Sequence
atgc intronic sequence ATGC exonic sequenceCTTAAGAAGGGTCCATGCTGCTCAAAAGGATGATGATATGCCTCCGATTGAAGCCATTCTAGCTCCATTGGAAGCTGAGCTTAAGCTAGCTCGCTCTGAGgtatgttttactcatttgaagtccaaatttctacttgcaaatcggatattaatttatgatgtttctgtgaag
Basic information
species | Arabidopsis thaliana |
transcript | AT1G68060.1 |
intron # | 4 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G68060.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os12g44340.1 (Oryza sativa), 5'ss of exon 4
CTTAAGAAGGGTCCATGCTGCTCAAAAGGATGATGATATGCCTCCGATTGAAGCCATTCTAGCTCCATTGGAAGCTGAGCTTAAGCTAGCTCGCTCTGAGgtatgttttactcatttgaagtccaaa----tttctacttgcaaatcggatattaatttatgatgtttctgtgaag------------------------
| ||||||| ||||| || || ||||||||||| ||||| || ||||| |||||||| || |||||||||||||| || || |||||||| |||||||| | | | | | | | ||||| ||| || || | ||| | || || |
ACTTCGAAGGGTTCATGCAGCACAGAAGGATGATGACATGCCCCCTATTGAGGCCATTCTTGCGCCATTGGAAGCTGAACTGAAACTAGCTCGTCATGAGgtatttcatccaagtgtatacctggattctctttcttcttttctttccaatcagtaccaatgttcttcatgcatcggtctttgtgtcaagatgcttgctt
upper sequence: AT1G68060.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os06g14080.1 (Oryza sativa), 5'ss of exon 4
CTTAAGAAGGGTCCATGCTGCTCAAAAGGATGATGATATGCCTCCGATTGAAGCCATTCTAGCTCCATTGGAAGCTGAGCTTAAGCTAGCTCGCTCTGAGgt-atgttttactcatttgaagtccaaatttctacttgcaaatcggata--ttaatttatgatgtttctgtgaag---------------------------------------------------------------------------------------------------------------------------
|| | || || ||||| || |||||||||||||| ||||| || |||||||||||||| || || | ||||||||||| ||||| ||||| ||||| | ||| ||| ||| || | | | | | ||||||| | ||| || | |
TTTGCGGAGAGTACATGCAGCCCAAAAGGATGATGACATGCCACCAATTGAAGCCATTCTCGCACCGCTTGAAGCTGAGCTAAAGCTTGCTCGGCAAGAGgtgaaactttgttcacccatcccccattttctatcattttgtttgtgtggtttaatttcttatgctttcctaacagttactgattattttcatcctctggtttgcctaaacggctaattagttgccttagtttcttttcattggtttgtgtattttctatgatcaaataagatgaccagttaacttggttcactttag
upper sequence: AT1G68060.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os02g50320.2 (Oryza sativa), 5'ss of exon 4
CTTAAGAAGGGTCCATGCTGCTCAAAAGGATGATGATATGCCTCCGATTGAAGCCATTCTAGCTCCATTGGAAGCTGAGCTTAAGCTAGCTCGCTCTGAGgta----tgttttactcatttg-------aagtccaaatttctacttgcaaatcg---gatattaat-ttatgatgtttctgtgaag--------------------------------------------------------------------------------------------------------------
| |||| || ||||| || ||||| |||||||||||||| || |||||||| ||||| |||||| | |||||||| || ||||| ||||| |||||| ||| ||||||| || | | ||| |||| | || | | | | || || ||| || ||| |
TCTGCGAAGAGTGCATGCAGCCCAAAAAGATGATGATATGCCACCTATTGAAGCTATTCTTGCTCCACTTGAAGCTGAACTAAAGCTTGCTCGTCAAGAGgtaatactgtgttactcaaatggccaggcatggccatattttattgttcattttgtttggtgttgatattacaatattttctcacacttatttagattttgcctcttgcttccatagtcctaattcaacttctccattccaccacatgcatgttcactataattgtctaaagaataagatttgctttttttcttcag
upper sequence: AT1G68060.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G039325_T01 (Zea mays), 5'ss of exon 4
CTTAAGAAGGGTCCATGCTGCTCAAAAGGATGATGATATGCCTCCGATTGAAGCCATTCTAGCTCCATTGGAAGCTGAGCTTAAGCTAGCTCGCTCTGAGgtatgttttactcatttgaagtccaaatttctacttgcaaat-cggatattaatttatgatgtttctgtgaag---------------------------------------------------------------------------------------------------------------
|| | || || ||||| || || || |||||||| ||||| || |||||||||||||| || ||| | ||||||||||| ||||| ||||| |||||| ||| || ||| || | | || ||| | | | || ||| | |||||| | |
TTTGCGGAGAGTACATGCAGCCCAGAAAGATGATGACATGCCACCAATTGAAGCCATTCTTGCACCACTTGAAGCTGAGCTAAAGCTTTCTCGCCAGGAGgtaatacttagtcttttatggtt-ggttctttatttgtgtttgtgcagatgtctttcataggtttctattacatttgcaaatattttacgcctccagtcaccctcgatgatctaattacccttttccaatttgtcatgtatttcctgcggatgaagtgtatgacaagttaaatcttgttttcag
upper sequence: AT1G68060.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA08G05100.1 (Glycine max), 5'ss of exon 4
CTTAAGAAGGGTCCATGCTGCTCAAAAGGATGATGATATGCCTCCGATTGAAGCCATTCTAGCTCCATTGGAAGCTGAGCTTAAGCTAGCTCGCTCTGAGgtatgttttactcat--ttgaagtccaaatttctacttgcaaatcggatattaatttatgatgtttctgtgaag------------------------------------------------------
| ||||||||||||||||||| ||||||||||| |||||||| || || |||||||| ||||| |||| ||||| |||||||| || || ||||||| || | | || | | ||| | | || | || || | |||| | |||||
TCTTCGAAGGGTCCATGCTGCTCAGAAGGATGATGACATGCCTCCTATAGAGGCCATTCTTGCTCCTCTGGAGGCTGAACTTAAGCTTGCGCGGCAAGAGgtattattactttgttcttctactttgaatggtgattccca---tgagaataaaatgatgaaggggac-tgaagctgacttgtcataggtgatttatgtcattattttcttcaatttgtttcgaacag
upper sequence: AT1G68060.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA05G34560.1 (Glycine max), 5'ss of exon 4
CTTAAGAAGGGTCCATGCTGCTCAAAAGGATGATGATATGCCTCCGATTGAAGCCATTCTAGCTCCATTGGAAGCTGAGCTTAAGCTAGCTCGCTCTGAGgtat-gttttactcatttgaagtccaaatttctacttgcaaatcggatattaatttatgatgtttctgtgaag-------------------------------------------------
| ||||||||||||||||||| ||||| ||||| |||||||| || || |||||||| ||||| |||| ||||| |||||||| || || ||||||| || ||| | | | | | | | | | | | | | || | | | |
TCTTCGAAGGGTCCATGCTGCTCAGAAGGACGATGACATGCCTCCTATAGAGGCCATTCTTGCTCCTCTGGAGGCTGAACTTAAGCTTGCACGGCAAGAGgtattattacactggtcttctatgaacagtgattcccatgagaagaa-actgatgaaggggaccgaagctgacttgtcataggtgatttatgtcattattttcttcaatttgtttcttacag
upper sequence: AT1G68060.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA07G26540.1 (Glycine max), 5'ss of exon 4
CTTAAGAAGGGTCCATGCTGCTCAAAAGGATGATGATATGCCTCCGATTGAAGCCATTCTAGCTCCATTGGAAGCTGAGCTTAAGCTAGCTCGCTCTGAGgtat-gttttactcatttgaagtccaaatt----tctacttgcaaatcggatatt--aatttatgatgtttctgtgaag-----------------------------------------
| ||||||||||||||||| || || |||||||| |||||||| || ||||| ||||| || || ||||||||||| || ||||| ||||| ||||||| || || ||| ||| || ||| || || | || | | || || ||| | | ||
TCTTAGAAGGGTCCATGCTGCCCAGAAAGATGATGACATGCCTCCAATAGAAGCAATTCTTGCACCTTTGGAAGCTGAACTCAAGCTTGCTCGGCAAGAGgtattaccttgttc--ttggagttcatattataatcccctggagaaagagctgttggaaggactgaaactggcttaaaatgagtggttttttactttgtacttccatttattccttgcag
upper sequence: AT1G68060.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA02G09390.1 (Glycine max), 5'ss of exon 4
CTTAAGAAGGGTCCATGCTGCTCAAAAGGATGATGATATGCCTCCGATTGAAGCCATTCTAGCTCCATTGGAAGCTGAGCTTAAGCTAGCTCGCTCTGAGgtat-gttttactcatttgaagtccaaatt----tctacttgcaaatcggatatt--aatttatgatgtttctgtgaag-----------------------------------------
| |||||||||| ||||| || || |||||||| |||||||| || ||||| ||||| ||||| ||||||||||| || ||||| ||||| ||||||| || || ||| ||| || ||| || || | || | | | || | | | | ||
TCTTCGAAGGGTCCACGCTGCCCAGAAAGATGATGACATGCCTCCAATAGAAGCAATTCTTGCTCCTTTGGAAGCTGAACTCAAGCTTGCTCGGCAAGAGgtattaccttgttc--ttggagttcatattgtaatcccctggagaaagagctgatggaaggacttaaactggcttaaaatgagtaattttttgatttgtacttccatttattccttgcag
upper sequence: AT1G68060.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv01s0011g05790.t01 (Vitis vinifera), 5'ss of exon 4
CTTAAGAAGGGTCCATGCTGCTCAAAAGGATGATGATATGCCTCCGATTGAAGCCATTCTAGCTCCATTGGAAGCTGAGCTTAAGCTAGCTCGCTCTGAGgtatgttttactcatttgaagtccaaatttctacttgcaaatcggatattaatttatgatgtttctgtgaag----------------------------------------------
| |||||||| |||||||| || |||||||| ||||||||||| |||||||| ||||| || || ||||| |||||||| ||||| ||||| |||||| | || ||| || | ||| || || | | | || | | || || | || || |
TCTTAGAAGGGTTCATGCTGCGCAGAAGGATGACGATATGCCTCCCATTGAAGCGATTCTTGCACCGTTGGAGGCTGAGCTCAAGCTTGCTCGGCAGGAGgtagttattg--catgtggcctttaaacttttaatgacgattctt-tctcaaagtaaaactcctcatagatgataaatagtagttatatgattgtttggctgtattggttcttttcagMapped 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|124722362|gb|EH813764.1|EH813764EST: TGAGCTTAAGCTAGCTCGCTCTGAG ATTGGGAAGCTTCAAGAAGATAACAGAGCTTTGGATCGTCTCACTAAATCA
genomic: TGAGCTTAAGCTAGCTCGCTCTGAGgtatgtttta ... ttctgtgaagATTGGGAAGCTTCAAGAAGATAACAGAGCTTTGGATCGTCTCACTAAATCA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CTTAAGAAGGGTCCATGCTGCTCAAAAGGATGATGATATGCCTCCGATTGAAGCCATTCTAGCTCCATTGGAAGCTGAGCTTAAGCTAGCTCGCTCTGAGgtatgttttactcatttgaagtccaaatttctacttgcaaatcggatattaatttatgatgtttctgtgaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT