Sequence
atgc intronic sequence ATGC exonic sequencegtaaagaaactctgctcttctcgtttccactgaaatatagtaaacttagtcacattgtaaccgtcatggtgaatcacagGGATATTGGATGGTCAAGCGGGCTGTTGGAACAAAAGCCTGCTTGCTCGGTAAAGCTGTGACCTGTAAGTACCTGAGGCAGGATAACTTTTTGGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G35180.4 |
intron # | 22 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G35180.4 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: GRMZM2G160927_T01 (Zea mays), 3'ss of exon 7
gtaaaga-aactctgctcttct-cgtttccactg-aaatatagtaaacttagtcacattgtaaccgtcatggtgaatca---cagGGATATTGGATGGTCAAGCGGGCTGTTGGAACAAAAGCCTGCTTGCTCGGTAAAGCTGTGACCTGTAAGTACCTGAGGCAGGATAACTTTTTGGAG
||| | || ||| | | | | || || | |||| || ||| | ||| | ||| | ||||| ||||||||||| ||||| ||||| ||||||||||| ||| | || || ||||| || || || || || || | |||||||||||| |||||
gtatgcatgtcttagctgatgtacagtattaccatgcatgtggtaa-tttgttcatgtc--aacttttgcatgaaattatgtcagGGTTATTGGATGGTTAAGCGTGCTGTAGGAACAAAAGCTTGCCTTCTGGGCAAAGCAGTAACGTGCAATTATCTTCGCCAGGATAACTTTCTGGAG
upper sequence: AT5G35180.4 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: GLYMA15G26120.1 (Glycine max), 3'ss of exon 7
------------gtaaagaaactc---tgctcttctcgtttccactgaaatatagtaaacttagtcacattgtaaccgtcatggtgaatcacagGGATATTGGATGGTCAAGCGGGCTGTTGGAACAAAAGCCTGCTTGCTCGGTAAAGCTGTGACCTGTAAGTACCTGAGGCAGGATAACTTTTTGGAG
||| | || ||| || | ||| || ||||| | || || | ||| | || |||||||||||||||||||||| ||||| ||||||||||| ||| | || || |||||||| || ||||| ||| | | || ||||| ||||| |||
gtgtgtgattctttaagatgattcatatgccttttttatttattttg---tatagca---ttgagcaaccaatggttttca--acggat-gtagGGATATTGGATGGTCAAGCGAGCTGTAGGAACAAAAGCTTGCCTACTAGGGAAAGCTGTCACTTGTAAATACTTTAAACAAGATAATTTTTTTGAG
upper sequence: AT5G35180.4 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: GLYMA17G11250.1 (Glycine max), 3'ss of exon 19
-----------gtaaagaaactctgctcttctcgtttccactgaaatatagtaaacttagtcacattgtaaccgtcatggtgaatcacagGGATATTGGATGGTCAAGCGGGCTGTTGGAACAAAAGCCTGCTTGCTCGGTAAAGCTGTGACCTGTAAGTACCTGAGGCAGGATAACTTTTTGGAG
|| ||| | | | | | ||| |||| | || |||| | || ||| ||| |||||||||||||||||||||| | ||||| ||||| ||||| ||| | | || ||||||||||| ||||| ||| | || || ||||| |||||||||
gtgtgtgatcctcaatgaagtgttatatatgccctatttgatgactgatagca---tttgtcagttgatagttttca-attga--tacagGGATATTGGATGGTCAAGAGAGCTGTAGGAACCAAAGCTTGCCTCTTAGGAAAAGCTGTGACTTGTAAATACTTTAGACAAGATAATTTTTTGGAG
upper sequence: AT5G35180.4 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: GLYMA13G22460.1 (Glycine max), 3'ss of exon 19
----------gtaaagaaactctgctcttctcgtttccactgaaatatagtaaacttagtcacattgtaaccgtcatggtgaatcacagGGATATTGGATGGTCAAGCGGGCTGTTGGAACAAAAGCCTGCTTGCTCGGTAAAGCTGTGACCTGTAAGTACCTGAGGCAGGATAACTTTTTGGAG
|||| || | | | | | ||| | || || |||| | || ||| ||| |||||||||||||||||||||| | ||||| ||||| ||||| ||| | | || ||||||||||| ||||| ||| | || || ||||| |||||||||
gtgtgagatcctaaatgaagtgttatatatatgccctatttgatgactgatagcatttgtcagctaatagttttcaaattga--tacagGGATATTGGATGGTCAAGAGAGCTGTAGGAACCAAAGCTTGCCTCTTAGGAAAAGCTGTGACTTGTAAATACTTTAGACAAGATAATTTTTTGGAG
upper sequence: AT5G35180.4 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: PP1S376_46V6.1 (Physcomitrella patens), 3'ss of exon 18
------gtaaagaaactctgctcttctcgtttccactgaaatata---gtaaacttagtcacattgtaac-----------cgtcatggtgaat-cacagGGATATTGGATGGTCAAGCGGGCTGTTGGAACAAAAGCCTGCTTGCTCGGTAAAGCTGTGACCTGTAAGTACCTGAGGCAGGATAACTTTTTGGAG
|| | | | || | | | | || | | | |||| | |||| | | | | ||| | | |||| ||||||||||| ||||| |||||||| |||||||| ||| | || || |||||||| || ||||| ||| || | ||||| ||| | |||
tgtttattatggcacgtttgattatgttttctctttcaagacgaataggtaatacctactgccttgtgaatcagtttctaacattacattgatttcttagGGTTATTGGATGGTGAAGCGTGCTGTTGGTACAAAAGCATGCCTACTGGGCAAAGCTGTCACTTGTAATTACTTGCGTAGAGATAATTTTCTTGAG
upper sequence: AT5G35180.4 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: PP1S141_3V6.1 (Physcomitrella patens), 3'ss of exon 18
------------gtaaagaaactctgctcttctcgtttccactgaaatatagtaaacttagtcaca--------ttgtaaccgtcatggtgaatc-acagGGATATTGGATGGTCAAGCGGGCTGTTGGAACAAAAGCCTGCTTGCTCGGTAAAGCTGTGACCTGTAAGTACCTGAGGCAGGATAACTTTTTGGAG
|| | | | | || | | | || || | | | | || | | | | | | |||| |||||| || |||||||| ||||| |||||||| ||||||||||| | || ||||| ||||| || ||||| ||| || | | |||||||| | |||
tttttttgaaagacaatgtgattttatgttttttttcgagatggatgcatgatgcatacactgttgggaatcttttctcaacacctcgttcaatccacagGGTTACTGGATGGTGAAGCGTGCTGTTGGTACAAAAGCCTGTCTACTGGGTAATGCTGTCACTTGTAATTACTTGCGCAAAGATAACTTCCTTGAGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|164075632|gb|ES071715.1|ES071715EST: TAAGCTAATTCCAAGTATTGTTCAG GGATATTGGATGGTCAAGCGGGCTGTTGGAACAAAAGC
genomic: TAAGCTAATTCCAAGTATTGTTCAGgtaaagaaac ... tgaatcacagGGATATTGGATGGTCAAGCGGGCTGTTGGAACAAAAGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttccactgaaatatagtaaacttagtcacattgtaaccgtcatggtgaatcacagGGATATTGGATGGTCAAGCGGGCTGTTGGAACAAAAGCCTGCTTGCTCGGTAAAGCTGTGACCTGTAAGTACCTGAGGCAGGATAACTTTTTGGAG
ttgtaac putative branch site (score: 2)
aaatatagtaaactta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaagaaactctgctcttctcgtttccactgaaatatagtaaacttagtcacattgtaaccgtcatggtgaatcacagGGATATTGGATGGTCAAGCGGGCTGTTGGAACAAAAGCCTGCTTGCTCGGTAAAGCTGTGACCTGTAAGTACCTGAGGCAGGATAACTTTTTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG