Sequence
atgc intronic sequence ATGC exonic sequencegtaagtttttttttgctcttcatttgatcatttccgataaaaattttgagagaacttaacgttaacgtttcttcttcgatatcatttacttagGGACCACAATATGTTTGCACTACTTTCTGGACTTTTGTTTGTACCAACTGCAGTGGAATACA
Basic information
species | Arabidopsis thaliana |
transcript | AT4G13350.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G13350.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os02g11820.1 (Oryza sativa), 3'ss of exon 2
-------------gtaagtttttttttgctcttcatttg-atcatttccgataaaaattttgagagaacttaacgttaacgtttcttcttcgatatcatttacttagGGACCACAATATGTTTGCACTACTTTCTGGACTTTTGTTTGTACCAACTGCAGTGGAATACA
|| || ||| | | | | || || || | || | |||||| | | ||| | || | | ||| || |||||||||||||||| || || | ||||||||| || |||||||||| ||||||||| |||
gtagacttaattagtgggtatttgtgtaatactgatgtgcattactttgtttcctaatttttt-----ttgtatattactgaatcacatatattgatattaac--agGGACCACAATATGTCTGTACAAATTTCTGGACCTTCATTTGTACCAATTGCAGTGGAGCACA
upper sequence: AT4G13350.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G043056_T01 (Zea mays), 3'ss of exon 2
----------gtaagtttttttttgctcttcatttgatcatttccgataaaaattttgagagaacttaacgttaacgtttcttcttcgatatcatttacttagGGACCACAATATGTTTGCACTACTTTCTGGACTTTTGTTTGTACCAACTGCAGTGGAATACA
||| | || | |||| | | | || | | || | || || | || | | | |||| |||||||||||||||| ||||| | ||||||||| |||||||||||||| ||||||||| |||
acatatcttgctaatatgttacaagagtaatattttgttagtgcctcctctactgttcc---acctgaaggaaaaaataacactgatatgctgatttgaacagGGACCACAATATGTCTGCACAAATTTCTGGACCTTTGTTTGTACCAATTGCAGTGGATCACA
upper sequence: AT4G13350.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G341732_T02 (Zea mays), 3'ss of exon 3
-------gtaagtttttttttgctcttcatttgatcatttccgat--aaaaattttgagagaacttaacgttaacgtttcttcttcgatatcatttacttagGGACCACAATATGTTTGCACTACTTTCTGGACTTTTGTTTGTACCAACTGCAGTGGAATACA
||| | || | | ||| | ||| || | || ||| || || || | | | |||| ||||||||||||||| ||||| | ||||||||| || ||||||||||| ||||||||| |||
tatcttgctaatatattatgagaataatgttttgttattgccttccctactgttccacctgaagaaaaaagcaagaacactgatatgctg--atttgaacagGGACCACAATATGCCTGCACAAATTTCTGGACCTTCGTTTGTACCAATTGCAGTGGAGCACA
upper sequence: AT4G13350.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA07G09750.2 (Glycine max), 3'ss of exon 2
----------gtaagtttttttttgctcttcatttgatcatttccgataaaaattttgagagaactta-acgttaacgtttcttcttcgatatcatttacttagGGACCACAATATGTTTGCACTACTTTCTGGACTTTTGTTTGTACCAACTGCAGTGGAATACA
| ||| || | || | || | | | ||| ||| | ||| | |||| | ||||||| | || ||| |||||||||||||||| ||||| | |||||||| |||||||| || |||||||||||||||||
agcattttgattgcgttcttcagaacctagaatggaaattattgcatttgatattgtgactggtcttttatattaat-tatcttcttt--tctcttttgaa-agGGACCACAATATGTGTGCACAAACTTCTGGACGTTTGTTTGCACAAACTGCAGTGGAATACA
upper sequence: AT4G13350.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA05G35310.1 (Glycine max), 3'ss of exon 2
-gtaagtttttttttgctcttc------atttgatcatttccgataaaaattttgagagaacttaacgt-taacgtttcttcttcgatatcatttacttagGGACCACAATATGTTTGCACTACTTTCTGGACTTTTGTTTGTACCAACTGCAGTGGAATACA
| || || | | | |||| | |||| | | ||| | || | | | | || ||| | || || |||||||||||||||||| ||||| | ||||||||| |||||||| || ||||| || ||||||||
attgcattcttctgaacctagctaggaaattttttaatttgatgttgaggtttgagactagtttgttgcattaaatccttttttctttctctcttg-ttagGGACCACAATATGTGTGCACAAATTTCTGGACGTTTGTTTGCACTAACTGTAGCGGAATACA
upper sequence: AT4G13350.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G04420.2 (Glycine max), 3'ss of exon 1
gtaagtttttttttgctct--tcatttgatcatt---tccgataaaaat-tttgagagaacttaacgtta--acgtttcttcttcgatatcatttacttagGGACCACAATATGTTTGCACTACTTTCTGGACTTTTGTTTGTACCAACTGCAGTGGAATACA
| || || | ||| | || || | ||| || ||||||| | || | | | | || ||| | || || |||||||||||||||||||||| | | ||||||||| |||||||| | ||||| || ||||||||
attgcattcttctgaatctagctaggaaattgttgaatttgatgttgatatttgagactagtttgctgcattaaatccttttttctttctctcttg-ttagGGACCACAATATGTTTGCTCAAATTTCTGGACGTTTGTTTGCATTAACTGTAGCGGAATACA
upper sequence: AT4G13350.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ33278 (Selaginella moellendorffii), 3'ss of exon 3
gtaagtttttttttgctcttcatttgatcatttccgataaaaattttgagagaacttaacgttaacgtttcttcttcgatatcatttacttagGGACCACAATATGTTTGCACTACTTTCTGGACTTTTGTTTGTACCAACTGCAGTGGAATACA
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---------------------gtacagtcttcttgcttgtttctttctgggtcgttctttgttgacaaggctcttttggtgtgatttttccagGGACCACAATATGTTTGCACAACTTTCTCAACTTTTGTGTGCATGGCTTGTGGTGGAGTCCAMapped 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|116423227|gb|EG465819.1|EG465819EST: GTCTTCTTAAACTTCCTGAGAATAAGAGGTGTATAAACTGTAACAGCCTT GGACCACAATATGTTTGCACTACTTTCTGGACTTTTGTTTGTACCAACTGC
genomic: GTCTTCTTAAACTTCCTGAGAATAAGAGGTGTATAAACTGTAACAGCCTTgtaagttttt ... atttacttagGGACCACAATATGTTTGCACTACTTTCTGGACTTTTGTTTGTACCAACTGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaaattttgagagaacttaacgttaacgtttcttcttcgatatcatttacttagGGACCACAATATGTTTGCACTACTTTCTGGACTTTTGTTTGTACCAACTGCAGTGGAATACA
cgttaac putative branch site (score: 3)
tttactt putative PPT
atatcatttactta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtttttttttgctcttcatttgatcatttccgataaaaattttgagagaacttaacgttaacgtttcttcttcgatatcatttacttagGGACCACAATATGTTTGCACTACTTTCTGGACTTTTGTTTGTACCAACTGCAGTGGAATACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA