Sequence
atgc intronic sequence ATGC exonic sequencegtaattatgcttttactgctctttcagttgcatttttcgtcttactaatagctgtttcttttcttaaataatcgtcaaccagGTTGTAGCTATAGCAAGTGCCGCACTTGATGGATTCAAGAATGAAGCTAAGAAGATGGTAGTTGCATTAGTTGATATGGAGCGTGCATTTGTACCACCTC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G59610.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os02g50550.1 (Oryza sativa), 3'ss of exon 11
--gtaattatgcttttactgctctttcagttgcatttttcgtcttactaatagctgtttcttttcttaaata----atcgtcaacc------agGTTGTAGCTATAGCAAGTGCCGCACTTGATGGATTCAAGAATGAAGCTAAGAAGATGGTAGTTGCATTAGTTGATATGGAGCGTGCATTTGTACCACCTC
| | || | | | | || | || | ||| ||| | || | ||| || |||| || | || |||| ||| | |||| ||||| | ||| || || ||||||||||||||| | ||||||||||||||||| ||||| ||||| |
gtaccactttgttctatttcaccaacttacaatgcattctacttccctttcacctgcttcctgagcacaacatcccatcatctcttttctgaagGTCGTTGAAATTGCAACCAATGCATTGGATGTCTTCAAAAGTGATGCAAAAAAGATGGTAGTTGCACTTGTTGATATGGAGCGTGCCTTTGTCCCACCAC
upper sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA09G00430.2 (Glycine max), 3'ss of exon 11
-------------------------------------------------------------------------------------------gtaattatgcttttactgctctttcagttgcatttttcgtcttactaatagctgtttcttttcttaaataa--tcgtcaa---------ccagGTTGTAGCTATAGCAAGTGCCGCACTTGATGGATTCAAGAATGAAGCTAAGAAGATGGTAGTTGCATTAGTTGATATGGAGCGTGCATTTGTACCACCTC
|||| | ||| || |||| || | || || | | | || | ||| |||| | || | | ||||||| ||||| |||| | ||||||| || || || ||||||||| | ||||| ||||| |||||| | ||||||||||||||||| ||||| |||||||
gtattgtacttcatttctgtttttctgtttctatttgatacctgtattaatatattattttaaatttgagtcttttcttgttgcatatagttcccttatacattttct--tcttaaaggtatcccttaggtggggactgcactttctctttcttttagataacattgtttaaaaatctttcaagGTTGTGGCTATTGCAACTTCCGCACTAGAAGGGTTTAAGAATGAATCGAAGAAAATGGTTGTTGCACTCGTTGATATGGAGCGTGCTTTTGTCCCACCTC
upper sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA12G37100.1 (Glycine max), 3'ss of exon 11
------------------------------------------------------------------------------------gta-attatgcttttactgctctttcagttgcatttttcgtcttactaatagctgtttcttttcttaaataatcgtc------aacc-----agGTTGTAGCTATAGCAAGTGCCGCACTTGATGGATTCAAGAATGAAGCTAAGAAGATGGTAGTTGCATTAGTTGATATGGAGCGTGCATTTGTACCACCTC
| | || | | |||| | || || | | || || | || || |||| |||| | | || | ||||||| ||||| |||| ||||| || || || || ||||||||| | ||||| ||||| |||||| ||||||||||||||||||| ||||| |||||||
gtatggtacttcattgttgtttttctgtttctacttgatacctgtattaatatatcatgttaaatttgagtcttttttcttgttgcatatagttcctttatacattttcttcttaaaggtatcccctaggtggggagtgcactttctctttcataaccttgtttaaaaatctttcaagGTTGTGGCTATTGCAACCGCCGCGCTAGAAGGGTTTAAGAATGAATCAAAGAAAATGGTGGTTGCACTAGTTGATATGGAGCGTGCTTTTGTCCCACCTC
upper sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA17G00480.1 (Glycine max), 3'ss of exon 11
gtaattatgcttttactgctctttcagttgcattt--ttcgtcttactaatagctgtttcttttcttaaataat-cgtcaaccagGTTGTAGCTATAGCAAGTGCCGCACTTGATGGATTCAAGAATGAAGCTAAGAAGATGGTAGTTGCATTAGTTGATATGGAGCGTGCATTTGTACCACCTC
| || || || | | || ||| | | | || | ||| || | || || | | | | || |||| || || |||||| | || || || | ||| || |||||| | || || ||||| |||||| ||||||||||||||||||||||||| ||||| |
------gtaacattgatgtgctgtaacttacatgtaacttggtttgtttttagaaattaccttgctcatttgttgcaatttttagATTGTGGCAATTGCAAGTTCAGCCCTAGAGGCATTTAAAAATGAATCCAAAAAAATGGTGGTTGCACTAGTTGATATGGAGCGTGCATTTGTTCCACCAC
upper sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA07G40300.1 (Glycine max), 3'ss of exon 11
gtaattatgcttttactgctctttcagttgcattt---ttcgtcttactaatagctgtttcttttcttaaataat-cgtcaaccagGTTGTAGCTATAGCAAGTGCCGCACTTGATGGATTCAAGAATGAAGCTAAGAAGATGGTAGTTGCATTAGTTGATATGGAGCGTGCATTTGTACCACCTC
| | ||| || | |||| ||| | || || | | ||| || || || | | | | ||| |||| || || |||||| | || || || | ||| || |||||| | || || ||||| |||||| ||||||||||||||||||||||||| || || |
------gtaacaatgctgtgctgtaagttacatgtaacttggtttgttttttagaaattatcttgctcatttgttgcaattttcagATTGTGGCAATTGCAAGTTCAGCCCTAGAGGCATTTAAAAATGAATCCAAAAAAATGGTGGTTGCACTAGTTGATATGGAGCGTGCATTTGTTCCTCCCC
upper sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv18s0089g00350.t01 (Vitis vinifera), 3'ss of exon 11
--------------------------------------------------------------------gtaattatgcttttactgctctttcagttgcatttttcgtcttactaatagctgtttcttttcttaaataatcgtcaaccagGTTGTAGCTATAGCAAGTGCCGCACTTGATGGATTCAAGAATGAAGCTAAGAAGATGGTAGTTGCATTAGTTGATATGGAGCGTGCATTTGTACCACCTC
|||||| | | | | || | | ||| | ||| | || | ||| |||| | | | | ||||||| || || |||| ||| ||||| |||| |||||||||||||||||||| ||||| ||||| |||| ||||||||||| || ||||| || ||||
gtatattttctttgattgcgcacctgttcttgtgctggcagtatttatttatatattcaggattgtgcgtaattttaatccttcatacctaaaaaatctattcgattttttattt-tatttttttattttttattttttatttttattagGTTGTGGCAATTGCAACTGCTGCACTAGATGTGTTCAAGAATGAAGCTAAGAAAATGGTGGTTGCCCTAGTGGATATGGAGCGAGCTTTTGTGCCCCCTC
upper sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv12s0035g01740.t01 (Vitis vinifera), 3'ss of exon 11
--------------------------------------------------gtaattatgctt---ttactgctctttcagttgcatttt--tcgtcttactaatagctgtttcttttcttaaataatcgtcaaccagGTTGTAGCTATAGCAAGTGCCGCACTTGATGGATTCAAGAATGAAGCTAAGAAGATGGTAGTTGCATTAGTTGATATGGAGCGTGCATTTGTACCACCTC
| |||| || || | | || |||| | ||| | | || | || | ||| || ||||| | | ||||||||||| || || ||| | | ||||| || || || |||||||| || ||||| ||||| |||||| | ||||||||||||||||||||||| || ||||
gtaatcatgctgcaaatgctgcccctttttttttttaagagattccctcctttgatatgtttaatttgatatttttcaagttcaagtttgttggcttttgtggtacaactcacttgtcataaat--ttttaaaccagGTTGTGGCAATTGCATCTACTGCACTGGAAGGGTTTAAGAATGAGGCAAAGAAAATGGTTGTTGCACTTGTTGATATGGAGCGTGCATTTGTTCCCCCTCMapped 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|125213926|gb|EL228665.1|EL228665EST: CCGCGAATGCCACACCTGGTCTTGGGAGATATCCTCCTTTTAAGAGAGAG GTTGTAGCTATAGCAAGTGCCGCACTTGATTGGATTCAAGAATGAAG
genomic: CCGCGAATGCCACACCTGGTCTTGGGAGATATCCTCCTTTTAAGAGAGAGgtaattatgc ... cgtcaaccagGTTGTAGCTATAGCAAGTGCCGCACTTGAT-GGATTCAAGAATGAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgcatttttcgtcttactaatagctgtttcttttcttaaataatcgtcaaccagGTTGTAGCTATAGCAAGTGCCGCACTTGATGGATTCAAGAATGAAGCTAAGAAGATGGTAGTTGCATTAGTTGATATGGAGCGTGCATTTGTACCACCTC
tactaat putative branch site (score: 1)
tttcttttcttaaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattatgcttttactgctctttcagttgcatttttcgtcttactaatagctgtttcttttcttaaataatcgtcaaccagGTTGTAGCTATAGCAAGTGCCGCACTTGATGGATTCAAGAATGAAGCTAAGAAGATGGTAGTTGCATTAGTTGATATGGAGCGTGCATTTGTACCACCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG