Sequence
atgc intronic sequence ATGC exonic sequencegttaacttcagtatttgatatatatgttgttcctttttcctttgatatgtgcttagtggaaagaagagccaattatttcgattctatttgtctgacagCTCTCTGTCGAAAGGCTTAGTTCCATGAAGAAATATGTTTTTGGATTAGGCTCCGCGCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G00630.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G00630.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA07G08030.1 (Glycine max), 3'ss of exon 4
gttaacttcagtatttgatatatatgttgttcctttttc-ctttgat-atgtgcttagtggaaagaagagccaattatttcgattctatttgtctgacagCTCTCTGTCGAAAGGCTTAGTTCCATGAAGAAATATGTTTTTGGATTAGGCTCCGCGCAG
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-----gtggagcttcctata-agatcttgttctgccttagctttgatcatctctgtagtaagaaataaactgaagc-tctgaactgtattttt---atagCTCTCTGTTGAAAGGCTTAGTTCAATGAAGAAATATGTCTTTGGATTAGGCTCTGCTCAG
upper sequence: AT4G00630.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA09G39770.1 (Glycine max), 3'ss of exon 8
gttaacttcagtatttgatatatat--gttgttcctttttcctttgatatgtgcttagtggaaagaagagccaatt---atttcgattctatttgtc-tgacagCTCTCTGTCGAAAGGCTTAGTTCCATGAAGAAATATGTTTTTGGATTAGGCTCCGCGCAG
|| | |||| | | | | ||||||| | || || | | | | | |||| | ||| ||||| | |||||||||| |||||||||||||| |||||||||||||| |||||||||||||| || |||
gtggggattcctattagttctggttcagttgttctatgttaactttgtccatcaccattatctaaggagctgaattgaggctcttatttgctttgttgttttagCTCTCTGTTGAAAGGCTTAGTTCAATGAAGAAATATGTCTTTGGATTAGGCTCTGCACAG
upper sequence: AT4G00630.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA18G46420.1 (Glycine max), 3'ss of exon 12
gttaacttcagtatttgatatatat--gttgttcctttttcctttgatatgtgcttagtggaaagaagagccaatta----tttcgattctatttgtctgacagCTCTCTGTCGAAAGGCTTAGTTCCATGAAGAAATATGTTTTTGGATTAGGCTCCGCGCAG
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gtggggattcttattagttctggttcagttgttctatgttaactttgtccatcaccattatcgaaagagctaaattgaggctcttatttgcttttttgttttagCTCTCGGTTGAAAGGCTTAGTTCAATGAAGAAATATGTCTTTGGATTTGGCTCTGCACAG
upper sequence: AT4G00630.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv15s0046g03390.t01 (Vitis vinifera), 3'ss of exon 3
gttaacttca-gtatttgatatatatgttgttcctttttcctttgata------tgtgcttagtggaaagaagagccaattatttcga-ttctatttgtctgacagCTCTCTGTCGAAAGGCTTAGTTCCATGAAGAAATATGTTTTTGGATTAGGCTCCGCGCAG
|| ||| || | | ||| | | || || || || | | | | ||| ||| | | | | || ||| |||| | || | ||||| ||||| |||||||| ||||||||||||||||||||||||||||| ||| | || |||
gtggactccataaaatctttatttctttttttatttgttaatctaagacaatgatgttctttataaatgaataaaaaaaaaattgaaccttctgtctgcattgcagCTATCTGTTGAAAGGCTGAGTTCCATGAAGAAATATGTTTTTGGATTGGGCACTGCTCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatatgtgcttagtggaaagaagagccaattatttcgattctatttgtctgacagCTCTCTGTCGAAAGGCTTAGTTCCATGAAGAAATATGTTTTTGGATTAGGCTCCGCGCAG
ctttgat putative branch site (score: 5)
ttctattt putative PPT
aattattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttaacttcagtatttgatatatatgttgttcctttttcctttgatatgtgcttagtggaaagaagagccaattatttcgattctatttgtctgacagCTCTCTGTCGAAAGGCTTAGTTCCATGAAGAAATATGTTTTTGGATTAGGCTCCGCGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA