Sequence
atgc intronic sequence ATGC exonic sequencegtaaatttcttgttttttgaaagctaaccaatggctccattttatggaattatatcttacctggcttttaatttttgtattagGCATGATTTCCAGTTTTTCAATAACCAAAGGCTAAATGAATTGTACGAAAAGGAAGTGCGGTACCTCATG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 17
lower sequence: LOC_Os01g27040.1 (Oryza sativa), 3'ss of exon 17
------------gtaaatttcttgttttttgaaagctaaccaatggctccatt---------ttatggaattatatcttacctggcttttaatttttgtattagGCATGATTTCCAGTTTTTCAATAACCAAAGGCTAAATGAATTGTACGAAAAGGAAGTGCGGTACCTCATG
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gtaagttttctcttgcctctttcattttgtgaaaaaaaaatcatgattaccttgtttgctctctttagaactac-tgtcagctcatattgtttttgtttgtcagACATGATTTCCAGTTCTTCAACAACCAAAGGCTCAATGAATTGTATGAAAAGGAAGTCCGGTACCTTATG
upper sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 17
lower sequence: 13113.m00246 (Oryza sativa), 3'ss of exon 17
------------gtaaatttcttgttttttgaaagctaa----ccaatggctccattt------tatggaattatatcttacctggcttttaatttttgtattagGCATGATTTCCAGTTTTTCAATAACCAAAGGCTAAATGAATTGTACGAAAAGGAAGTGCGGTACCTCATG
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gtaagttttctcttgcctctttcattttgtgaaaaaaaaaatcatgattaccttgtttgctctctttagaactac-tgtcagctcatattgtttttgtttgtcagACATGATTTCCAGTTCTTCAACAACCAAAGGCTCAATGAATTGTATGAAAAGGAAGTCCGGTACCTTATG
upper sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 17
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 17
gtaaatttcttgtttt-ttgaaagctaaccaatggctccattttatggaattatatcttacctggcttttaatttttgtattagGCATGATTTCCAGTTTTTCAATAACCAAAGGCTAAATGAATTGTACGAAAAGGAAGTGCGGTACCTCATG
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gtaagcatctctttgaactgattgctttcttg-gattgtagttgatgttttcatctgctttatatgttttgcctctgtttttagGCATGATTTCCAATTCTTTAACACACAAAGGCTGAATGAGTTGTATGAGAAAGAAGTGCGGTACCTCATGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|32929959|gb|CF034771.1|CF034771EST: GGTGCACCAACGAAGCCTAGGGAGCCAAGGATTCCAAGAATGCCGCACTT GCATGATTTCCAGTTTTTCAATAACCAAAGGCTAAATGAATTGT
genomic: GGTGCACCAGCGAAGCCTAGGGAGCCAAGGATTCCAAGAATGCCGCACTTgtaaatttct ... tttgtattagGCATGATTTCCAGTTTTTCAATAACCAAAGGCTAAATGAATTGT
EST:
gi|211502860|gb|FK981747.1|FK981747EST: GGTGCACCAACGAAGCCTAGGGAGCCAAGGATTCCAAGAATGCCGCACTT GCATGATTTCCAGTTTTTCAATAACCAAAGGCTAAATGAATTGTACGAMAA
genomic: GGTGCACCAGCGAAGCCTAGGGAGCCAAGGATTCCAAGAATGCCGCACTTgtaaatttct ... tttgtattagGCATGATTTCCAGTTTTTCAATAACCAAAGGCTAAATGAATTGTACGAAAA
EST:
gi|33094019|gb|CF054013.1|CF054013EST: GGTGCACCAACGAAGCCTAGGGAGCCAAGGATTCCAAGAATGCCGCACTT GCATGATTCCCAGTTTTTCAATAACCAAAGGCTAAATGAATTGTAC
genomic: GGTGCACCAGCGAAGCCTAGGGAGCCAAGGATTCCAAGAATGCCGCACTTgtaaatttct ... tttgtattagGCATGATTTCCAGTTTTTCAATAACCAAAGGCTAAATGAATTGTAC
RNA-Seq data
ATGC Supported by RNA-Seq exonic block that spans over the splice site
atgs Truncated intron sequence
Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.
Found data for 4 RNA-Seq libraries.
Block sizes:
48 (upstream exon),
49 (downstream exon)
Score:
314CTACTCTGAGTCTGATTACTTTAAGCAAGCGCTTCGCCAAGGTGCACCAGCGAAGCCTAGGGAGCCAAGGATTCCAAGAATGCCGCACTTgtaaatttct ... tttgtattagGCATGATTTCCAGTTTTTCAATAACCAAAGGCTAAATGAATTGTACGAAAAGGAAGTGCGGTACCTCATG
Block sizes:
42 (upstream exon),
49 (downstream exon)
Score:
153CTACTCTGAGTCTGATTACTTTAAGCAAGCGCTTCGCCAAGGTGCACCAGCGAAGCCTAGGGAGCCAAGGATTCCAAGAATGCCGCACTTgtaaatttct ... tttgtattagGCATGATTTCCAGTTTTTCAATAACCAAAGGCTAAATGAATTGTACGAAAAGGAAGTGCGGTACCTCATG
Block sizes:
47 (upstream exon),
49 (downstream exon)
Score:
205CTACTCTGAGTCTGATTACTTTAAGCAAGCGCTTCGCCAAGGTGCACCAGCGAAGCCTAGGGAGCCAAGGATTCCAAGAATGCCGCACTTgtaaatttct ... tttgtattagGCATGATTTCCAGTTTTTCAATAACCAAAGGCTAAATGAATTGTACGAAAAGGAAGTGCGGTACCTCATG
Block sizes:
46 (upstream exon),
47 (downstream exon)
Score:
164CTACTCTGAGTCTGATTACTTTAAGCAAGCGCTTCGCCAAGGTGCACCAGCGAAGCCTAGGGAGCCAAGGATTCCAAGAATGCCGCACTTgtaaatttct ... tttgtattagGCATGATTTCCAGTTTTTCAATAACCAAAGGCTAAATGAATTGTACGAAAAGGAAGTGCGGTACCTCATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caatggctccattttatggaattatatcttacctggcttttaatttttgtattagGCATGATTTCCAGTTTTTCAATAACCAAAGGCTAAATGAATTGTACGAAAAGGAAGTGCGGTACCTCATG
ttttaat putative branch site (score: 164)
tttttgt CT-rich tract
attttatggaattata TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaatttcttgttttttgaaagctaaccaatggctccattttatggaattatatcttacctggcttttaatttttgtattagGCATGATTTCCAGTTTTTCAATAACCAAAGGCTAAATGAATTGTACGAAAAGGAAGTGCGGTACCTCATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA