Sequence
atgc intronic sequence ATGC exonic sequencegtctcataggccaacaaccactcagtatataattacaatttgattagtaatatactaatattttttatatctgaaaatgaaatttctaaagttttttcaaacttggttcatttgatagCAGACACCACCAACATGGAAGGTGGCAAGCTCGAATTGGTAGAGTGGCTGGAAACAAAGATCTATATCTTGGAACCTTCA
Basic information
species | Glycine max |
transcript | GLYMA17G17010.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G17010.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G021573_T02 (Zea mays), 3'ss of exon 6
gtctcataggccaacaaccactcagtatataattacaatttgattagtaatatactaatattttttatatctgaaaatgaaatttctaaagttttttcaaacttggttcatttgatagCAGACACCACCAACATGGAAGGTGGCAAGCTCGAATTGGTAGAGTGGCTGGAAACAAAGATCTATATCTTGGAACCTTCA
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gttcgtctgtgcagggattgcgc--caccgcatctcgcttcc-ttattattgtgcggacaactaacgtaagtgaagagatcgtctcaa-------tgcacac---gctaactgcattgcagGCACCACCAGCAAGGAAGATGGCAGTCTCGGATTGGAAGAGTCGCTGGAAACAAGGATCTATACCTCGGCACTTTCA
upper sequence: GLYMA17G17010.1 (Glycine max), 3'ss of exon 7
lower sequence: AT4G37750.1 (Arabidopsis thaliana), 3'ss of exon 6
gtctcataggccaacaaccactcagtatataattacaatttgattagtaatatactaatattttttatatctgaaaatgaaatttctaaagttttttcaaacttggttcatttgatagCAGACACCACCAACATGGAAGGTGGCAAGCTCGAATTGGTAGAGTGGCTGGAAACAAAGATCTATATCTTGGAACCTTCA
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--------------------------------gtccttttaaattacatttatataactttatataatacat-agtttaataatgtgaatattgactttgtgtgagtt--ttttgtactagACATCACCAGCATGGAAGGTGGCAAGCACGGATTGGTAGAGTCGCTGGAAACAAAGATCTCTACCTTGGAACTTTTG
upper sequence: GLYMA17G17010.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv07s0151g00440.t01 (Vitis vinifera), 3'ss of exon 6
gtctcataggccaacaaccactcagtatataattacaatttgattagtaatatactaatatttttt------atatctgaaaatgaaatttctaaagttttttcaaacttggttcatttgatagCAGACACCACCAACATGGAAGGTGGCAAGCTCGAATTGGTAGAGTGGCTGGAAACAAAGATCTATATCTTGGAACCTTCA
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--------gtcttactattattttctgcttatgtctcatcttgt-aattgtattgtcatgttctctgagagaaaaggcgaaaaaaaatcccctgaaatctcttt---cctgcttcgattcttagcagACATCACCAACATGGACGGTGGCAAGCTCGAATTGGCAGAGTTGCAGGGAACAAGGACCTTTATCTTGGGACATTCA
upper sequence: GLYMA17G17010.1 (Glycine max), 3'ss of exon 7
lower sequence: EFJ26861 (Selaginella moellendorffii), 3'ss of exon 6
gtctcataggccaacaaccactcagtatataattacaatttgattagtaatatactaatattttttatatctgaaaatgaaatttctaaagttttttcaaacttggttcatttgatagCAGACACCACCAACATGGAAGGTGGCAAGCTCGAATTGGTAGAGTGGCTGGAAACAAAGATCTATATCTTGGAACCTTCA
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--------------------------------------------------------------gtaagcgtgccgtaaatccttctcctttgcgattcctaacaagctttaaatcat-gcagACACCATCAACAAGGACGCTGGCAAGCCCGGATTGGAAGAGTAGCCGGCAACAAAGATCTTTACCTCGGAACTTTCA
upper sequence: GLYMA17G17010.1 (Glycine max), 3'ss of exon 7
lower sequence: EFJ21317 (Selaginella moellendorffii), 3'ss of exon 6
gtctcataggccaacaaccactcagtatataattacaatttgattagtaatatactaatattttttatatctgaaaatgaaatttctaaa--gttttttcaaacttggttcatttgatagCAGACACCACCAACATGGAAGGTGGCAAGCTCGAATTGGTAGAGTGGCTGGAAACAAAGATCTATATCTTGGAACCTTCA
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----------------------------------------------------------------gtaagcgtggcgtgaatccttctacttcgcgattcctaacaagctttaaatcat-gcagACACCATCAACAAGGACGCTGGCAAGCCCGGATTGGAAGAGTAGCCGGCAACAAAGATCTTTACCTCGGAACTTTCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttatatctgaaaatgaaatttctaaagttttttcaaacttggttcatttgatagCAGACACCACCAACATGGAAGGTGGCAAGCTCGAATTGGTAGAGTGGCTGGAAACAAAGATCTATATCTTGGAACCTTCA
ttctaaa putative branch site (score: 2)
ttcattt putative PPT
aaaatgaaatttctaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctcataggccaacaaccactcagtatataattacaatttgattagtaatatactaatattttttatatctgaaaatgaaatttctaaagttttttcaaacttggttcatttgatagCAGACACCACCAACATGGAAGGTGGCAAGCTCGAATTGGTAGAGTGGCTGGAAACAAAGATCTATATCTTGGAACCTTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA