Sequence
atgc intronic sequence ATGC exonic sequencegtaaatcttgaagctaattacgaaaccaatctcgagtatatctctctcttcaaagttgttaaatgtctttgtgtgtggtgtttttatgcagGAAGGAACATCGAATTACTTCAAAGGATTGATGCTCATTCTTTGCTATTTGATAGTCGCCGCTAGTTTCTTTGTACACGAAGATCCTCATCAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G55730.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G55730.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA08G44910.1 (Glycine max), 3'ss of exon 9
--------------------------gtaaatcttgaagcta----attacgaa----accaatctcgagtatatctctctcttcaaagttgtt-aaatgtctttg-tgtgtggtgtttttatgcagGAAGGAACATCGAATTACTTCAAAGGATTGATGCTCATTCTTTGCTATTTGATAGTCGCCGCTAGTTTCTTTGTACACGAAGATCCTCATCAAG------
| || || || || |||||||| | |||| | | ||| | | | || || | | | || | | | | | ||||||||||||| | ||||||||||||||| | ||||| |||||||||||| ||||||| || || ||||| | |||||| | |||| | ||||
gtttgtattcaaacataaaaaaaagaatgaaaattaaaagtatggtattacgaatgttaacaatgacttgattattagtatggtgaagactgaagagacaacactgacatttattatgcatttgcagGAAGGAACTGCTAATTACTTCAAAGGACTAATGCTTATTCTTTGCTATCTGATAGTGGCAGCCAGTTTTTATGTACATGTAGATTCCTCTCAATAAGTTA
upper sequence: AT1G55730.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA18G08030.1 (Glycine max), 3'ss of exon 11
-----------------------------------------------gtaaatcttgaagctaattacgaaaccaatctcgagtatatctctctcttcaaagttgttaaa---tgtctttgtg-----tgtggtgtttttatgcagGAAGGAACATCGAATTACTTCAAAGGATTGATGCTCATTCTTTGCTATTTGATAGTCGCCGCTAGTTTCTTTGTACACGAAGATCCTCATCAAG------
|| || | || | | || | | || || | | | | | ||| | | ||||| | | | | | ||||||||||||| | |||||||||||||| | ||||| |||||||||||| ||||||| || || ||||| | |||||| | |||| | ||||
gtttgtattcaatcataaaaaaaagaataaaaattaaaagtatggtattaggaacctaaaacacatagatagcacatgttaacaatgccttgattattagtatgataaaaagataacattgtgacatatttattatgaatttgcagGAAGGAACTGCTAATTACTTCAAAGGGCTAATGCTTATTCTTTGCTATCTGATAGTGGCAGCCAGTTTTTATGTACATGTAGATTCCTCTCAATAAGTTA
upper sequence: AT1G55730.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA08G44920.1 (Glycine max), 3'ss of exon 9
------------------gtaaatcttgaagctaattacgaaaccaatc-tcgagtatatctctctcttcaaagttgttaa----atgtctttgtgtgtggtgtttttatgcagGAAGGAACATCGAATTACTTCAAAGGATTGATGCTCATTCTTTGCTATTTGATAGTCGCCGCTAGTTTCTTTGTACACGAAGATCCTCATCAAG--
||| | | ||||| | | | | | | || | | | | |||||| || | || | | | | | ||||||||||||| | ||||||||||||||| | |||| |||||||||||| ||||||| || || ||||| | |||||| |||| | ||||
gtttgtattcaaagataaaagaatgaaaatgaaaattatgctattaggaacccaaaacatgtagacaatgacatatgttaacattgtgacatta-atttattatgcatttgcagGAAGGAACTGCCAATTACTTCAAAGGACTACTGCTTATTCTTTGCTATCTGATAGTGGCTGCCAGTTTTTATGTACATTTAGATTCCTCTCAATAA
upper sequence: AT1G55730.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv19s0015g01320.t01 (Vitis vinifera), 3'ss of exon 10
-----------------------------gtaaatcttgaagctaattacgaaaccaatctcgagtatatctctctcttcaaagttgtta-aatgtctt---tgtgtgtggtgtttt-tatgcagGAAGGAACATCGAATTACTTCAAAGGATTGATGCTCATTCTTTGCTATTTGATAGTCGCCGCTAGTTTCTTTGTACACGAAGATCCTCATCAAG---
|| | |||| | | | | || ||| ||||| || | | | ||| ||| | | | |||||| | |||||||||| || || |||||||| |||||| | |||||||||||||||||| | ||||| || || |||||||||||||| | |||||| | ||
gtttgtattcaatgaaggaacacagatctatatactttgatagtggtgtcttgtagatattcatcattatttctctgtttggttatttcacaataacttacatattcctcttgttttgtttgcagGAAGGCACTTCTAATTACTTTAAAGGACTAATGCTCATTCTTTGCTATCTAATAGTTGCAGCAAGTTTCTTTGTACATGTCGATCCTACTTTAGTAG
upper sequence: AT1G55730.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: PP1S245_10V6.1 (Physcomitrella patens), 3'ss of exon 11
------------------------------gtaaatcttgaagctaattacgaaaccaatctcgagtatatctc-tctcttcaaagttgttaaatgtctttgtgtg-tggtgtttttatg-------cagGAAGGAACATCGAATTACTTCAAAGGATTGATGCTCATTCTTTGCTATTTGATAGTCGCCGCTAGTTTCTTTGTACACGAAGATCCTCATCAAG------
| | || |||| | | | | | | | | | |||| || | | | | | | | || || ||||| || ||||| |||||||| || || |||||||| ||||||||||||||||| || | || || ||||| || |||| || || | |
gtgggtggttttctccatttccttcgattaactgacagtataggggattatgtctgcgttgttagattttcttagtattctcaatcttcctcattccggctctaaactcacgaccttgtggttgtcacagGAGGGCACATCAAATTACTTTAAGGGCTTGATGCTGATTCTTTGCTATTTGATTGTGGGAGCCAGCTTCTTCGTGCACGTCGACATTCCGGACGCGCACCMapped 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|116460063|gb|EG502655.1|EG502655EST: AGACGGCTACTCTGTTCATAACTGTTATTGTTGTAGCTTTCTTTTTCCAG GAAGGAACATCGAATTACTTCAAAGGATTGATGCTCATTTTTTGCTATTTG
genomic: AGACGGCTACTCTGTTCATAACTGTTATTGTTGTAGCTTTCTTTCTCCAGgtaaatcttg ... ttttatgcagGAAGGAACATCGAATTACTTCAAAGGATTGATGCTCATTCTTTGCTATTTG
EST:
gi|164064350|gb|ES066319.1|ES066319EST: AGACGGCTACTCTGTTCATAACTGTTATTGTTGTAGCTTTCTTTCTCCAG GAAGGAACATCGAATTACTTCAAAGGATTGATGCTCA
genomic: AGACGGCTACTCTGTTCATAACTGTTATTGTTGTAGCTTTCTTTCTCCAGgtaaatcttg ... ttttatgcagGAAGGAACATCGAATTACTTCAAAGGATTGATGCTCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatatctctctcttcaaagttgttaaatgtctttgtgtgtggtgtttttatgcagGAAGGAACATCGAATTACTTCAAAGGATTGATGCTCATTCTTTGCTATTTGATAGTCGCCGCTAGTTTCTTTGTACACGAAGATCCTCATCAAG
tgttttt CT-rich tract
ttgttaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaatcttgaagctaattacgaaaccaatctcgagtatatctctctcttcaaagttgttaaatgtctttgtgtgtggtgtttttatgcagGAAGGAACATCGAATTACTTCAAAGGATTGATGCTCATTCTTTGCTATTTGATAGTCGCCGCTAGTTTCTTTGTACACGAAGATCCTCATCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA