Sequence
atgc intronic sequence ATGC exonic sequence...atatggttttcttttgctacaacttgctttttagttcttatgcatattgctatagtgcacagtaaagcatcagaataagattaattttctcttgctccagGAAGGATGTGGTGCCATTGTCGAATGGTGTACTTGCCGATGTCGTATTTGTATGGAAAAAGGTTTGTGGGTCCCATAACGTCCACTGTTTTATCACTGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G07050.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G07050.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G065494_T01 (Zea mays), 3'ss of exon 5
atatggttttcttttgctacaacttgctttttagttcttatgcatattgctatagtgcacagtaaagcatcagaataagattaattttctcttgctccagGAAGGATGTGGTGCCATTGTCGAATGGTGTACTTGCCGATGTCGTATTTGTATGGAAAAAGGTTTGTGGGTCCCATAACGTCCACTGTTTTATCACTGAG
|||| | | | | | | | |||| || | | | | | | | || || || | | |||| ||||||||||| ||||||||||||||||| ||||| |||| || | ||||| || |||||||| |||| || || | || || | | ||
ctatgttgcattaccatagtctttcggtagtctgctcttggttgctatgttgttacttttgctgatacgatacactattatggtttacaatgtcttacagGGAGGATGTGGTGTCATTGTCGAATGGTGTATTTGCCAATGTGCTACATCTATGGGAAGAGGTTTGTTGGTCGAATCACACCACTCGTGTTGGAATTAAG
upper sequence: AT2G07050.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G023798_T02 (Zea mays), 3'ss of exon 3
------atatggttttcttttgctacaacttgctttttagttcttatgcatattgctatagtgcacagtaaagcatcagaataagattaattttctcttgctccagGAAGGATGTGGTGCCATTGTCGAATGGTGTACTTGCCGATGTCGTATTTGTATGGAAAAAGGTTTGTGGGTCCCATAACGTCCACTGTTTTATCACTGAG
||| | | | | | | | | || ||| | || || || | || | | | | | | || | | |||||| ||| ||||||||||| ||||||||||||||||| ||||| |||| || | ||||| || |||||||| || | || || | | | || | | ||
attaccataggtccatagtctttcagtagtgtgctcttggtttctttgttgtttcctttttctcata-tgatacgcttttgt--ggtttacaatgtcttgc---agGGAGGATGTGGTGTCATTGTCGAATGGTGTATTTGCCAATGTGCTACATTTATGGGAAGAGGTTTGTTGGCCGAATCACACCACTTCTGTTGGAATTAAG
upper sequence: AT2G07050.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA01G00430.2 (Glycine max), 3'ss of exon 6
--atatggttttcttttgctacaacttgc-tttttagttcttatgcatattgctatagtgcacagtaaa-gcatcagaataagattaattttctcttgctccagGAAGGATGTGGTGCCATTGTCGAATGGTGTACTTGCCGATGTCGTATTTGTATGGAAAAAGGTTTGTGGGTCCCATAACGTCCACTGTTTTATCACTGAG
| ||||| ||||| | | | || || | | || ||| | || |||| ||| |||| | | || || | | |||||||||||||||| || || || ||||| || ||||||||||| || || ||||| || |||||||| ||||| || | | || || ||||| ||||
taaattggttgtctttagtcattgtgaacattgtttgatgttccattcattctttatgtaaacaggaaataaatcatatt----tttatgctaatgcattacagGAAGGATGTGGTGTCACTGCCGGATGGTCTATTTGCCGATGTCCTACTTATATGGCAAGAGGTTTGTTGGTCCAATCTCACCAACAGTATTATCTTTGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attgctatagtgcacagtaaagcatcagaataagattaattttctcttgctccagGAAGGATGTGGTGCCATTGTCGAATGGTGTACTTGCCGATGTCGTATTTGTATGGAAAAAGGTTTGTGGGTCCCATAACGTCCACTGTTTTATCACTGAG
gattaat putative branch site (score: 3)
ttttctcttgctcc CT-rich tract
agaataagattaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atatggttttcttttgctacaacttgctttttagttcttatgcatattgctatagtgcacagtaaagcatcagaataagattaattttctcttgctccagGAAGGATGTGGTGCCATTGTCGAATGGTGTACTTGCCGATGTCGTATTTGTATGGAAAAAGGTTTGTGGGTCCCATAACGTCCACTGTTTTATCACTGAG
- - - - - - - - ctacaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - acagtaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aataaga