490	HIT000327117	3	Pyruvate kinase family protein.	5-5,5-6-3,5-6-4	-	auto
HIX0042028	HIT000099040	4	Conserved hypothetical protein.	5-2,5-3,5-5,5-6-1	-	manual
HIX0043567	HIT000064221	3	Homeobox domain containing protein.	5-5,5-6-3	-	manual
HIX0159184	HIT000332427	4	Conserved hypothetical protein.	5-1,5-3,5-5	-	auto
HIX0028063	HIT000046651	4	Conserved hypothetical protein.	5-2,5-3,5-5,5-6-1	-	manual
HIX0018463	HIT000084380	3	Ras family protein.	5-1,5-3,5-5	-	manual
HIX0017710	HIT000013787	5	Hypothetical protein.	5-1,5-2,5-3,5-5,5-6-1	-	manual
HIX0019573	HIT000026389	3	Protein of unknown function DUF1193 family protein.	5-1,5-2,5-3,5-5	-	manual
HIX0042975	HIT000061896	4	Conserved hypothetical protein.	5-1,5-5	-	manual
HIX0080315	HIT000017555	3	Zinc finger, C2H2-type domain containing protein.	5-5	-	manual
HIX0055480	HIT000327092	4	Conserved hypothetical protein.	5-5,5-6-3	-	auto
HIX0041483	HIT000216695	3	Replication initiation factor family protein.	5-5	-	manual
HIX0027949	HIT000052647	4	Conserved hypothetical protein.	5-1,5-2,5-3,5-5	-	manual
HIX0159189	HIT000063765	2	PHD finger protein 2 (GRC5).	5-5,5-6-3,5-6-4	-	auto
HIX0097813	HIT000259351	3	Chlorophyll A-B binding protein family protein.	5-5	-	auto
HIX0159191	HIT000249427	2	Transgelin-2 (SM22-alpha homolog).	5-2,5-3,5-5	-	auto
HIX0042029	HIT000031758	5	Hypothetical protein.	5-2,5-3,5-5	-	auto
HIX0159192	HIT000045138	5	Hypothetical protein.	5-2,5-5	-	auto
HIX0061037	HIT000332435	4	Conserved hypothetical protein.	5-5	-	auto
HIX0044950	HIT000070322	3	Potassium channel, voltage dependent, Kv4.2 family protein.	5-2,5-3,5-5,5-6-3,5-6-4	-	auto
HIX0023407	HIT000015937	4	Conserved hypothetical protein.	5-5,5-6-1,5-6-2,5-6-4	-	auto
HIX0080399	HIT000065455	4	Conserved hypothetical protein.	5-5	-	auto
HIX0112563	HIT000386642	5	Hypothetical protein.	5-1,5-2,5-3,5-5,5-6-1	-	manual
HIX0159194	HIT000393102	4	Conserved hypothetical protein.	5-5	-	auto
HIX0159195	HIT000332095	2	IGHM protein.	5-5,5-6-4	-	auto
HIX0097979	HIT000392343	4	Conserved hypothetical protein.	5-2,5-5	-	manual
HIX0080309	HIT000026018	4	Conserved hypothetical protein.	5-2,5-3,5-5,5-6-1	-	manual
HIX0043236	HIT000063482	3	Protein of unknown function DUF1234 family protein.	5-5,5-6-3,5-6-4	-	auto
HIX0049630	HIT000252513	4	Conserved hypothetical protein.	5-2,5-3,5-5,5-6-1	-	manual
HIX0054342	HIT000321000	3	ATPase, P-type, K/Mg/Cd/Cu/Zn/Na/Ca/Na/H-transporter family protein.	5-5,5-6-3,5-6-4	-	auto
HIX0159197	HIT000191412	2	Cytochrome P450 2A6 (EC 1.14.14.1) (CYPIIA6) (Coumarin 7-hydroxylase) (P450 IIA3) (CYP2A3) (P450(I)).	5-2,5-3,5-5	-	auto
HIX0159199	HIT000191957	2	Immunglobulin heavy chain variable region (Fragment).	5-5,5-6-3	-	auto
HIX0068099	HIT000195934	3	ATPase, V1 complex, subunit B family protein.	5-2,5-3,5-5,5-6-1,5-6-2,5-6-4	-	auto
HIX0159200	HIT000334029	1	Uncharacterized serine/threonine-protein kinase SgK494 (EC 2.7.11.1) (Sugen kinase 494). Isoform 2.	5-4,5-5	-	manual
HIX0037289	HIT000336562	3	Mammalian taste receptor family protein.	5-2,5-3,5-5,5-6-1	-	auto
HIX0113155	HIT000393254	5	Hypothetical protein.	5-1,5-5,5-6-1	-	auto
HIX0019325	HIT000038191	3	Twist family protein.	5-2,5-5,5-6-2,5-6-3,5-6-4	-	manual
HIX0060419	HIT000074350	3	Glyceraldehyde 3-phosphate dehydrogenase family protein.	5-5	-	auto
HIX0060255	HIT000056150	3	GPCR kinase domain containing protein.	5-1,5-2,5-3,5-5	-	manual
HIX0042074	HIT000193050	3	Homeobox domain containing protein.	5-5	-	manual
HIX0159202	HIT000250723	1	Dynein light chain 1, cytoplasmic (Dynein light chain LC8-type 1) (8 kDa dynein light chain) (DLC8) (Protein inhibitor of neuronal nitric oxide synthase) (PIN).	5-4,5-5	-	manual
HIX0022691	HIT000047610	4	Conserved hypothetical protein.	5-3,5-5	-	auto
HIX0159205	HIT000022694	2	Carboxyl-ester lipase.	5-2,5-5	-	auto
HIX0042026	HIT000094695	4	Conserved hypothetical protein.	5-2,5-3,5-5,5-6-1	-	manual
HIX0051085	HIT000099581	4	Conserved hypothetical protein.	5-5,5-6-1	-	auto
HIX0159206	HIT000017288	4	Conserved hypothetical protein.	5-2,5-3,5-5	-	auto
HIX0021405	HIT000079603	3	Zinc finger, C2H2-type domain containing protein.	5-2,5-3,5-5,5-6-1	-	auto
HIX0075704	HIT000332430	4	Conserved hypothetical protein.	5-1,5-3,5-5	-	auto
HIX0050885	HIT000037321	4	Conserved hypothetical protein.	5-2,5-3,5-5	-	manual
HIX0159209	HIT000026212	4	Conserved hypothetical protein.	5-1,5-5	-	auto
HIX0159210	HIT000195782	2	Mucin-3A precursor (MUC-3A) (Intestinal mucin-3A).	5-1,5-5	-	auto
HIX0080322	HIT000045447	3	RNA polymerase II, heptapeptide repeat, eukaryotic containing protein.	5-5,5-6-1	-	manual
HIX0159211	HIT000332425	4	Conserved hypothetical protein.	5-1,5-5	-	auto
HIX0159212	HIT000392815	2	Imuunoglobulin mu-chain D-J4-region (Fragment).	5-5,5-6-4	-	auto
HIX0017615	HIT000006117	4	Conserved hypothetical protein.	5-1,5-2,5-3,5-5,5-6-1	-	manual
HIX0159213	HIT000061897	4	Conserved hypothetical protein.	5-1,5-5	-	manual
HIX0072430	HIT000251585	4	Conserved hypothetical protein.	5-3,5-5	-	auto
HIX0046983	HIT000243957	3	Steroid/nuclear receptor, oncofetal protein p65 family protein.	5-5	-	manual
HIX0159215	HIT000324082	5	Hypothetical protein.	5-1,5-5	-	manual
HIX0159216	HIT000332437	4	Conserved hypothetical protein.	5-1,5-5	-	auto
HIX0061364	HIT000011443	5	Hypothetical protein.	5-1,5-5	-	manual
HIX0028061	HIT000046507	4	Conserved hypothetical protein.	5-1,5-2,5-3,5-5	-	manual
HIX0017743	HIT000022348	4	Conserved hypothetical protein.	5-2,5-3,5-5	-	manual
HIX0097994	HIT000393071	4	Conserved hypothetical protein.	5-5	-	auto
HIX0159217	HIT000090650	2	Plus agglutinin (Fragment).	5-2,5-3,5-5	-	auto
HIX0159218	HIT000250428	5	Hypothetical protein.	5-2,5-3,5-5	-	manual
HIX0027993	HIT000043320	5	Hypothetical protein.	5-1,5-2,5-3,5-5,5-6-1	-	manual
HIX0159219	HIT000332098	2	Anti-FactorVIII scFv (Fragment).	5-2,5-3,5-5	-	auto
HIX0055510	HIT000327141	4	Conserved hypothetical protein.	5-5,5-6-3,5-6-4	-	auto
HIX0159220	HIT000325725	2	Immunglobulin heavy chain variable region (Fragment).	5-2,5-3,5-5,5-6-4	-	auto
HIX0041484	HIT000061895	4	Conserved hypothetical protein.	5-1,5-5	-	manual
HIX0159222	HIT000246382	2	Integrin-linked protein kinase (EC 2.7.11.1).	5-5,5-6-3,5-6-4	-	auto
HIX0052343	HIT000215687	3	Gonadotropin, beta chain family protein.	5-5,5-6-3,5-6-4	-	auto
HIX0055478	HIT000327090	4	Conserved hypothetical protein.	5-2,5-5,5-6-3,5-6-4	-	auto
HIX0159228	HIT000255501	2	ATP synthase protein 8 (ATPase subunit 8) (A6L).	5-5	-	auto
HIX0017611	HIT000018015	5	Hypothetical protein.	5-2,5-3,5-5,5-6-1	-	manual
HIX0159230	HIT000392895	2	Immunglobulin heavy chain variable region (Fragment).	5-2,5-3,5-5	-	auto
HIX0028051	HIT000046129	5	Hypothetical protein.	5-1,5-2,5-3,5-5,5-6-1	-	manual
HIX0159232	HIT000049837	2	SJCHGC03017 protein.	5-2,5-5	-	auto
HIX0159233	HIT000063098	2	Rheumatoid factor C6 heavy chain (Fragment).	5-2,5-3,5-5	-	auto
HIX0159234	HIT000017517	2	Pherophorin-S precursor.	5-1,5-2,5-5	-	manual
HIX0159235	HIT000191941	2	Immunglobulin heavy chain variable region (Fragment).	5-5,5-6-3	-	auto
HIX0159236	HIT000332103	2	Imuunoglobulin mu-chain D-J4-region (Fragment).	5-5,5-6-3	-	auto
HIX0023340	HIT000005681	3	Protein of unknown function DUF1630 family protein.	5-1,5-5,5-6-1	-	manual
HIX0051547	HIT000192814	3	Aromatic amino acid hydroxylase family protein.	5-5,5-6-3,5-6-4	-	auto
HIX0159237	HIT000334596	1	T-complex protein 1 subunit delta (TCP-1-delta) (CCT-delta) (Stimulator of TAR RNA-binding).	5-4,5-5	-	manual
HIX0060170	HIT000018866	3	Sushi/SCR/CCP domain containing protein.	5-2,5-5,5-6-1	-	auto
HIX0029968	HIT000091421	3	SH2 motif domain containing protein.	5-2,5-3,5-5,5-6-1	-	auto
HIX0159238	HIT000072102	1	RNase K.	5-4,5-5	-	manual
HIX0028055	HIT000046236	5	Hypothetical protein.	5-1,5-2,5-3,5-5,5-6-1	-	manual
HIX0159240	HIT000332431	4	Conserved hypothetical protein.	5-1,5-5	-	auto
HIX0159242	HIT000332429	4	Conserved hypothetical protein.	5-1,5-3,5-5	-	auto
HIX0159243	HIT000218979	1	Methionine aminopeptidase 2 (EC 3.4.11.18) (MetAP 2) (MAP 2) (Peptidase M 2) (Initiation factor 2-associated 67 kDa glycoprotein) (p67) (p67eIF2).	5-4,5-5,5-6-3,5-6-4	-	manual
HIX0053957	HIT000222065	3	Isocitrate/isopropylmalate dehydrogenase family protein.	5-5,5-6-3,5-6-4	-	auto
HIX0053189	HIT000218438	3	ABC transporter-like domain containing protein.	5-2,5-3,5-5,5-6-3,5-6-4	-	auto
HIX0018300	HIT000017407	5	Hypothetical protein.	5-1,5-2,5-3,5-5,5-6-1	-	manual
HIX0159249	HIT000218478	2	Homeobox-like sequence. Part of tandem repeat (Fragment).	5-1,5-5	-	manual
HIX0112556	HIT000386444	3	TMC family protein.	5-2,5-3,5-5,5-6-3	-	auto
HIX0050926	HIT000091700	4	Conserved hypothetical protein.	5-2,5-3,5-5	-	manual
HIX0159252	HIT000332438	4	Conserved hypothetical protein.	5-1,5-2,5-5	-	auto
HIX0045747	HIT000076540	3	Ornithine decarboxylase antizyme family protein.	5-5,5-6-3,5-6-4	-	auto
HIX0061387	HIT000013837	3	Homeobox domain containing protein.	5-1,5-2,5-3,5-5	-	manual
HIX0028276	HIT000055328	5	Hypothetical protein.	5-1,5-2,5-3,5-5	-	manual
HIX0159253	HIT000191834	2	Mucin-6 precursor (MUC-6) (Gastric mucin-6).	5-1,5-2,5-5	-	auto
HIX0028096	HIT000048362	4	Conserved hypothetical protein.	5-2,5-3,5-5,5-6-1	-	manual
HIX0159255	HIT000042835	1	Stomatin-like 3.	5-4,5-5	-	manual
HIX0159257	HIT000220924	2	Immunglobulin heavy chain variable region (Fragment).	5-5,5-6-3	-	auto
HIX0159258	HIT000061898	2	Mucin (Fragment).	5-1,5-5	-	manual
HIX0045028	HIT000071453	4	Conserved hypothetical protein.	5-1,5-5	-	manual
HIX0028253	HIT000053809	3	Krueppel-associated box domain containing protein.	5-5,5-6-1	-	auto
HIX0061651	HIT000045110	4	Conserved hypothetical protein.	5-2,5-3,5-5	-	auto

2. Chimeric (fusion) transcripts

Description: A normal mRNA sequence is aligned on the single location of the genome. However, the alignment of a fused type mRNA is split into two parts and mapped on the different locations of the genome (e.g. the 5’part of the transcript is mapped on the chromosome 1, but the 3’ part is mapped on the chromosome 2). Several possibilities should be considered for the formation of such chimeric/fusion transcript as follws;
1. experimental artifact (cDNA/cDNA recombination)
2. transcription from the rearranged genome (translocation, transposition, segmental duplication)
3. trans-splicing
We identified chimeric transcripts in the unmapped mRNAs by examining the alignment result. We further analyzed the splice site motif of the fusion boundary, consensus with exon/intron structure, and overlapping status with normal transcripts etc. These data are considered to be helpful for classifying the chimeric transcripts according to the type of fusion (discrimination between trans-splicing and others etc.).

[Download (2)-1] Annotation summary for the chimeric (fusion) transcripts

File name: um_dlfile2.txt
Format:
1. HIT
2. Accession #
3. Internal ID for Chimera alignment
4. Cluster-ID (chimera cluster)
5. Alignment position for the 5’ part (genome coordinate)
6. Alignment position for the 5’ part (transcript coordinate)
7. Alignment position for the 3’ part (genome coordinate)
8. Alignment position for the 3’ part (transcript coordinate)
9. Alignment position for the 3’ part
10.Total identity
11.Total coverage
12.Splice site motif for the fusion boundary
13.Overlapping transcript for the 5’ part
14.Overlapping transcript for the 3’ part

[Download (2)-2] Alignment file for chimeric (fusion) transcripts

File name: um_dlfile3.txt
Header lines:
>tID chim-id tDesc ident cover qstt qend tstt tend qleng
- tID --- H-InvDB's transcript ID (HIT*********)
- chim-id --- internal ID for chimera alignment
- tDesc --- absolute coordinate of the fused genome in the reference genome format=chrom1:stt1(strand +or-)end1__chrom2:stt2(strand +or-)end2
- ident --- total identity for the chimeric alignment
- cover --- total coverage for the chimeric alignment
- qstt --- chimera alignment start position (transcript position)
- qend --- chimera alignment end position (transcript position)
- tstt --- chimera alignment start position (fused genome position)
- tend --- chimera alignment end position (fused genome position)
- qleng --- length of the chimera transcript

Header line starts with ">". All lines are described in tab-delimited format.
The chimeraAln format describes an alignment for the chimeric transcript, which is mapped onto the multiple locations of the genome. Each set of chimeAln alignments starts with a header line (the line starts with ">"), contains two or more alignment data lines, and terminates with a junction data line.

[Download (2)-3] Overlaps between H-InvDB transcripts and chimeric (fusion) transcripts
File name: um_dlfile4.txt
Header lines
>tID chim-id tDesc
     tID --- H-InvDB's transcript ID (HIT*********)
     chim-id --- internal ID for chimera alignment
     tDesc --- absolute coordinate of the fused genome in the reference genome format=chrom1:stt1(strand +or-)end1__chrom2:stt2(strand +or-)end2
The chimeraAln format describes an alignment for the chimeric transcript, which is mapped onto the multiple locations of the genome. Each set of chimeAln alignments starts with a header line (the line starts with ">"), contains representative overlapping transcripts lines, and overlap status lines if any overlaps.

3. Partially mapped transcripts

[Download (3)] Overlaps between H-InvDB transcripts and partially mapped transcripts
File name: um_dlfile5.txt
Format:
1: HIT
2: overlapping transcripts (comma delimited)