Sequence
atgc intronic sequence ATGC exonic sequencegtaagtctttatatccatttgatgcatgtcttttgtctctgtttctcgctcttggggttcaccaaaaattgaatctttttagctggaaacgtaccacgaatctcaaagtaacattttttataagatggattaggaaaagcaactgtatttcccctttttggttggtaaaagtctgatttttttgtttaatttgcagTGTGAGGTGTTCAGTGTCTGGTGGAAATGGAACTGCTGGAAAGAGAACGACTCTTCATGATCTATATGAGAAGGAAGGTCAGAGTCCTTGGTATGATAAT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G13420.1 |
intron # | 1 |
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 1
lower sequence: GLYMA08G47790.3 (Glycine max), 3'ss of exon 1
gtaagtctttatatccatttgatgcatgtcttttgtctctgtttctcgctcttggggttcaccaaaaattgaatctttttagctggaaacgtaccacgaatctcaaagtaacatttt-ttataagatggattaggaaaagcaactgtatttcccctttttggttggtaaaagtctgattttt--ttgtttaatttgcagTGTGAGGTGTTCAGTGTCTGGTGGAAATGGAACTGCTGGAAAGAGAACGACTCTTCATGATCTATATGAGAAGGAAGGTCAGAGTCCTTGGTATGATAAT
||| |||| ||| || || ||| || | || | || | | | | || | | | |||| || |||| | || ||| | | || || | | ||| ||||||| | ||| |||||| || ||||||||||| |||||||| ||||| |||||||| ||||||||||||
--------------------------------------------------------------------------------------------------gctcttcaagtgacaattagtttgaaggtgtagtattgtttcttatcttaaactgctcatgtaggaggcatatatttgatgcttgattgtcttcatt-cagGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGTGCTTCATGATCTTTATGAGAAAGAAGGGCAGAGTCCATGGTATGATAAT
upper sequence: AT5G13420.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA18G53700.1 (Glycine max), 3'ss of exon 1
gtaagtctttatatccatttgatgcatgtcttttgtctctgtttctcgctcttggggttcaccaaaaattgaatctttttagctggaaacgtaccacgaatctcaaagtaacattttttataagatggattaggaaaagcaactgtatttcccctttttggttggtaaaagtctgatttttttgtttaatt-tgcagTGTGAGGTGTTCAGTGTCTGGTGGAAATGGAACTGCTGGAAAGAGAACGACTCTTCATGATCTATATGAGAAGGAAGGTCAGAGTCCTTGGTATGATAAT
| | |||| ||| || | | | || ||| | | | || | | | | || ||| | |||| || | | | | ||| | | || || | | ||| ||||||| | ||| |||||| || ||||||||||| |||||||| ||||| |||||||| |||||||||||
----------------------------------------------------------------------------------------------aatgcccacttaagtgacaattagtttgaa--ggtgtagtattgtttcttaaacatctctcatatagaaggcaaatatttgatgcttgattgtgttcattcaGGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGTGCTTCATGATCTTTATGAGAAAGAAGGGCAGAGTCCATGGTATGATAA-
upper sequence: AT5G13420.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv01s0150g00190.t01 (Vitis vinifera), 3'ss of exon 1
gtaagtctttatatccatttgatgcatgtcttttgtctctgtttctcgctcttggggttcaccaaaaattgaatctttttagctggaaacgtaccacgaatctcaaagtaacattttttataagatggattaggaaaagcaactgtatttcccctttttggttggtaaaagtctgatttttttgtttaatt--tgcagTGTGAGGTGTTCAGTGTCTGGTGGAAATGGAACTGCTGGAAAGAGAACGACTCTTCATGATCTATATGAGAAGGAAGGTCAGAGTCCTTGGTATGATAAT
| ||| | | || ||| | ||| ||| || | | | | ||| | || ||| ||| | ||| || | |||||| || ||||| || |||||||||| ||||||||| |||||||||||||| |||||| ||| ||| ||||| || |||||||||||
----------------------------------------------------------------------------------------------ttgttgtttcatttttctctaattctaaagtttaatttttaaaggct----ttctctgattgtaaagtttgagaagttctcattccgtatgttatttattacagTGTCAGATGTTCCCAACTTGAGGGAAATGGAAGCCAAATAAAGAGAACAACTCTTCATGATCTCTATGAGCAGGGAGGGCAGAGCCCATGGTATGATAACMapped 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|164053794|gb|ES149686.1|ES149686EST: TCTTCTCAGCTTTCTCTTCGTTATAACCAACGATCAATACCTTCCCTCTC TGTGAGGTGTTCAGTGTC
genomic: TCTTCTCAGCTTTCTCTTCGTTATAACCAACGATCAATACCTTCCCTCTCgtaagtcttt ... taatttgcagTGTGAGGTGTTCAGTGTC
EST:
gi|124975980|gb|EL049432.1|EL049432EST: TCTTCTCAGCTTTCTCTTCGTTATAACCAACGATCAATACCTTCCCTCTC TGTGAGGTGTTCAGT
genomic: TCTTCTCAGCTTTCTCTTCGTTATAACCAACGATCAATACCTTCCCTCTCgtaagtcttt ... taatttgcagTGTGAGGTGTTCAGT
EST:
gi|116415992|gb|EG458584.1|EG458584EST: TCTTCTCAGCTTTCTCTTCGTTATAACCAACGATCAATACCTTCCCTCTC TGTGAGGTGTTCAGTGTCTGGTGGAAATGGAACTGCTGGAAAGAGAACGAC
genomic: TCTTCTCAGCTTTCTCTTCGTTATAACCAACGATCAATACCTTCCCTCTCgtaagtcttt ... taatttgcagTGTGAGGTGTTCAGTGTCTGGTGGAAATGGAACTGCTGGAAAGAGAACGAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actgtatttcccctttttggttggtaaaagtctgatttttttgtttaatttgcagTGTGAGGTGTTCAGTGTCTGGTGGAAATGGAACTGCTGGAAAGAGAACGACTCTTCATGATCTATATGAGAAGGAAGGTCAGAGTCCTTGGTATGATAAT
gtttaat putative branch site (score: 4)
tttttttgttt CT-rich tract
taaaagtctgattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtctttatatccatttgatgcatgtcttttgtctctgtttctcgctcttggggttcaccaaaaattgaatctttttagctggaaacgtaccacgaatctcaaagtaacattttttataagatggattaggaaaagcaactgtatttcccctttttggttggtaaaagtctgatttttttgtttaatttgcagTGTGAGGTGTTCAGTGTCTGGTGGAAATGGAACTGCTGGAAAGAGAACGACTCTTCATGATCTATATGAGAAGGAAGGTCAGAGTCCTTGGTATGATAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA