Sequence
atgc intronic sequence ATGC exonic sequencegtaagaatattttcataatgattgcatgtcttcctgtcccctgaagcctcttaatttgcccagaattcatgtgtcctgatatgcaaagttacttcataaatacagATTGTTGTTTCTACACAAAGGAAAGATTGTTTGGGAAGGAATGACTCATGAATTTACAACTTCAACTAATCCAATTGTCCAGCAG
Basic information
species | Glycine max |
transcript | GLYMA09G38730.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G38730.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM5G868168_T02 (Zea mays), 3'ss of exon 8
gtaagaatattttcataatgattgcatgtcttcctgtcccctgaagcctcttaatttgcccagaattcatgtgtcctgatatgcaaagttacttcataaatacagATTGTTGTTTCTACACAAAGGAAAGATTGTTTGGGAAGGAATGACTCATGAATTTACAACTTCAACTAATCCAATTGTCCAGCAG
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--------------gtaaagaacaaatgctacacttttcactccatgacctcagttgtct----attgctgggttggtatctg-atatttgctt------ttcagGTTGCTATTTCTTCATGAGGGGAAGGTTGTTTGGGAAGGAATGACACATGAGTTCACAACATCAGCTAATCCAATTGTTCAACAG
upper sequence: GLYMA09G38730.1 (Glycine max), 3'ss of exon 8
lower sequence: AT1G65410.1 (Arabidopsis thaliana), 3'ss of exon 8
gtaagaatattttcataatgattgcatgtcttcctgtcccctgaagcctcttaatttgcccagaattcatgtgtcctgatatgcaa-agttacttcataaatacagATTGTTGTTTCTACACAAAGGAAAGATTGTTTGGGAAGGAATGACTCATGAATTTACAACTTCAACTAATCCAATTGTCCAGCAG
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-----------------------gttccgcttctagtccatattacaagatacgtttttgcagcttttgcttcatcccttgagtaatatttgtttcttctattcagGTTATTGTTTCTGTATGAAGGAAAGATCGTTTGGCAAGGAATGACACATGAATTCACAACCTCAACTAATCCAATAGTTCAACAG
upper sequence: GLYMA09G38730.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv04s0023g00290.t01 (Vitis vinifera), 3'ss of exon 8
gtaagaatattttcataatgattgcatgtct-----tcctgtcccctga-agcctcttaatttgcccagaattcatgtgtcctgatatgcaaagttacttcataaatacagATTGTTGTTTCTACACAAAGGAAAGATTGTTTGGGAAGGAATGACTCATGAATTTACAACTTCAACTAATCCAATTGTCCAGCAG
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gtagtgcttcatacaaatgagatgcatttctgaaagtacaaggctttgtcaggaatttatgtggctttgttctgacatatcctaaactg-attgccattgttattatatagGCTGTTGTTTCTTTATGATGGGAAAATCGTCTGGGAAGGAATGACTGATGAATTCACCACTTCAACAAACCCAATTGTTCAGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaatttgcccagaattcatgtgtcctgatatgcaaagttacttcataaatacagATTGTTGTTTCTACACAAAGGAAAGATTGTTTGGGAAGGAATGACTCATGAATTTACAACTTCAACTAATCCAATTGTCCAGCAG
tcctgat putative branch site (score: 3)
ttacttcataaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagaatattttcataatgattgcatgtcttcctgtcccctgaagcctcttaatttgcccagaattcatgtgtcctgatatgcaaagttacttcataaatacagATTGTTGTTTCTACACAAAGGAAAGATTGTTTGGGAAGGAATGACTCATGAATTTACAACTTCAACTAATCCAATTGTCCAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA