Sequence
atgc intronic sequence ATGC exonic sequencegtttaaacatcactatttgtggatcattatattatgaagcaattccttatgagatattcaatttgggtaacttgtatgtttgtagGGAGAAGAAATTTGTGTTGCTTTGCAAACACATATAAATGATGTCATGTTGCGTCGTTACTCCAAAGCTCGATCTGCTGCCAATAGCTTGGTTAATGGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G65930.2 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G65930.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA01G35950.1 (Glycine max), 3'ss of exon 12
----------------------------------gtttaaacatcactatttgtggatcattatattatgaagcaattccttatgagatattcaatttgggtaac-ttgtatg----tttgtagGGAGAAGAAATTTGTGTTGCTTTGCAAACACATATAAATGATGTCATGTTGCGTCGTTACTCCAAAGCTCGATCTGCTGCCAATAGCTTGGTTAATGGAG
||| || | | |||| |||| | || ||| ||| ||| |||| || | || || ||| |||| ||||||||||||||||||| ||| | || ||||| ||||||||||| ||| |||| || || |||||||||||||||||||| | | | |||| ||
gtattagcatgctcagggacattctactctaccaatttcttaatttcggcctttggac--ttat-tcatatcttcattactttggagttattttatattattagtattttatcattctttgaagGGAGAAGAAATTTGTGTAGCTCTTCAGACACACATAAATGATGTAATGCTGCGCCGCTATTCCAAAGCTCGATCTGCTGCGGGTGGTCCTTTGAATGAAG
upper sequence: AT5G65930.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA09G32740.1 (Glycine max), 3'ss of exon 12
gtttaaacatcactatttgtggatcattatattatgaagca--attccttatgagatattcaattt---gggtaacttgtatgtttg---tagGGAGAAGAAATTTGTGTTGCTTTGCAAACACATATAAATGATGTCATGTTGCGTCGTTACTCCAAAGCTCGATCTGCTGCCAATAGCT-TGGTTAATGGAG
| | || ||||| ||| || | | || | || ||| || |||| | | || || | | |||| |||||||||||||||||||| ||| | || ||||||||||||||||| ||| |||| ||||| || ||||| ||||| ||||| | | ||||| ||
----gtataatacc-tttgttgatgatgtcac-acaaacccttgtttctttggaattattttgcctcactgatattttatctatttgttgtagGGAGAAGAAATTTGTGTAGCTCTTCAGACACATATAAATGATGTAATGCTGCGCCGTTATTCGAAAGCACGATCAGCTGCTGCTGGTGGTGGTTCTCTGA-
upper sequence: AT5G65930.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA11G09480.1 (Glycine max), 3'ss of exon 12
-----------------------------------gtttaaacatcactatttgtggatcattatattatgaagcaattccttatgagatattcaatttg---ggtaacttgta--tgtttgtagGGAGAAGAAATTTGTGTTGCTTTGCAAACACATATAAATGATGTCATGTTGCGTCGTTACTCCAAAGCTCGATCTGCTGCCAATAGCTTGGTTAATGGAG
||| | || | | | |||| || | || ||| ||| || |||| |||| |||| || | | |||| ||||||||||||||||||| ||| | || ||||| |||||||| || |||||||| || || ||||||||||||||||||| | | | |||| ||
gtattggcatgttcagggacactgtactcttcctagttctta-atttcgacctttggac--ttgactcatatcttcattactttgaagttattttattttattggtattttatcattctttgaagGGAGAAGAAATTTGTGTAGCTCTTCAGACACACATAAATGACGTAATGTTGCGACGCTATTCCAAAGCTCGATCTGCTGTGGGTGAATCTTTGAATGAAG
upper sequence: AT5G65930.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA16G21340.1 (Glycine max), 3'ss of exon 15
gtttaaacatcactatttgtggatcattatattatgaagcaattccttatgagatattcaatttgggtaacttgtatgtttgtagGGAGAAGAAATTTGTGTTGCTTTGCAAACACATATAAATGATGTCATGTTGCGTCGTTACTCCAAAGCTCGATCTGCTGCCAATAGCTTGGTTAATGGAG---
|| ||| | | | || || || | || | |||| || || | | | || | |||| ||||||||||||||||||||||| ||| | || ||||| ||||||||||| ||| ||||||| || || ||||| |||| ||||| | | | || |||
gtataa-tacctttgttgatgttgcacaaactttctttggaattattt-tgtcacactggtattttatctcttgg----ttgtagGGAGAAGAAATTTGTGTAGCTCTTCAGACACACATAAATGATGTAATGCTGCGTCGCTATTCGAAAGCAAGATCAGCTGCTGGTGGT---GGTAGTGGTTCTC
upper sequence: AT5G65930.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 11
------------------------------------------------gtttaaacatcactatttgtggatcattatattatgaagcaattccttatgagatattcaatttgggtaacttgtatgtt-tgtagGGAGAAGAAATTTGTGTTGCTTTGCAAACACATATAAATGATGTCATGTTGCGTCGTTACTCCAAAGCTCGATCTGCTGCCAATAGCTTGGTTAATGGAG
|||| | || | || | || | || | | || | |||| || | | || || || || ||||||||||||||||||||||| | || || |||||||||||||| ||||||||||| || || ||||| || |||||||| | | ||| | |||||||
gttcttaatcttttgagtttctatatgtatatatataacatttttagagttttagtctcttttttcttttatgtattccttgtttgcctatcaaaaaattattatttgatagagttctattccattttatgcagGGAGAAGAAATTTGTGTTGCTCTTCAGACGCATATAAATGATGTTATGTTGCGTCGCTATTCTAAAGCACGGTCTGCTGCTAGTGGCTCTATGAATGGAG
upper sequence: AT5G65930.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S199_47V6.1 (Physcomitrella patens), 3'ss of exon 13
--gtttaaacatcac-tatttgtgg-atcattatatta----tgaagcaatt-ccttatgagatattca-atttgggtaacttgt-atgtttg--------------tagGGAGAAGAAATTTGTGTTGCTTTGCAAACACATATAAATGATGTCATGTTGCGTCGTTACTCCAAAGCTCGATCTGCTGCCAATAGCTTGGTTAATGGAG
|||| | |||| | | || | | | |||| || || | ||||||| ||| | | | ||||| || | |||| || ||||||| || ||||||||||| |||||||| || |||||||| || |||||| | | || || | | || || ||||| | || | || |
gtatttataaatcaagtgtaagtcgtacggtcatatccaagctgctgcggtggttttatgagtcatttataacttggtaatttatgatgtgtgggattggcttcaaacagGGAGAGGACATTTGTGTTGCATTGCAAACGCACATAAATGACGTTATGTTGAGAAGGTATTCTAGGACACGCAATGTGCCCAATGGGCAGGCGCAGGGCG
upper sequence: AT5G65930.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S83_25V6.1 (Physcomitrella patens), 3'ss of exon 12
-------gtttaaacatcactatttgtg----gatcattatattatgaagc-aattcc--ttatgagatattcaatttgggtaacttgtatgtttg-tagGGAGAAGAAATTTGTGTTGCTTTGCAAACACATATAAATGATGTCATGTTGCGTCGTTACTCCAAAGCTCGATCTGCTGCCAATAGCTTGGTTAATGGAG
| | || || | | | | | || | |||| ||||||| | | || |||| | | | ||||||| || || ||||| ||| ||||||||||||||||||| || |||||| | | || || | | | || || ||||| | || | |
gtatctattcttaatgtctatggtcatactcaagcttctgcggtgtggatttaattttagttatgagtcaacaatttaatgtaaaatccctttgaaacagGGAGAGGACATATGTGTCGCTCTGCAAACACATATAAATGACGTAATGTTGAGGAGGTATTCAAGAACACGCAATGTGCCCAATGGGCAGGCGCAAGTGAMapped 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|125061157|gb|EL129796.1|EL129796EST: AAATGAGAGTCGCTGGTGTTCTTCACATATTTCAGTTCGAGACAAAACAG GGAGAAGAAATTTGT
genomic: AAATGAGAGTCGCTGGTGTTCTTCACATATTTCAGTTCGAGACAAAACAGgtttaaacat ... atgtttgtagGGAGAAGAAATTTGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attatgaagcaattccttatgagatattcaatttgggtaacttgtatgtttgtagGGAGAAGAAATTTGTGTTGCTTTGCAAACACATATAAATGATGTCATGTTGCGTCGTTACTCCAAAGCTCGATCTGCTGCCAATAGCTTGGTTAATGGAG
gggtaac putative branch site (score: 3)
atattcaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttaaacatcactatttgtggatcattatattatgaagcaattccttatgagatattcaatttgggtaacttgtatgtttgtagGGAGAAGAAATTTGTGTTGCTTTGCAAACACATATAAATGATGTCATGTTGCGTCGTTACTCCAAAGCTCGATCTGCTGCCAATAGCTTGGTTAATGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC