Sequence
atgc intronic sequence ATGC exonic sequence...ccctctttcattgtgtctaacttttatacttcttaaatttcgtaacttttgtagcattgtgcatgttctaaattttgattcatattgtgaattacttcagGTTATGATTGATTTCCAAGCAGCTGAAAAGAAGAGAGTTGATGAACCTGCATCTGATATTGGTCTGGAACCTCTATGCGCTATG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G71820.1 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G71820.2 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA03G03120.1 (Glycine max), 3'ss of exon 16
ccctctttcattgtgtctaac-ttttatacttcttaaatttcgtaacttttgtagcattgtgcatgttctaaattttgattcatattgtgaattacttcagGTTATGATTGATTTCCAAGCAGCTGAAAAGAAGAGAGTTGATGAACCTGCATCTGATATTGGTCTGGAACCTCTATGCGCTATG
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-tcactagaaatccatgaagtgctcctcatagcgcaatgtgtagtgcttactccttatatcggtagctttgtatcctaggttatactatgtatttttacagGTGATGATTGATTTTCAAGCAGCTGAAAAGAAGAGACTAGAAGAACCAGCTTCTGAAATTGGTCTGGAACCTTTATGTGCTATG
upper sequence: AT1G71820.2 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: Vv12s0034g02360.t01 (Vitis vinifera), 3'ss of exon 15
--ccctctttcattgtgtctaacttttat-acttcttaaatttcgtaacttttgtagcattgtgcatgttctaaattttgattcatattgtgaattacttcagGTTATGATTGATTTCCAAGCAGCTGAAAAGAAGAGAGTTGATGAACCTGCATCTGATATTGGTCTGGAACCTCTATGCGCTATG
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taaaccccttttttacttctcattgtggttgtctatcatggtttgtcaatgtcctatttaaaatcataattgatgttcagattcacttcatg---ttttttagGTAATGATTGATTTTCAAGCAGCTGAAAAGCGAAGACTTGAAGAACCTGCTTCTGAAATTGGTCTGGAATCTTTATGTGCAATG
upper sequence: AT1G71820.2 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: Vv03s0097g00670.t01 (Vitis vinifera), 3'ss of exon 15
--ccctctttcattgtgtctaacttttat-acttcttaaatttcgtaacttttgtagcattgtgcatgttctaaattttgattcatattgtgaattacttcagGTTATGATTGATTTCCAAGCAGCTGAAAAGAAGAGAGTTGATGAACCTGCATCTGATATTGGTCTGGAACCTCTATGCGCTATG
||| |||| || ||| | | | | | | | || || | | | || || | | || |||||| | ||| | || |||| ||||||||||| ||||||||||||||| ||| |||| |||||||| ||||| |||||||||||| || |||| || |||
aaccccctttttttacttctcattgtggttgtctatcatggtttgtcaatgtcctatttaaaatcacaattgatgttcggattcacttcgtg---ttttttagGTAATGATTGATTTTCAAGCAGCTGAAAAGCGAAGACTTGAAGAACCTGCTTCTGAAATTGGTCTGGAATCTTTATGTGCAATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttttgtagcattgtgcatgttctaaattttgattcatattgtgaattacttcagGTTATGATTGATTTCCAAGCAGCTGAAAAGAAGAGAGTTGATGAACCTGCATCTGATATTGGTCTGGAACCTCTATGCGCTATG
ttacttc CT-rich tract
ttctaaattttgattc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccctctttcattgtgtctaacttttatacttcttaaatttcgtaacttttgtagcattgtgcatgttctaaattttgattcatattgtgaattacttcagGTTATGATTGATTTCCAAGCAGCTGAAAAGAAGAGAGTTGATGAACCTGCATCTGATATTGGTCTGGAACCTCTATGCGCTATG
-cctcttt