Sequence
atgc intronic sequence ATGC exonic sequence...ggattttcagacactaacttagctgcttctctattaatagtcaaccaactaaatattacaagaagctacaacttcaccacgtttcttttctctgttacagGATGCATATCTTCCTCAGAGGCTTCTGGACAAACTGATGTTTATATATAATTATGTCGAAATGGCTCGTGTAACTGGTGTCCCTATTTCATTTCTTCTTG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G63960.2 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G63960.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA06G16110.1 (Glycine max), 3'ss of exon 12
--ggattttcagacactaacttagctgcttctctattaatagtcaaccaactaaatattacaagaagctacaacttcaccacgtttcttttctctgttacagGATGCATATCTTCCTCAGAGGCTTCTGGACAAACTGATGTTTATATATAATTATGTCGAAATGGCTCGTGTAACTGGTGTCCCTATTTCATTTCTTCTTG
||| || || | | | | | | | | | | ||| || | || | | || |||| || || ||| | | | | |||||||||||||| |||||| ||||| |||| ||| ||||||| || || |||||||| || |||||||| ||||| |||||||| ||||| ||||| |||
tcagatattgtgaatccattatgggtatattacatgtgaaaaaaaactaagtgaaataaattgaccattcaaaattcat-actttgcttgtgt-taatgcagGATGCATATCTCCCTCAGCGGCTTTTGGATAAATTGATGTTCATTTACAATTATGTGGAGATGGCTCGAGTAACAGGTGTCCCAATTTCTTTTCTACTTT
upper sequence: AT5G63960.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA04G38800.1 (Glycine max), 3'ss of exon 12
ggattttcagacactaacttagctgcttc--tctattaatagtcaaccaactaaatattacaagaagctacaacttcaccacgtttcttttctctgttacagGATGCATATCTTCCTCAGAGGCTTCTGGACAAACTGATGTTTATATATAATTATGTCGAAATGGCTCGTGTAACTGGTGTCCCTATTTCATTTCTTCTTG
| | | || | | | | | || | ||| || | || | | || |||| |||| || | |||||||||||||| |||||| ||||| |||| ||| ||||||| || || |||||||| || |||||||| ||||| |||||||| ||||| ||||| |||
gaaaaccatgccatttctgtgatgggtatattacatctgaaaaaaactaagtgaaataaattgaccattcaaaattcata--gtttgcttgtctaaatgcagGATGCATATCTCCCTCAGCGGCTTTTGGATAAATTGATGTTCATTTACAATTATGTGGAGATGGCTCGAGTAACAGGTGTCCCAATTTCTTTTCTACTTT
upper sequence: AT5G63960.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: PP1S14_182V6.1 (Physcomitrella patens), 3'ss of exon 12
--------------------------------------------------------ggattttcagacactaacttag-ctgcttctctattaatagtcaaccaactaaatattacaagaagc------tacaacttcaccacgt--ttcttttctctgt-tacagGATGCATATCTTCCTCAGAGGCTTCTGGACAAACTGATGTTTATATATAATTATGTCGAAATGGCTCGTGTAACTGGTGTCCCTATTTCATTTCTTCTTG
| | || | | ||| | || | | || | || | | | || || | | |||| | | | || | | | |||||| || |||||||||||| | | |||||||| || |||| |||||| |||||||| || ||||||||||| |||||||| ||||| || ||||||||||
gtatgtgtatcttgatctagtcacatgagtggtctttaacttgtattagctgtatttgttgtttatctggccgcgtaggccatttttttggcaacaacttgagtacatagcctaataaagagtgcgtctcgtacactgaccatgaggtaccttcatttatgcacagGACGCTTATCTTCCTCAGCGATTACTGGACAAGCTTATGTATATATACAATTATGTTGAGATGGCTCGTGTTACTGGTGTTCCTATCTCCTTTCTTCTTG
upper sequence: AT5G63960.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: EFJ15982 (Selaginella moellendorffii), 3'ss of exon 11
ggattttcagacactaacttagctgcttctctattaatagtcaaccaactaaatattacaagaagctacaacttcaccacgtttcttttctctgttacagGATGCATATCTTCCTCAGAGGCTTCTGGACAAACTGATGTTTATATATAATTATGTCGAAATGGCTCGTGTAACTGGTGTCCCTATTTCATTTCTTCTTG
| | | || | ||| | | | |||||||||| |||||||| ||||| |||||||| | || || || ||||||||||||||||| ||| |||||||||| | ||||| || || || ||||| |||||||||
-------------------------------------------gtgagccgcacttt----ggttctatgtttatattttccatgttttctctgt--cagGATGCGTATCTGCCTCAGAGATTACTCGAAAAGCTGATGTTTATATATAACTATATCGAAATGGCAAGAGTAACAGGAGTTCCCATTTCGTTTCTTCTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caactaaatattacaagaagctacaacttcaccacgtttcttttctctgttacagGATGCATATCTTCCTCAGAGGCTTCTGGACAAACTGATGTTTATATATAATTATGTCGAAATGGCTCGTGTAACTGGTGTCCCTATTTCATTTCTTCTTG
aactaaa putative branch site (score: 2)
cttcaccacgtttctt putative PPT
aaatattacaagaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggattttcagacactaacttagctgcttctctattaatagtcaaccaactaaatattacaagaagctacaacttcaccacgtttcttttctctgttacagGATGCATATCTTCCTCAGAGGCTTCTGGACAAACTGATGTTTATATATAATTATGTCGAAATGGCTCGTGTAACTGGTGTCCCTATTTCATTTCTTCTTG
- - - - - acactaa
- - - - - - - - - - - - -cttctct
- - - - - - - - - - - - - - - - - - - -gtcaacc
- - - - - - - - - - - - - - - - - - - - - - - aactaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -acaagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctacaac