Sequence
atgc intronic sequence ATGC exonic sequenceGTTATTTTGGCCAGAACATTCGGAGTTTGTAAGGATAGCATCTAAATTTGGAGCAAAAATCATTCCTTTTGGAGTTGTTGGAGAAGATGATCTTTGTGAAgtaagcaaaaaaatctcttttccgttctactttcaacacctgcattcttaaaactcattttgtttcaattgggttttgagttaactcgtttgagcaatgg...
Basic information
species | Arabidopsis thaliana |
transcript | AT5G41120.1 |
intron # | 11 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G41120.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: LOC_Os09g33530.1 (Oryza sativa), 5'ss of exon 11
GTTATTTTGGCCAGAACATTCGGAGTTTGTAAGGATAGCATCTAAATTTGGAGCAAAAATCATTCCTTTTGGAGTTGTTGGAGAAGATGATCTTTGTGAAgtaagcaaaaaaatctcttttccgttctactttcaacacctgcattcttaaaactcattttgtttcaattgggtttt--gagttaactcgtttgagca-atgg-
||| ||||||||||| || || || ||||| ||||| ||||| | |||||||||| ||| || || |||||||| ||||||||||||||| | ||||| || || | | || | | | | | || | |||| | | | ||| | ||| |||| ||| | || || | |||
GTTGTTTTGGCCAGAGCAGTCTGAATTTGTGAGGATGGCATCAAGGTTTGGAGCAACAATAATACCATTTGGAGTAGTTGGAGAAGATGATATATGTGATgtgagtgcattcttactattaactaccaattattaatagatgcaaatct----cctttgctgtctacatttttttttgcgaggaacctttgctgtctacatgtt
upper sequence: AT5G41120.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GLYMA16G05580.1 (Glycine max), 5'ss of exon 11
GTTATTTTGGCCAGAACATTCGGAGTTTGTAAGGATAGCATCTAAATTTGGAGCAAAAATCATTCCTTTTGGAGTTGTTGGAGAAGATGATCTTTGTGAAgtaagcaaaaaaatctcttttccgttctactttcaacacctgcattcttaaaactc-attttgtttcaattgggttttgagtta--actcgtttgagcaatgg
|||||| ||||| ||||| || |||||||||||||| ||| | | ||||||||| ||||| | |||||||| || |||||||||||||| || || ||||||| | | | | | |||| | || ||| | | | || || || || | | | | | |||| |
GTTATTCTGGCCTGAACAATCCGAGTTTGTAAGGATGGCAGCAAGATTTGGAGCCAAAATAGTACCTTTTGGTGTAGTTGGAGAAGATGACATTGGTCAAgtaagttttggtcttttctgaaccaatcattttcctctatgaatttattatagcctgaaaatgcttgtatcaggcaaagcatgaccaattgtttttatat---
upper sequence: AT5G41120.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GLYMA16G05570.1 (Glycine max), 5'ss of exon 13
GTTATTTTGGCCAGAACATTCGGAGTTTGTAAGGATAGCATCTAAATTTGGAGCAAAAATCATTCCTTTTGGAGTTGTTGGAGAAGATGATCTTTGTGAAgtaagcaaaaaaatct-cttttccgttctactttcaacacctgcattcttaaaactcattttgtttcaattgggttttgagttaactcgtttgagcaatgg
|||||| ||||| |||| || |||||||||||||| ||| | | ||||||||| ||||| | |||||||| | |||||||||||||| ||| |||||||||| | | || || || || || | | || | || || || || |||| || || ||||
GTTATTCTGGCCTCAACAATCTGAGTTTGTAAGGATGGCAGCAAGATTTGGAGCCAAAATTGTACCTTTTGGTGCAGTTGGAGAAGATGACCTTGGTGAAgtaagttttggtcttttctgaaccaatccttttcttttacaaatctattatggcctgaaaatgattgtatcaggcaaagagt-gaccaattgtttttatgg
upper sequence: AT5G41120.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: Vv14s0068g01430.t01 (Vitis vinifera), 5'ss of exon 11
GTTATTTTGGCCAGAACATTCGGAGTTTGTAAGGATAGCATCTAAATTTGGAGCAAAAATCATTCCTTTTGGAGTTGTTGGAGAAGATGATCTTTGTGAAgtaagcaaaaaaatctcttttccgttctactttcaacacctgcattcttaaaactcattttgtt-tcaattgggttttgagttaactcgtttgagcaatgg--
||| |||||||||||||| || |||||||| | || || ||| |||||||| ||||| || || |||||||||||||||||||||||| || || | |||| | || || | || || | ||| | | | | | | | || | | || ||| | ||| | ||| || |
GTTGTTTTGGCCAGAACAATCTGAGTTTGTCCGAATTGCGGCTAGGTTTGGAGCCAAAATTATACCCTTTGGAGTTGTTGGAGAAGATGATTTTGGTCAGgtaaacttg---attactataatgtccttcaatcatagcttctttattgattattagttctcctaccagttgccatgcaagtaagttcgcatgcatgctaacaMapped 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|86087911|gb|DR383670.1|DR383670EST: GAGCAAAAATCATTCCTTTTGGAGTTGTTGGAGAAGATGATCTTTGTGAA ATGGTTTTAGATTATGATGATCAAATGAAGATCCCTTTCTTGAAGAATCTT
genomic: GAGCAAAAATCATTCCTTTTGGAGTTGTTGGAGAAGATGATCTTTGTGAAgtaagcaaaa ... atgtattcagATGGTTTTAGATTATGATGATCAAATGAAGATCCCTTTCTTGAAGAATCTT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GTTATTTTGGCCAGAACATTCGGAGTTTGTAAGGATAGCATCTAAATTTGGAGCAAAAATCATTCCTTTTGGAGTTGTTGGAGAAGATGATCTTTGTGAAgtaagcaaaaaaatctcttttccgttctactttcaacacctgcattcttaaaactcattttgtttcaattgggttttgagttaactcgtttgagcaatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tctctttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaactca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctcgtttg