Sequence
atgc intronic sequence ATGC exonic sequencegtgtgtcttattgtccgttttctttattatttgtacctctgatgtttatttgtatctttgatgttatgaatccacaatctcttctgatgttgttatgtgaatgagcagGTTCTTTGGCCAGAATGCGGTTGGCAGCCTGTATCGTTGACCGATTTAATTACCGGTGCATCTGTCAAGAAAGTTTACAGGAAGGCCACTCTCTGTATAC
Basic information
species | Arabidopsis thaliana |
transcript | AT4G12770.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G12770.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os01g25320.1 (Oryza sativa), 3'ss of exon 6
gtgtgtcttattgtccgttttctttattatttgtacctctgatgtttatttgtatctttgatgttatgaatccacaatctcttctgatgttgttatgtgaatgagcagGTTCTTTGGCCAGAATGCGGTTGGCAGCCTGTATCGTTGACCGATTTAATTACCGGTGCATCTGTCAAGAAAGTTTACAGGAAGGCCACTCTCTGTATAC
| ||| | | | | |||| | | | | || | ||| || | |||| | || | | |||||| | ||| |||||||||||||| ||||| || |||| |||||||| ||||| ||||| ||||| | |||||||||||||||| |||||||| || || | || || |
----ctactatggggtgaagtgaacacaatttaaa--tttaactttcctaactattattattattatctttttgcagtacttatgctctttgttaatttaatt--cagGTTCTTTGGCCTGAATGTGGGTGGCGACCTGTATCATTGACTGATTTGATTACAGCCGCATCTGTCAAGAAAGAATACAGGAAAGCAACATTATGCATCC
upper sequence: AT4G12770.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM5G839757_T01 (Zea mays), 3'ss of exon 6
gtgtgtcttattgtccgttttctttattatttgtacctctgatgtttatttgtatctttgatgttatga-atccacaatctcttctgatgttgttatg-tgaatgagcagGTTCTTTGGCCAGAATGCGGTTGGCAGCCTGTATCGTTGACCGATTTAATTACCGGTGCATCTGTCAAGAAAGTTTACAGGAAGGCCACTCTCTGTATAC
| | | | | | | ||||||| || || | ||| || || || | ||| ||| ||| || | || | |||| | ||| |||||||||||||||||||| || ||||| |||||||| | || ||||| ||
----ctttaaagacataacctatatttaatttgta-----gaagtatttttttaa-ttagaagaaatgtcgatgacattctattttaatttgtttattctttctgaacagGTTCTTTGGCCAGAATGTGGGTGGCAACCTGTATCCCTCACTGATTTGATC-------------------------------------------------
upper sequence: AT4G12770.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G158872_T01 (Zea mays), 3'ss of exon 6
gtgtgtcttattgtccgttttctttattatttgtacct--ctgatgtttatttgtatctttgatgttatgaatccacaatctcttctgatgttgt-tatgtgaatgagcagGTTCTTTGGCCAGAATGCGGTTGGCAGCCTGTATCGTTGACCGATTTAATTACCGGTGCATCTGTCAAGAAAGTTTACAGGAAGGCCACTCTCTGTATAC
| || | || | || | | | | | ||| | |||| || | | || |||| | | | | | | ||||| | ||| | |||||||||||||| || ||||| ||||||| ||||| ||||||||||| || || |||| ||||| ||||||||||| || || || || |
-----ttacatggaaggtgcttttaaaaaaacggaaataatgaatgccaaattgt--ctcaaggctcgtaaa----caattccatttactaatatgtatgttctgaaacagATACTTTGGCCAGAATGTGGATGGCAAGCTGTATCATTGACTGATTTAATTACTGGAGCTGCTGTTAAGAAGCAGTACAGGAAGGCAACACTGTGCATTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atctttgatgttatgaatccacaatctcttctgatgttgttatgtgaatgagcagGTTCTTTGGCCAGAATGCGGTTGGCAGCCTGTATCGTTGACCGATTTAATTACCGGTGCATCTGTCAAGAAAGTTTACAGGAAGGCCACTCTCTGTATAC
ttctgat putative branch site (score: 3)
ttatgaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtgtcttattgtccgttttctttattatttgtacctctgatgtttatttgtatctttgatgttatgaatccacaatctcttctgatgttgttatgtgaatgagcagGTTCTTTGGCCAGAATGCGGTTGGCAGCCTGTATCGTTGACCGATTTAATTACCGGTGCATCTGTCAAGAAAGTTTACAGGAAGGCCACTCTCTGTATAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA