Sequence
atgc intronic sequence ATGC exonic sequencegtaatatattgaatatcacgtcttttcgtcatggtgtgtttcattctatctaaaacggagatgtttttgtttaatcacataactgaacagGCGATAATTGATGCGGCTTCATATGTTCCACCTCCACCATCAGAAGAACAAAAGAAGAAAATAGTAAAGCT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G62850.3 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G62850.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G170532_T01 (Zea mays), 3'ss of exon 5
gtaatatattgaatatcacgtcttttcgtcatggtgtgtttcattctatctaaaacggagatgtttttgtttaatcacataactgaacagGCGATAATTGATGCGGCTTCATATGTTCCACCTCCACCATCAGAAGAACAAAAGAAGAAAATAGTAAAGCT
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---------------gtatgcttcttcaattcagtttcattttctagggctagaccacttacattactccacaatttgcc--ctgaacagGCAATCATTGATGCTGCATCATATGTTCCTCCACCCCCAACAGAAGACCAAAAGAAAAAGATTGAAAAAAT
upper sequence: AT1G62850.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA17G14410.1 (Glycine max), 3'ss of exon 5
----gtaatatattgaat---atcacgtcttttc--gtcatggtgtgtttcattctatctaaaacggagatgtttttgtttaatca-cataactgaacagGCGATAATTGATGCGGCTTCATATGTTCCACCTCCACCATCAGAAGAACAAAAGAAGAAAATAGTAAAGCT
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caacaacataaattgagttcatttacctcttttcttgtttctaaaaactggcttttacttagcaatggtgcttttctgtttatttaatggcaaaaaatagGAAATCATTGATGCGGCATCTTATGTTCCGCCGCCTCCCTCAGAAGAGCAAAAGAAGAAAATTGCGAAGAT
upper sequence: AT1G62850.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv02s0241g00090.t01 (Vitis vinifera), 3'ss of exon 6
-------gtaatat-attgaatatcacgtcttttcgtcatggtgtgtt--tcattctatctaaaacggagatgtttttgtttaatcacataactgaacagGCGATAATTGATGCGGCTTCATATGTTCCACCTCCACCATCAGAAGAACAAAAGAAGAAAATAGTAAAGCT
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tgtcattattgtgtgacttgctgttgattatttttgaagtgatgttttgttgagattaattttattattgattttccattattttgaatgaataaaacagGCAATTATTGATGCTGCTTCATATGTCCCACCGCCCCCATCAGAAGAGCAGAAGAAAAAAATTGCCAAGTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgtttcattctatctaaaacggagatgtttttgtttaatcacataactgaacagGCGATAATTGATGCGGCTTCATATGTTCCACCTCCACCATCAGAAGAACAAAAGAAGAAAATAGTAAAGCT
acataac putative branch site (score: 3)
atgtttttgtttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatatattgaatatcacgtcttttcgtcatggtgtgtttcattctatctaaaacggagatgtttttgtttaatcacataactgaacagGCGATAATTGATGCGGCTTCATATGTTCCACCTCCACCATCAGAAGAACAAAAGAAGAAAATAGTAAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA