Sequence
atgc intronic sequence ATGC exonic sequencegtggctaaaatccttaagtctaaatcactgtcgataatgaaaagataattccaaaatttttaactgatgatctctgttatgtacgcagGAAGGGTCATCGAATTACTTCAAAGGATTGATGCTGATTCTTTGTTATTTGATAGTAGCTGCCAGTTTCTTTGTACACGAAGATCCTCACCAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G13320.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G13320.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os02g04630.1 (Oryza sativa), 3'ss of exon 10
gtggctaaaatccttaagtctaaatcactgtcg---ataatgaaaaga---taattccaaa--atttttaactgatgatctctgttatgtacg--cagGAAGGGTCATCGAATTACTTCAAAGGATTGATGCTGATTCTTTGTTATTTGATAGTAGCTGCCAGTTTCTTTGTACACGAAGATCCTCA--CCAAG-
|| ||||||| || | | | | || | || ||| || | ||| || | ||||| || | | | | | | || ||||| ||| | || |||| | |||||||||||||| |||| |||||| ||||||||||||||||||| | |||||| | ||||| | |||||
gtaa-taaaatcattgtgcaaagagagcattcttttaaaacaaaatgagtttgatttcacatgattttaaaacgttcttttaaatcacacactttcagGATGGGACTTCAAATTGTGTGAAAGGATTGATGCTATTTCTCTGTTATCTGATAGTAGCTGCCAGTTTTTATGTACATGCTGATCCAAATTCCAAGG
upper sequence: AT3G13320.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA08G44920.1 (Glycine max), 3'ss of exon 9
-------------------------gtggctaaaatccttaagtctaaatcactgtcgataatgaaaa-gataattccaaaatttttaactgatgatctctgttatgtacgcagGAAGGGTCATCGAATTACTTCAAAGGATTGATGCTGATTCTTTGTTATTTGATAGTAGCTGCCAGTTTCTTTGTACACGAAGATCCTCACCAAG--
||||| | | | | | || || || || | | || || | || | || | | | | ||||||||| | | ||||||||||||||| | |||| |||||||| ||| ||||||| ||||||||||| | |||||| |||| | |||
gtttgtattcaaagataaaagaatgaaaatgaaaattatgctattaggaacccaaaacatgtagacaatgacatatgttaacattgtgac-attaatttattatgcatttgcagGAAGGAACTGCCAATTACTTCAAAGGACTACTGCTTATTCTTTGCTATCTGATAGTGGCTGCCAGTTTTTATGTACATTTAGATTCCTCTCAATAA
upper sequence: AT3G13320.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA08G44910.1 (Glycine max), 3'ss of exon 9
----------------------gtggctaaaatccttaagtctaa-atcac---tgtcgataatgaaaagataattccaaaatttttaactga-----------tgatctctgttatgtac--gcagGAAGGGTCATCGAATTACTTCAAAGGATTGATGCTGATTCTTTGTTATTTGATAGTAGCTGCCAGTTTCTTTGTACACGAAGATCCTCACCAAG------
| | ||| |||| | || || ||| | ||||| ||| ||| | | ||||| ||| | | ||||| | ||||||||| | | ||||||||||||||| | ||||| |||||||| ||| ||||||| || |||||||| | |||||| | |||| | |||
gtttgtattcaaacataaaaaaaagaatgaaaattaaaagtatggtattacgaatgttaacaatgacttgattattagtatggtgaagactgaagagacaacactgacatttattatgcatttgcagGAAGGAACTGCTAATTACTTCAAAGGACTAATGCTTATTCTTTGCTATCTGATAGTGGCAGCCAGTTTTTATGTACATGTAGATTCCTCTCAATAAGTTA
upper sequence: AT3G13320.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA18G08030.1 (Glycine max), 3'ss of exon 11
-------------------------------------------gtggctaaaatccttaagt--ctaaatcac---tgtcgataatgaaaagataattc------caaaatttttaactgatga--tctctgttatgta--cgcagGAAGGGTCATCGAATTACTTCAAAGGATTGATGCTGATTCTTTGTTATTTGATAGTAGCTGCCAGTTTCTTTGTACACGAAGATCCTCACCAAG------
| || | ||| || || || | ||| | |||| ||| ||| |||| | | | ||| | | | ||||| | ||||||||| | | |||||||||||||| | ||||| |||||||| ||| ||||||| || |||||||| | |||||| | |||| | |||
gtttgtattcaatcataaaaaaaagaataaaaattaaaagtatggtattaggaacctaaaacacatagatagcacatgttaacaatgccttgattattagtatgataaaaagataacattgtgacatatttattatgaatttgcagGAAGGAACTGCTAATTACTTCAAAGGGCTAATGCTTATTCTTTGCTATCTGATAGTGGCAGCCAGTTTTTATGTACATGTAGATTCCTCTCAATAAGTTA
upper sequence: AT3G13320.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv19s0015g01320.t01 (Vitis vinifera), 3'ss of exon 10
---------------------------------------gtggctaaaatccttaagtctaaatcactgtcgataatgaaaagataattccaaaatttttaactgatgatctctgttatgtacgcagGAAGGGTCATCGAATTACTTCAAAGGATTGATGCTGATTCTTTGTTATTTGATAGTAGCTGCCAGTTTCTTTGTACACGAAGATCCTCACCAAG---
| | || | | |||| | | | | | ||| || ||| | || || |||| ||| ||||||||| | || |||||||| |||||| | ||||| |||||||| ||| | ||||| || || |||||||||||||| | |||||| ||
gtttgtattcaatgaaggaacacagatctatatactttgatagtggtgtcttgtagatattcatcattatttct--ctgtttggttatttcacaataacttacatattcctcttgttttgtttgcagGAAGGCACTTCTAATTACTTTAAAGGACTAATGCTCATTCTTTGCTATCTAATAGTTGCAGCAAGTTTCTTTGTACATGTCGATCCTACTTTAGTAG
upper sequence: AT3G13320.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: PP1S245_10V6.1 (Physcomitrella patens), 3'ss of exon 11
------------------------------------------gtggctaaaatccttaagtctaaatcactgtcgataatgaaaagataattc--caaaatttttaactgatgatctctgttatgtacgcagGAAGGGTCATCGAATTACTTCAAAGGATTGATGCTGATTCTTTGTTATTTGATAGTAGCTGCCAGTTTCTTTGTACACGAAGATCCTCACCAAG------
| || | | || || || | | || | || | || | | |||| | || || ||| | | ||||| || |||| |||||||| || || ||||||||||||||||| |||||||| || | ||||| ||||| || |||| || || | |
gtgggtggttttctccatttccttcgattaactgacagtataggggattatgtctgcgttgttagatt-ttcttagtattctcaatcttcctcattccggctctaaactcacgacct-tgtggttgtcacagGAGGGCACATCAAATTACTTTAAGGGCTTGATGCTGATTCTTTGCTATTTGATTGTGGGAGCCAGCTTCTTCGTGCACGTCGACATTCCGGACGCGCACCMapped 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|86088412|gb|DR384171.1|DR384171EST: AGACGGCGATGCTGTTCATCACTGTTATAGTAGTAGCATTTTTTCTCCAG GAAGGGTCATCGAATTACTTCAAAGGATTGATGCTGATTCTTTGTTATTTG
genomic: AGACGGCGATGCTGTTCATCACTGTTATAGTAGTAGCATTTTTTCTCCAGgtggctaaaa ... atgtacgcagGAAGGGTCATCGAATTACTTCAAAGGATTGATGCTGATTCTTTGTTATTTG
EST:
gi|124934528|gb|EL011591.1|EL011591EST: AGACGGCGATGCTGTTCATCACTGTTATAGTAGTAGCATTTTTTCTCCAG GAAGGGTCATCGAATTACTTCAAAGGATTGATGCTGATTCTTTG
genomic: AGACGGCGATGCTGTTCATCACTGTTATAGTAGTAGCATTTTTTCTCCAGgtggctaaaa ... atgtacgcagGAAGGGTCATCGAATTACTTCAAAGGATTGATGCTGATTCTTTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ataatgaaaagataattccaaaatttttaactgatgatctctgttatgtacgcagGAAGGGTCATCGAATTACTTCAAAGGATTGATGCTGATTCTTTGTTATTTGATAGTAGCTGCCAGTTTCTTTGTACACGAAGATCCTCACCAAG
aaaagataattccaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtggctaaaatccttaagtctaaatcactgtcgataatgaaaagataattccaaaatttttaactgatgatctctgttatgtacgcagGAAGGGTCATCGAATTACTTCAAAGGATTGATGCTGATTCTTTGTTATTTGATAGTAGCTGCCAGTTTCTTTGTACACGAAGATCCTCACCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA