Sequence
atgc intronic sequence ATGC exonic sequencegtatctttttgtgattgtcttagacttgtggttgttaacaacatgctattaaaactttagagttcttctttatatgaaaagttgtctgatatgttaatggtatacctgacatgcactattagGACACTTGTGGAATCGGGAAAGGACATTGAAAGTGCGTATTGGGAACTTGTGGTGAAGGATATTCAGGATGCCTGCAAACTTTTTGAGCCAATCTATGAC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G13420.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G13420.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G47790.3 (Glycine max), 3'ss of exon 3
gtatctttttgtgattgtcttagacttgtggttgttaacaacatgctattaaaactttagagttcttctttatatgaaaagttgtctgatatgttaatggtatacctgacatgcactattagGACACTTGTGGAATCGGGAAAGGACATTGAAAGTGCGTATTGGGAACTTGTGGTGAAGGATATTCAGGATGCCTGCAAACTTTTTGAGCCAATCTATGAC
| ||| | | ||| | || | || || ||| | || | | || ||| | || || ||| ||| || || ||| ||||||| || | || || |||||||||||||| |||||||||||||| ||||||||||| || ||||| |||||| | ||||| |||||||||||
---------------gatattaaa---aggaaaaataaaataattttttttggtctcatatgttaataattctct-aattgttcttaaat-tgctaaaatcatattattcaatcatg--cagGGAACTTGTGCAAGCAGGGAAAGACATTGAAAGTGCATATTGGGAACTTGTAGTGAAGGATATCCAAGATGCTTGCAAATTATTTGAACCAATCTATGAT
upper sequence: AT5G13420.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA18G53700.1 (Glycine max), 3'ss of exon 3
gtatctttttgtgattgtcttagacttgtggttgttaacaacatgctattaaaactttagagttcttctttatatgaaaagttgtctgatatgttaatggtatacctgacatgcactattagGACACTTGTGGAATCGGGAAAGGACATTGAAAGTGCGTATTGGGAACTTGTGGTGAAGGATATTCAGGATGCCTGCAAACTTTTTGAGCCAATCTATGAC
| || | | || ||| ||||| ||||| || |||| | || | | || || || ||| ||| ||| | | ||| || ||| ||||||| || | || || |||||||||||||| |||||||||||||| ||||||||||| || ||||| |||| ||| ||||| |||||||||||
gaatatgctagtaatt--------cttgtt-ttgttcttaaattgctctattgacctagcaatttcctttcctac---------tcttata-actaaaaacaaattatacaatcatg--caGGGAACTTGTGCAAACAGGGAAAGACATTGAAAGTGCATATTGGGAACTTGTAGTGAAGGATATCCAAGATGCTTGCAGACTATTTGAACCAATCTATGA-
upper sequence: AT5G13420.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv01s0150g00190.t01 (Vitis vinifera), 3'ss of exon 3
gtatctttttgtgattgtcttagacttgtggttgttaacaacatgctattaaaactttagagttcttctttatatgaaaagttgtctgatatgttaatggtatacctgacatgcactattagGACACTTGTGGAATCGGGAAAGGACATTGAAAGTGCGTATTGGGAACTTGTGGTGAAGGATATTCAGGATGCCTGCAAACTTTTTGAGCCAATCTATGAC
| || | | |||| | | || || || || | ||||| || || | ||| | || |||| | || | | ||| |||||| | | ||||| |||||||||||||| || ||||| |||||||||||||| || || ||||| |||| |||||||||||||||||||||
-----------tagttattctgctcttgcaggacctgg-aatccaatacta--acatccgagttgatccttcagagttggtaaatctaacattttaa----acctttggattctgc----agGGAACTTGTACTAGCAGGAAAAGACATTGAAAGTGCATACTGGGAGCTTGTGGTGAAGGACATCCAAGATGCGTGCAGACTTTTTGAGCCAATCTATGATMapped 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|125324207|gb|EL338287.1|EL338287EST: ATCTTCCAAAAAGCCATTTCCACTTCAAATGCTTATAATGATCAATTCAG GACACTTGTGGAATCGGGAAAGGACATTGAAAGT
genomic: ATCTTCCAAAAAGCCATTTCCACTTCAAATGCTTATAATGATCAATTCAGgtatcttttt ... gcactattagGACACTTGTGGAATCGGGAAAGGACATTGAAAGT
EST:
gi|116415992|gb|EG458584.1|EG458584EST: ATCTTCCAAAAAGCCATTTCCACTTCAAATGCTTATAATGATCAATTCAG GACACTTGTGGAATCGGGAAAGGACATTGAAAGTGCGTATTGGGAACTTGT
genomic: ATCTTCCAAAAAGCCATTTCCACTTCAAATGCTTATAATGATCAATTCAGgtatcttttt ... gcactattagGACACTTGTGGAATCGGGAAAGGACATTGAAAGTGCGTATTGGGAACTTGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttatatgaaaagttgtctgatatgttaatggtatacctgacatgcactattagGACACTTGTGGAATCGGGAAAGGACATTGAAAGTGCGTATTGGGAACTTGTGGTGAAGGATATTCAGGATGCCTGCAAACTTTTTGAGCCAATCTATGAC
acctgac putative branch site (score: 3)
atatgttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatctttttgtgattgtcttagacttgtggttgttaacaacatgctattaaaactttagagttcttctttatatgaaaagttgtctgatatgttaatggtatacctgacatgcactattagGACACTTGTGGAATCGGGAAAGGACATTGAAAGTGCGTATTGGGAACTTGTGGTGAAGGATATTCAGGATGCCTGCAAACTTTTTGAGCCAATCTATGAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG