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Transcript Information


[Identification] [Tissues] [cDNA Mapping] [Sequences]

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):

Identification

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

Tissues

Tissue associations are derived from CAGE tags located up to 20bp upstream or downstream of the TSS of the transcript. Currently there are CAGE tags available from several tissues from mouse and human. 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)

cDNA Mapping

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

Sequences

The Sequences table provides the nucleotide sequence of the transcript and the corresponding protein sequence:

The nucleotide sequence can be downloaded for further analysis either to your local disk or to your personal sequence directory on our server.

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

download Download sequence file (4.0Kb)
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  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).