Sequence
atgc intronic sequence ATGC exonic sequence...tcatgtagatattaataaagattataatagtttcagactatataataattactctctttttcttattttgacaatactcaacaaatgaacaaattcacagGTGGGCTGCTATAGCCTCTCAGCTACCAGGAAGAACAGACAATGAGATCAAGAACTTATGGAACACCCACTTAAAGAAACGTCTCATTTGCATGGGCCTG
Basic information
species | Glycine max |
transcript | GLYMA07G07960.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G07960.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G61250.1 (Arabidopsis thaliana), 3'ss of exon 2
tcatgtagatattaataaagattataatagtttcagactatataataattactctctttttcttattttgacaatactcaacaaatgaacaaattcacagGTGGGCTGCTATAGCCTCTCAGCTACCAGGAAGAACAGACAATGAGATCAAGAACTTATGGAACACCCACTTAAAGAAACGTCTCATTTGCATGGGCCTG
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-------gtcttttactttgcttctc-caccttccttctctactctagctatcttcttcttcattgtctga----attctgcttttttttgtttcctcagGTGGGCTGCTATTGCAGCACAGCTTCCAGGAAGAACAGACAACGAGATCAAGAACTTATGGAACACTCATTTGAAGAAACGTCTTTTATCTATGGGTCTT
upper sequence: GLYMA07G07960.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv15s0046g03190.t01 (Vitis vinifera), 3'ss of exon 2
--tcatgtagatattaataaagattataatagtttcagact-atataataattactctctttttcttat-----tttgacaatactcaacaaatgaacaaattcacagGTGGGCTGCTATAGCCTCTCAGCTACCAGGAAGAACAGACAATGAGATCAAGAACTTATGGAACACCCACTTAAAGAAACGTCTCATTTGCATGGGCCTG
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ctttggttaggt-tttctgcaatttgtcac--tctgacattgatggaatattttcatatttcatgttatgaacttttaacaatacttgatacacta-----tgttcagGTGGGCTGCCATTGCCTCTCAACTGCCCGGAAGGACCGATAATGAGATCAAGAACCTATGGAACACCCACTTGAAGAAGCGCCTGCTTGGAATGGGGCTT
upper sequence: GLYMA07G07960.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S389_40V6.1 (Physcomitrella patens), 3'ss of exon 1
-tcatgtagatattaataaagattataatagtttcagactatataataattactctctttttcttattttgacaatactcaacaaatgaaca--aattcacagGTGGGCTGCTATAGCCTCTCAGCTACCAGGAAGAACAGACAATGAGATCAAGAACTTATGGAACACCCACTTAAAGAAACGTCTCATTTGCATGGGCCTG
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tttgttttgttttgttttt---ttgtgtttttttgtgtgtgtgtgcgagtgcgtggagcacagaaaaattgattttttggaatgtgttgttgttgattcgcagATGGTCTGCCATAGCTAGCCATCTTCCTCGCCGCACTGACAACGAGATCAAGAACTACTGGAACACACACTTGAAGAAGCGTCTCATGCAAATGGGAATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taattactctctttttcttattttgacaatactcaacaaatgaacaaattcacagGTGGGCTGCTATAGCCTCTCAGCTACCAGGAAGAACAGACAATGAGATCAAGAACTTATGGAACACCCACTTAAAGAAACGTCTCATTTGCATGGGCCTG
ttttgac putative branch site (score: 3)
tctttttcttatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcatgtagatattaataaagattataatagtttcagactatataataattactctctttttcttattttgacaatactcaacaaatgaacaaattcacagGTGGGCTGCTATAGCCTCTCAGCTACCAGGAAGAACAGACAATGAGATCAAGAACTTATGGAACACCCACTTAAAGAAACGTCTCATTTGCATGGGCCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
tcatgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctcaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatgaac