Sequence
atgc intronic sequence ATGC exonic sequencegtcagtttctttgatctcttttgtcctgtttagggaaaatcctcagttcctcataaatttagacttgatatgttgcagGTGGCAGACTTTGGATCTCTTGAACTCTCACCCGTCGATGGAAGAACTCTGACAGACTTTATGCACACCAGAGGCTTGCAAATGCATTCCTTGGGAAGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G28080.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G28080.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA04G24430.1 (Glycine max), 3'ss of exon 9
gtcagtttctt--tgatctcttttgtcctgtttagggaaaatcctc-----agttcctcataaatttagacttgatatgttgcagGTGGCAGACTTTGGATCTCTTGAACTCTCACCCGTCGATGGAAGAACTCTGACAGACTTTATGCACACCAGAGGCTTGCAAATGCATTCCTTGGGAAGAG
|| |||||||| || | ||| | | || | || | | | | ||| ||| |||||| || | |||||||||| ||||| || |||||||||||||| || |||||||| || |||| || || ||||| ||||| |||||||||||| |||||| ||| |||
gttagtttcttaatgttgaatttgtttatattaaaaccaagttattttgtaatgtgttcagttattgttacttgaaat-tcatagGTGGCAGATTTTGGGTCCCTTGAACTCTCACCTGTTGATGGAAGGACGTTGACTGATTTCATGCATACCAGGGGCTTGCAAATGTCTTCCTTAGGACGAG
upper sequence: AT4G28080.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA06G30000.1 (Glycine max), 3'ss of exon 10
gtcagtttctt--tgatctcttttgtcctgtttagggaaaatcctc-----agttcctcataaatttagacttgatatgttgcagGTGGCAGACTTTGGATCTCTTGAACTCTCACCCGTCGATGGAAGAACTCTGACAGACTTTATGCACACCAGAGGCTTGCAAATGCATTCCTTGGGAAGAG
|| |||||||| || | ||| | | |||| || | | | | | | ||| |||| | || | |||||||||| ||||| || |||||||||||||| || |||||||| || |||| || || ||||| || || |||||||||||| |||||| ||| |||
gttagtttcttaatgttgaatttgtttatatttaaaccaagttattttgtaatgtgtttagttattgttacttcaaat-tcatagGTGGCAGATTTTGGGTCCCTTGAACTCTCACCTGTTGATGGAAGGACGTTGACTGATTTCATGCATACTAGGGGCTTGCAAATGTCTTCCTTAGGACGAG
upper sequence: AT4G28080.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv11s0037g00840.t01 (Vitis vinifera), 3'ss of exon 12
gtcagtttctt--tgatctct-tttgtcctgtttagggaaaatcctcagttcctcataaatttagacttgatatgttgc-agGTGGCAGACTTTGGATCTCTTGAACTCTCACCCGTCGATGGAAGAACTCTGACAGACTTTATGCACACCAGAGGCTTGCAAATGCATTCCTTGGGAAGAG
|| ||| ||| | || | |||| || | | || | | || | | | |||| | | || | |||||||||| ||||| || |||||||| ||||| ||||||||||| ||| ||||||| |||||||||||||| || ||||||||| ||| ||||| | |
gttggttccttaataattattatttgctttgccttgtgatc-ttttaagacttttaaatatttgatttaactttgatattagGTGGCAGATTTTGGCTCCCTTGAACTTTCACCTGTCGATGGAAGGACTTTGACAGATTTTATGCACACCAGGGGTTTGCAAATGTGTTCGTTGGGTCGTG
upper sequence: AT4G28080.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: PP1S363_15V6.1 (Physcomitrella patens), 3'ss of exon 12
-------------------------------------------------------------------------------gtcagtttctttgatctcttttgtcctgtttagggaaaatcctcagttcctcataa-------atttagacttgatatgtt----gcagGTGGCAGACTTTGGATCTCTTGAACTCTCACCCGTCGATGGAAGAACTCTGACAGACTTTATGCACACCAGAGGCTTGCAAATGCATTCCTTGGGAAGAG
| || || || | || || | |||| || || | | | | | | | ||| || |||||||||||||||||||| ||||| |||||||| || |||||| | ||||| ||||| || |||||||| | || | || |||| ||||||||| ||||
gtaagttcatgtggattaaggaatacgtatgtcgagactgattgataccattaatgtacggaggtgatttgagagtccacttagcactcagcatagctgtgactttgcacagcaataatctggagctcattttgaccaccgcaaccatggtcgctatttttgtaacagGTGGCAGACTTTGGATCCCTTGAGCTCTCACCAGTGGATGGACGTACTCTTACAGATTTCATGCACACTCGGGGTCTACAGATGCGTTCCTTGGGGAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcctgtttagggaaaatcctcagttcctcataaatttagacttgatatgttgcagGTGGCAGACTTTGGATCTCTTGAACTCTCACCCGTCGATGGAAGAACTCTGACAGACTTTATGCACACCAGAGGCTTGCAAATGCATTCCTTGGGAAGAG
acttgat putative branch site (score: 5)
ataaatttagactt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcagtttctttgatctcttttgtcctgtttagggaaaatcctcagttcctcataaatttagacttgatatgttgcagGTGGCAGACTTTGGATCTCTTGAACTCTCACCCGTCGATGGAAGAACTCTGACAGACTTTATGCACACCAGAGGCTTGCAAATGCATTCCTTGGGAAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA