Sequence
atgc intronic sequence ATGC exonic sequence...tctgttaattaattaagcatgcagtttagtatatacgaacataggtttttcttgatttaaactgtggacttgtattaattcttgaatttgggaaatgcagATGGGCTCACATTGCAAGCCACTTGCCAGGTCGAACTGACAATGAAATAAAGAACTATTGGAACTCATGGATAAAAAAGAAAATAAGAAAGACTTCTTCG
Basic information
species | Glycine max |
transcript | GLYMA08G02080.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G02080.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G325907_T01 (Zea mays), 3'ss of exon 2
tctgttaattaattaagcatgcagtttagtata-tacgaacataggtt--tttcttgatttaaactgtggacttgtattaattcttgaatttgggaaatgcagATGGGCTCACATTGCAAGCCACTTGCCAGGTCGAACTGACAATGAAATAAAGAACTATTGGAACTCATGGATAAAAAAGAAAATAAGAAAGACTTCTTCG
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--tgaaaatgaaggctaaatccaaaggaatgcaacacctaggctagctagctagttgatgtgtac-atgaccacagccatgtcccccggttctctctctgcagGTGGGCCCACATTGCCAGCCACTTGCCCGGGCGGACGGACAACGAGATCAAGAACTACTGGAACTCGTGGATCAAGAAGAAGATCCGGAAGCCGGCGATG
upper sequence: GLYMA08G02080.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv02s0025g00320.t01 (Vitis vinifera), 3'ss of exon 2
tctgttaa-ttaattaagcatgcagtttagt-atatacgaa-cataggtttttcttgatttaaactgtggacttgtattaattcttgaatttgggaaatgcagATGGGCTCACATTGCAAGCCACTTGCCAGGTCGAACTGACAATGAAATAAAGAACTATTGGAACTCATGGATAAAAAAGAAAATAAGAAAGACTTCTTCG
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ttcgtgaagttacttccaaacccaccgtattcatgaactaatcacaaactttgaggtgtttcag-tcttcttaaggactgacatttg--tttgggaattgtagATGGGCTCATATTGCAAGTCACTTGCCTGGAAGAACAGACAATGAGATAAAGAATTACTGGAATTCGTGGATCAAAAAGAAGATAAGGAAGCCGTCGGCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttttcttgatttaaactgtggacttgtattaattcttgaatttgggaaatgcagATGGGCTCACATTGCAAGCCACTTGCCAGGTCGAACTGACAATGAAATAAAGAACTATTGGAACTCATGGATAAAAAAGAAAATAAGAAAGACTTCTTCG
tattaat putative branch site (score: 2)
tattaattcttgaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tctgttaattaattaagcatgcagtttagtatatacgaacataggtttttcttgatttaaactgtggacttgtattaattcttgaatttgggaaatgcagATGGGCTCACATTGCAAGCCACTTGCCAGGTCGAACTGACAATGAAATAAAGAACTATTGGAACTCATGGATAAAAAAGAAAATAAGAAAGACTTCTTCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - gcatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - actgtgg