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The Transcript Info page presents information relevant for one transcript identified by its Genomatix TranscriptID. The data includes general information about the name, the genomic location, and the length of UTRs and coding sequence. It also provides information about the tissues the transcript is expressed in. The detailed data about the cDNA mapping used for the annotation process and the sequences of the transcript and the resulting protein are shown.
Below is an example output for transcript GXT_22214872 (one transcript from the genes SFRS1):
The Identification table provides you with the key features of the transcript like e.g. identifiers, length, number of exons, genomic location, and the Genomatix transcript quality. The length of the UTRs and the coding sequence (CDS) are derived from the transcript sequence by in silico methods. Conflicts with the UTR/CDS annotated for the related RefSeq/GenBank sequence are indicated.
| Identification | |
|---|---|
| Organism |  Homo sapiens |
| cDNA Accession | AK225711 |
| LocusID | GXL_36015 (see More Gene Info) |
| Symbol | SRSF1 |
| GeneId | 6426 |
| Description | serine/arginine-rich splicing factor 1 |
| Transcript length | 2026 bp |
| Number of exons | 4 |
| Transcript quality | gold (experimentally verified 5' complete transcript) |
| Genomic location | NC_000017 (-) 56080854 - 56084585 |
| 5' UTR | 87 bp |
| CDS | 606 bp (201 aa) |
| 3' UTR | 1333 bp |
Tissue associations are derived from CAGE tags located up to 20 bp upstream or downstream of the TSS of the transcript. Currently there are CAGE tags available from several tissues from mouse and human (see CAGE tag statistics). The numbers following the tissue names indicate how often the respective tissue was annotated for this transcript.
| Tissues (based on CAGE tags) |
|---|
| liver (79) adrenal gland (38) bone marrow (35) lung (29) large intestine (26) cerebrum (19) colon (18) cecum (16) embryo (16) brain (11) thymus (10) blood (9) kidney (6) adipose (6) muscle (5) mammary gland (4) rectum (4) small intestine (4) frontal lobe (3) testis (3) parietal lobe (2) spleen (1) cerebellum (1) |
Transcripts in ElDorado are annotated by mapping the sequence
of a cDNA from e.g. RefSeq or GenBank to the respective genomic sequence.
The cDNA sequences may differ from the genomic sequences either by point mutations
or insertions/deletions. Thus the resulting transcript annotated in ElDorado
is not necessarily identical to the cDNA sequence used for the mapping. Gaps
either in the cDNA or the genomic sequence located in the CDS of the transcript
may result in frameshifts and the loss of the coding potential of the transcript. If such discrepancies have been found, they are shown in the "cDNA Mapping" table. The detailed output
of the mapping process can be accessed by the link "detailed mapping" in
the last row of the table.
If the cDNA sequences does not differ from the genomic sequence, the cDNA mapping table is not displayed.
| cDNA Mapping | |
|---|---|
| The annotation of GXT_22214872 is based on mapping of AK225711. | |
| 5' not aligned | 0 bp |
| 3' not aligned | 16 bp |
| Point mutations | 1 |
| Gaps in cDNA | 0 |
| Gaps in genomic sequence | 0 |
| Details | detailed mapping |
The Sequences table provides the nucleotide sequence of the transcript and the corresponding protein sequence:
| Sequences | |
|---|---|
| cDNA sequence | Protein sequence, predicted |
1 agacgtggtg ccgctgcggg ctcgctctgc cgtgcgctag gcttggtggg 51 aaggcctgtt ctcgagtccg cgcttttcgt caccgccATG TCGGGAGGTG 101 GTGTGATTCG TGGCCCCGCA GGGAACAACG ATTGCCGCAT CTACGTGGGT 151 AACTTACCTC CAGACATCCG AACCAAGGAC ATTGAGGACG TGTTCTACAA 201 ATACGGCGCT ATCCGCGACA TCGACCTCAA GAATCGCCGC GGGGGACCGC 251 CCTTCGCCTT CGTTGAGTTC GAGGACCCGC GAGACGCGGA AGACGCGGTG 301 TATGGTCGCG ACGGCTATGA TTACGATGGG TACCGTCTGC GGGTGGAGTT 351 TCCTCGAAGC GGCCGTGGAA CAGGCCGAGG CGGCGGCGGG GGTGGAGGTG 401 GCGGAGCTCC CCGAGGTCGC TATGGCCCCC CATCCAGGCG GTCTGAAAAC 451 AGAGTGGTTG TCTCTGGACT GCCTCCAAGT GGAAGTTGGC AGGATTTAAA 501 GGATCACATG CGTGAAGCAG GTGATGTATG TTATGCTGAT GTTTACCGAG 551 ATGGCACTGG TGTCGTGGAG TTTGTACGGA AAGAAGATAT GACCTATGCA 601 GTTCGAAAAC TGGATAACAC TAAGTTTAGA TCTCATGAGG TAGGTTATAC 651 ACGTATTCTT TTCTTTGACC AGAATTGGAT ACAGTGGTCT TAAcagtgga 701 atttcaaggt aaggattcag gcaaggttgt ccaagtaaat tgccagattt 751 ctggttttag ttacattgta ttcattcagc atgtctgaag atagatgaaa 801 gcttagatct ttcaatggaa agttctgtct atccaatagg gagaaactgc 851 ctacatccgg gttaaagttg atgggcccag aagtccaagt tatggaagat 901 ctcgatctcg aagccgtagt cgtagcagaa gccgtagcag aagcaacagc 951 aggagtcgca gttactcccc aaggagaagc agaggatcac cacgctattc 1001 tccccgtcat agcagatctc gctctcgtac ataagatgat tggtgacact 1051 ttttgtagaa cccatgttgt atacagtttt cctttattca gtacaatctt 1101 ttcatttttt aattcaaact gttttgttca gaatgggcta aagtgttgaa 1151 ttgcattctt gtaatatccc cttgctccta acatctacat tcccttcgtg 1201 tctttgataa attgtatttt aagtgatgtc atagacagga ttgtttaaat 1251 ttagttaact ccatactctt cagactgtga tattgtgtaa atgtctatct 1301 gccctggttt gtgtgaactg ggatgttggg ggtgtttgtg gttatcttac 1351 ctggggaagt tcttatgttt atcttgcttt tcatgtgtct ttctgtagac 1401 atatctgaag agatggatta agaatgcttt ggattaagga ttgtggagca 1451 catttcaatc attttaggat tgtcaaaagg aggattgagg aggatcagat 1501 caataatgga ggcaatggtt tggattggag agggctcact ggatcccaat 1551 ccttggagct ggatcattgg attcaaatca taatgtggat aggataggga 1601 ggatgaatta ccaggattca tggagcggga tcagattacc aggaacatag 1651 gagtggattc ctgccccaac caaaccgcat tcgtgtggat ttttttattc 1701 aacttaattg gctattccaa agattttttt tttcctattt ttgacgattg 1751 gagcccttaa gatgcacgat ggaattgtgt tttgcgtttt ttggtaaaag 1801 gagcaaagcg aggacctgga gataaacgct ggagcaatct ccttggaagg 1851 attcagcacg agtagatggt aaacatttaa aggggaaagg gggggtttgt 1901 ttaaaatagt aaatcagtaa gtcacttcta aatttaaaga aaacaaaatt 1951 ggagttgaag aataagtagg tttccaattg gctattgccg ttttctttga 2001 aaaaataaac attttttaaa aaacta | 1 MSGGGVIRGP AGNNDCRIYV GNLPPDIRTK DIEDVFYKYG AIRDIDLKNR 51 RGGPPFAFVE FEDPRDAEDA VYGRDGYDYD GYRLRVEFPR SGRGTGRGGG 101 GGGGGGAPRG RYGPPSRRSE NRVVVSGLPP SGSWQDLKDH MREAGDVCYA 151 DVYRDGTGVV EFVRKEDMTY AVRKLDNTKF RSHEVGYTRI LFFDQNWIQW 201 S |
| Legend: Exons are alternately coloured BLACK and BLUE. Nucleotides in lower case indicate the UTR. The CDS is given in upper case. Mouse over shows the corresponding exon numbers. Nucleotides highlighted in yellow indicate SNPs (mouse over shows alleles). | |
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