Sequence
atgc intronic sequence ATGC exonic sequence...aactttaaccattcgttggtgtaccataagatggtgacagctagatttagtttaaaaggagtgttgttggtttctcattgtcttgctttgttctttgcagATCGTGGCTACTATTCAGTAGAGACAGTTTCTCTATTGGTGGCACTAAAAGTGCGATACAGGGATAGACTTACAATCTTACGAGGGAATCACGAGAGTCG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G10430.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G10430.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G133464_T01 (Zea mays), 3'ss of exon 1
aactttaaccattc-gttggtgtaccataagatggtgacagctagatttagtttaaaaggagtgttgttggtttctcattgtcttgctttgttctttgcagATCGTGGCTACTATTCAGTAGAGACAGTTTCTCTATTGGTGGCACTAAAAGTGCGATACAGGGATAGACTTACAATCTTACGAGGGAATCACGAGAGTCG
| || ||| || | ||| | || | | || || | | | || | | ||| || | | |||| | | | || |||||||||||||||||||||||| || ||||||||||| || ||||| | ||||| || ||||| |||||| ||||||| | |||| ||||| ||||| |
-ggataaataatttagtagatgttcattactttatttccatgtataatacatctagcataactgtcatttttgttaaattgattgtgtctcttggctgcagATCGTGGCTACTATTCAGTCGAAACAGTTTCTCTGTTAGTGGCTTTGAAAGTCCGTTACAGAGATAGAATTACAATACTTAGAGGAAATCATGAGAGCAG
upper sequence: AT1G10430.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G038195_T01 (Zea mays), 3'ss of exon 1
aactttaaccattcgttg-gtgtacca-taagatggtgacagcta--gatttagtttaaaaggagtgttgttggtttctcattgtcttgctttgttctt---tgcagATCGTGGCTACTATTCAGTAGAGACAGTTTCTCTATTGGTGGCACTAAAAGTGCGATACAGGGATAGACTTACAATCTTACGAGGGAATCACGAGAGTCG
| | |||| | ||| | ||| | || || | | || ||| | | | | || || | | || | | |||| ||||||||||||||| |||||||| || || |||||||| || ||||| | ||||| || ||||| |||||| ||||||| | ||||| ||||| ||||| |
-------attttgtgttgagggtataagtaatttagtaggagttccttactttatttccatgtgtaatacgtctttgctaaattcattacgtgtctcttgactgcagATCGTGGCTATTATTCAGTTGAAACGGTTTCTCTGTTAGTGGCTTTGAAAGTCCGTTACAGAGATAGAATTACAATACTTCGAGGAAATCATGAGAGCAG
upper sequence: AT1G10430.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G119546_T01 (Zea mays), 3'ss of exon 1
-aactttaaccattcgttggtgtaccataagatggtgacagctagatttagtttaaaaggagtgttgttggtttctcattgtcttgctttgttctttgcagATCGTGGCTACTATTCAGTAGAGACAGTTTCTCTATTGGTGGCACTAAAAGTGCGATACAGGGATAGACTTACAATCTTACGAGGGAATCACGAGAGTCG
| | ||| || | ||| | || ||| |||||| | | | | | | | || | |||||| ||||||||||| ||||| ||||| || || |||||||||| |||||||| || || || || ||| | ||||| || |||| ||||| |||||| |
ctggggaagcttaccgtcttcatatc-taaactttctactgctttcgatagttttatttgtttccataccacagttgagttgactatgggtttttctgcagACCGTGGCTACTACTCAGTGGAGACTGTGTCCTTATTGGTGGCTCTAAAAGTACGTTATAGAGACAGAATCACAATATTGAGAGGAAATCATGAGAGTAG
upper sequence: AT1G10430.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA02G02990.1 (Glycine max), 3'ss of exon 1
-aactttaaccattcgttggtgtaccataagatggtgacagctagatttagtttaaaaggagtgttgttggtttctcattgtcttgctttgttctttgcagATCGTGGCTACTATTCAGTAGAGACAGTTTCTCTATTGGTGGCACTAAAAGTGCGATACAGGGATAGACTTACAATCTTACGAGGGAATCACGAGAGTCG
||| | ||| | | | | || | | | | || || | | | | || | | || ||||| || || |||| ||||||||| ||||||||||| ||||| ||| | || |||||||| | ||||| || ||||| |||||| |||||||| | | || ||||||||||| ||
ctttttttatcatgcttcttttgatgatgttcagattaga-cttttttgcatatttgggaactgctatcatttcctcatggtactggcaaaaattttgtagATCGTGGGTACTATTCAGTGGAGACTGTTACGCTTTTGGTGGCCTTGAAAGTTCGTTACAGAGATAGAATTACAATCCTTAGGGGAAATCACGAGAGCCG
upper sequence: AT1G10430.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA08G40490.1 (Glycine max), 3'ss of exon 1
aactttaaccattcgttggtgtaccataagatggtgacagctagatttagtttaaaaggagtgttgttggtttctcattgtcttgctttgttctttgcagATCGTGGCTACTATTCAGTAGAGACAGTTTCTCTATTGGTGGCACTAAAAGTGCGATACAGGGATAGACTTACAATCTTACGAGGGAATCACGAGAGTCG
| | ||| || | | || | | | | || | | || | || ||||| | || || | |||||||||||| ||||||||||| ||||| ||| | || |||||||| | ||||| || ||||| |||||| | ||||| | | || ||||| || |||||
ggtcattatatttctttcttttgtcacgctgctcttaaggattttcagtgtctgtggatactgcttccaattcctcatgataatggcttaattcatgcagATCGTGGATACTATTCAGTGGAGACTGTTACACTTTTGGTGGCTTTGAAAGTCCGTTACAGAGATAGAATCACAATTCTCAGGGGAAATCATGAAAGTCG
upper sequence: AT1G10430.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S102_196V6.1 (Physcomitrella patens), 3'ss of exon 1
aactttaaccattcgttggtgtaccataagatggtgacagctagatttagtttaaa-aggagtgttgttggtttctcattgtcttgctttgttctttgcagATCGTGGCTACTATTCAGTAGAGACAGTTTCTCTATTGGTGGCACTAAAAGTGCGATACAGGGATAGACTTACAATCTTACGAGGGAATCACGAGAGTCG
||| | | | | || | | ||||| | | |||| ||| | | || | || | | | | ||| || | ||||||||||||| || ||||| || ||||| || || || || ||||| || || ||||| || |||||||| | |||||||| |||||||| |||||||| |
aacgtca-tgaaactctgaggcctcccaagatactaattttagtatttgttttgttcatgggtctcattagatagttaagcatttgtttgctctgttgcagATCGTGGATATTATTCTGTCGAGACTGTGTCGCTCTTAGTGGCCCTGAAGGTGCGGTATAGGGATAGGATCACAATCTTGCGAGGGAACCACGAGAGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttagtttaaaaggagtgttgttggtttctcattgtcttgctttgttctttgcagATCGTGGCTACTATTCAGTAGAGACAGTTTCTCTATTGGTGGCACTAAAAGTGCGATACAGGGATAGACTTACAATCTTACGAGGGAATCACGAGAGTCG
tcttgctttgttcttt CT-rich tract
tttaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aactttaaccattcgttggtgtaccataagatggtgacagctagatttagtttaaaaggagtgttgttggtttctcattgtcttgctttgttctttgcagATCGTGGCTACTATTCAGTAGAGACAGTTTCTCTATTGGTGGCACTAAAAGTGCGATACAGGGATAGACTTACAATCTTACGAGGGAATCACGAGAGTCG
- - - - - - - - - - - accataa
- - - - - - - - - - - - - - - - - - - - - -gatttag
- - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaggag