Sequence
atgc intronic sequence ATGC exonic sequence...aaggaaaaggagaactttcaaatttcataaataaccttagacctccatactttgatagttggttgcattaatccgtacttgtgatattatattcacttagGTGGGCTTCTATAGCATCCCAACTACCTGGAAGAACAGACAATGAGATTAAGAACTACTGGAATACCCATCTGAAGAAGCGTCTCCTTCGATCATGTTAT
Basic information
species | Glycine max |
transcript | GLYMA10G38090.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G38090.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv16s0050g00070.t01 (Vitis vinifera), 3'ss of exon 2
----------aaggaaaaggagaactttcaaatttcataaataaccttagacctccatactttgatagttggttgcattaatccgtacttgtgatattatattcacttagGTGGGCTTCTATAGCATCCCAACTACCTGGAAGAACAGACAATGAGATTAAGAACTACTGGAATACCCATCTGAAGAAGCGTCTCCTTCGATCATGTTAT
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ggaccctgttgatgcagtcccatcctcctatatttcgaggtcaatatggaccttccgcatttt-----ttgttttcat--atgtgaactgaatgtaagatatt---tcagGTGGGCTGCAATCGCTTCAAAAATACCTGGTAGAACGGACAATGAGATCAAGAACTTCTGGAACACCCATCTAAAGAAGCGCCTCCTGGGCAACCACCAA
upper sequence: GLYMA10G38090.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S389_41V6.1 (Physcomitrella patens), 3'ss of exon 2
aaggaaaaggagaactttcaa---atttcataaataaccttagacctccatactttgatagt-tggttgcattaatccgtacttgtgatattatattc---------acttagGTGGGCTTCTATAGCATCCCAACTACCTGGAAGAACAGACAATGAGATTAAGAACTACTGGAATACCCATCTGAAGAAGCGTCTCCTTCGATCATGTTAT
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gttcgcacggtcccattccagtgcatcgcaagcgcatactgctgctttaactgtgtgagaaagtgactcaaggacactgtctcagcgtttctgttttctgtcctgccatgcagATGGTCGACCATAGCAGCGCATCTGCCCGGACGGACTGACAACGAGATTAAAAACTACTGGAATACACACGTGAAGAAGCGTCTTCTGCAATTGGGAATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catactttgatagttggttgcattaatccgtacttgtgatattatattcacttagGTGGGCTTCTATAGCATCCCAACTACCTGGAAGAACAGACAATGAGATTAAGAACTACTGGAATACCCATCTGAAGAAGCGTCTCCTTCGATCATGTTAT
cattaat putative branch site (score: 3)
ttcactt putative PPT
atattatattcactta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaggaaaaggagaactttcaaatttcataaataaccttagacctccatactttgatagttggttgcattaatccgtacttgtgatattatattcacttagGTGGGCTTCTATAGCATCCCAACTACCTGGAAGAACAGACAATGAGATTAAGAACTACTGGAATACCCATCTGAAGAAGCGTCTCCTTCGATCATGTTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
aaggaaaa
- - - - - - - - - - - - - - aaataacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcatta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acttgtg