Sequence
atgc intronic sequence ATGC exonic sequenceAGCTCTTATTGCCCATTTCCAGAACTCAAGCTTAATGAACGAAGACAAACGTTGCCGACCTATTCTCTTCCACACTGATGGTCCAAATGCTGGTGATCAGgtaaagattaaagcttcatacaattccgtcttgtttggttcccattatccatatgcacttccttcacttcaagtgtgatttcattatatcataagattagtgagtaaaagaagattcatatgatttcctttgttgttatatcaccacag
Basic information
species | Arabidopsis thaliana |
transcript | AT5G61960.2 |
intron # | 13 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G61960.2 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: LOC_Os05g01240.2 (Oryza sativa), 5'ss of exon 14
AGCTCTTATTGCCCATTTCCAGAACTCAAGCTTAATGAACGAAGACAAACGTTGCCGACCTATTCTCTTCCACACTGATGGTCCAAATGCTGGTGATCAGgtaaagattaaagcttcatacaattccgtcttgtttggttcccattatccatatgcacttccttcact--tcaagtgtgatttcattatatcataagattagtgagtaaaagaagattcatatgatttcctttgttgttatatcaccacag---
||| | ||||| ||||| ||||| || ||| | ||||| ||||||||| | || |||||||| || ||||||| |||||||||||||| || |||||||| || | || | | | | |||| | || ||||||| || || | | | || | || || | | | | | | ||| ||| | | | |||| | | |
TGCTTTGATTGCTCATTTTCAGAATTCTAGCCTGATGAATGAAGACAAATGGTGTCGACCTATGCTTTTCCACAAAGATGGTCCAAATGCAGGAGATCAGgtgtgaat---atctctag-----tgcttattgtatacactaaatataccatatgagtgaccacttctgactgaccctattcgcacaaaatgattgacatggcggttttatacatattattattttctgataaagatacatattattattgcag
upper sequence: AT5G61960.2 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: LOC_Os02g31290.1 (Oryza sativa), 5'ss of exon 14
AGCTCTTATTGCCCATTTCCAGAACTCAAGCTTAATGAACGAAGACAAACGTTGCCGACCTATTCTCTTCCACACTGATGGTCCAAATGCTGGTGATCAGgtaaaga--ttaaagcttcatacaattccgtcttgtttggttcccattatccatatgcacttccttcacttcaagtgtgatttcattatatcataagattagtgagtaaaagaagattcatatgatttcctttgttgttatatcaccacag
|||||||||||| || ||||||||||| || || ||||| || ||||| || ||||| || || || ||||| | |||||||| ||||| || ||||||||| || || | || ||| | | | | | ||| | || || | || | | | ||
AGCTCTTATTGCTCACTTCCAGAACTCCAGTTTGATGAATGAGGACAAGCGCTGCCGCCCCATACTATTCCATTCGGATGGTCCTAATGCAGGAGATCAGgtatgatctttctctctctctctctctctctctctctctctctctctcgttgataaatggagttaaagcagcagatgacacttggacacagtttgctgtt---------------------------------------------------
upper sequence: AT5G61960.2 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: GRMZM2G459746_T01 (Zea mays), 5'ss of exon 14
AGCTCTTATTGCCCATTTCCAGAACTCAAGCTTAATGAACGAAGACAAACGTTGCCGACCTATTCTCTTCCACACTGATGGTCCAAATGCTGGTGATCAGgtaaagattaaagcttcatacaattccgtcttgtttggttcccattatccatatgcacttccttcacttcaagtgtgatttcattatatcataagattagtgagtaaaagaagattcatatgatttcctttgttgttatatcaccacag
|||||| ||||| |||||||||||||| || || ||||| || |||||||||||||| || || ||||||||| | |||||||| ||||| || ||||||||| | || || | ||| | || | || |||| || || | | || | | || | | || | | | || |||
AGCTCTGATTGCTCATTTCCAGAACTCTAGTTTGATGAATGAGGACAAACGTTGCCGCCCCATACTCTTCCACTCAGATGGTCCTAATGCAGGAGATCAGgtatgcttatttcttttttattttgtcgt-tggtactttccctgctatct---tgttctccagttacattatgtttcgctgcagtgcactgt--gacgagtcttct-------------------------------------------
upper sequence: AT5G61960.2 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: GRMZM2G451716_T01 (Zea mays), 5'ss of exon 14
AGCTCTTATTGCCCATTTCCAGAACTCAAGCTTAATGAACGAAGACAAACGTTGCCGACCTATTCTCTTCCACACTGATGGTCCAAATGCTGGTGATCAGgtaaagattaaagcttcatacaattccgtcttgtttggttcccattatccatatgcacttccttcacttcaagtgtgatttcattatatcataagattagtgagtaaaagaagattcatatgatttcctttgttgttatatcaccacag
|||||| |||| ||||||||||||||||| || ||||| || || ||||| ||||| ||||| ||||||||| |||||||||| ||||| || ||||| ||| | | | | | || | || | || | ||| || ||| | | | ||| | ||| | | || | ||| | ||
AGCTCTAGTTGCTCATTTCCAGAACTCAAGTTTGATGAATGAGGATAAACGCTGCCGCCCTATACTCTTCCACTCTGATGGTCCGAATGCAGGAGATCAAgtatgctctctacttgtccatcactctctattatctg--ttgcatcatg-gtatatgactatatggtgactagt---agttcctgaactctgctgcttatcgcata-------------------------------------------
upper sequence: AT5G61960.2 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: GRMZM5G814700_T01 (Zea mays), 5'ss of exon 4
AGCTCTTATTGCCCATTTCCAGAACTCAAGCTTAATGAACGAAGACAAACGTTGCCGACCTATTCTCTTCCACACTGATGGTCCAAATGCTGGTGATCAGgtaaagattaaagcttcatacaattccgtcttgtttggttcccattatccatatgcacttccttcacttcaagtgtgatttcattatatcataagattagtgagtaaaagaagattcatatgatttcctttgttgttatatcaccacag
||| || ||||| |||||||||||||| || || ||||| || |||||||| ||||| || || || |||||| | |||||||| ||||| || ||||||||| | ||| || || || ||| || | || || | | | | || | | || | | || || || | | || |||
AGCCCTGATTGCTCATTTCCAGAACTCTAGTTTGATGAATGAGGACAAACGCTGCCGCCCCATACTTTTCCACTCAGATGGTCCTAATGCAGGAGATCAGgtat-gctta---ttttgta---ttttgtcctgggtactttccctcctgtcttttt-ctccggttacattatgtactgttgtcttgtgagttgtgacaagtcttctct-----------------------------------------
upper sequence: AT5G61960.2 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: GLYMA08G01040.1 (Glycine max), 5'ss of exon 14
AGCTCTTATTGCCCATTTCCAGAACTCAAGCTTAATGAACGAAGACAAACGTTGCCGACCTATTCTCTTCCACACTGATGGTCCAAATGCTGGTGATCAGgtaaagattaaagcttcatacaattccgtcttgtttggttcccattatccatatgcacttccttcacttcaagtgtgatt--tcattatatcataagattagtgagtaaaagaagattcatatgatttcctttgttgttatatcaccacag
|||||||||| |||||||||||||||||| | ||||| ||||||||||||||||| |||||||||||||| || ||||| |||||||||||||||| |||||| | || || | | | | ||| | | ||| ||| ||| | | | ||| ||| ||| | | | |
TTCTCTTATTGCTCATTTCCAGAACTCAAGCCTGATGAATGAAGACAAACGTTGCCGTCCTATTCTCTTCCATACAGATGGCCCAAATGCTGGTGATCCGgtaaa--tcaagcttttgttc-------tttagttaagaactttgtat---tatctgattcttctggtggtgataaaattgatcaatatttttttgtctctgcag----------------------------------------------
upper sequence: AT5G61960.2 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: GLYMA04G37810.1 (Glycine max), 5'ss of exon 12
AGCTCTTATTGCCCATTTCCAGAACTCAAGCTTAATGAACGAAGACAAACGTTGCCGACCTATTCTCTTCCACACTGATGGTCCAAATGCTGGTGATCAGgtaaagattaaagcttcatacaattccgtcttgtttggttcccattatccatatgcacttccttcacttcaagtgtgatttcattatatcataagattagtgagtaaaagaagattcatatgatttcctttgttgttatatcaccacag
||||||||||| ||||||||||| |||||| | ||||| ||||| ||||| ||||| |||||||||||||| || ||||| |||||||||||||||| |||||| || | |||| | || | ||| ||| | ||| | || || | | | || | ||||||| || | ||| | | ||
TGCTCTTATTGCTCATTTCCAGAATTCAAGCCTGATGAATGAAGATAAACGGTGCCGTCCTATTCTCTTCCATACAGATGGCCCAAATGCTGGTGATCCGgtaaat--------------cagcttgttctttagttgtaactattttccttttgc--taactacaatgtat-tatggaactactatatcagcttgttcttcagttgtaattgtttt--------------------------------
upper sequence: AT5G61960.2 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: GLYMA06G17250.1 (Glycine max), 5'ss of exon 12
AGCTCTTATTGCCCATTTCCAGAACTCAAGCTTAATGAACGAAGACAAACGTTGCCGACCTATTCTCTTCCACACTGATGGTCCAAATGCTGGTGATCAGgtaaagattaaagcttcatacaattccgtcttgtttggttcccattatccatatgcacttccttcacttcaagtgtgatttcattatatcataagattagtgagtaaaagaagattcatatgatttcctttgttgttatatcaccacag
||||||||||| ||||| ||||| |||||| ||||||| ||||| ||||||||||| || ||||||||||| || ||||| |||||||||||||||| |||||| | | | | | || || ||| | | || | | | | | | | | | | | | | ||| | || | | ||
TGCTCTTATTGCTCATTTTCAGAATTCAAGCCTAATGAATGAAGATAAACGTTGCCGCCCCATTCTCTTCCATACAGATGGCCCAAATGCTGGTGATCCGgtaaa--tcagcttgttctttagttgtaact-attttgcttttgctaactaca---atgtattatggaactactatatctgcttgttattttccttttgctaacta-------------------------------------------
upper sequence: AT5G61960.2 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: Vv17s0000g00240.t01 (Vitis vinifera), 5'ss of exon 14
AGCTCTTATTGCCCATTTCCAGAACTCAAGCTTAATGAACGAAGACAAACGTTGCCGACCTATTCTCTTCCACACTGATGGTCCAAATGCTGGTGATCAGgtaaagattaaagcttcatacaattccgtcttgtttggttcccattatccatatgcacttccttcacttcaagtgtgatttcattatatcataagattagtgagtaaaagaagattcatatgatttcctttgttgttatatcaccacag
||||||||||| |||||||| ||||| ||||| ||||| || || ||||||||||| |||||||| || || ||||||||||||||||| |||||||||||| | | | | | | | | ||| ||| | ||| | | || ||| | ||| |||| || | || ||| || |
TGCTCTTATTGCTCATTTCCAAAACTCGAGCTTGATGAATGAGGATAAACGTTGCCGCCCTATTCTATTTCATACTGATGGTCCAAATGCAGGTGATCAGgtaggacatctgacataaagtatgttc--tctattttgttgttggatctcggatgtaaacct----gtttaagaata--ttctttat-tctaattggtaatgactatta----------------------------------------Mapped 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|125284872|gb|EL298957.1|EL298957EST: GTTGCCGACCTATTCTCTTCCACACTGATGGTCCAAATGCTGGTGATCAG GAACCATTTCCAATGGG
genomic: GTTGCCGACCTATTCTCTTCCACACTGATGGTCCAAATGCTGGTGATCAGgtaaagatta ... atcaccacagGAACCATTTCCAATGGG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AGCTCTTATTGCCCATTTCCAGAACTCAAGCTTAATGAACGAAGACAAACGTTGCCGACCTATTCTCTTCCACACTGATGGTCCAAATGCTGGTGATCAGgtaaagattaaagcttcatacaattccgtcttgtttggttcccattatccatatgcacttccttcacttcaagtgtgatttcattatatcataagattagtgagtaaaagaagattcatatgatttcctttgttgttatatcaccacag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG