Sequence
atgc intronic sequence ATGC exonic sequencegtttttatcttcttcgttctttgtctaacgttctgcataaaagtttgtcttggttcagtagtattgattctccttttgcttacctttgttggtggaatgacagGAGGATTTCCCACATAATGCACACCATAGAGAGATAGCAATTTCGATAAGCAATTACACATTGAAGCATGGTGATACGGGTTTGGTTATTGTTGGTGGAC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G51050.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G51050.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA11G07720.1 (Glycine max), 3'ss of exon 3
gtttttatcttcttcgttctttgtctaacgttctgcataaaagtttgtcttggttcagtagtattgattctccttttgcttacctttgttggtggaatgacagGAGGATTTCCCACATAATGCACACCATAGAGAGATAGCAATTTCGATAAGCAATTACACATTGAAGCATGGTGATACGGGTTTGGTTATTGTTGGTGGAC
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---------------gtatgatgttca--gttgtac-tatatgatcctgttattgtattaggtttggttgagcttactaattcttttagtggttg--ttatagGAGGATTTTCCACATAATGCTCACCATAGGGAAGTTGCAATCTCTATAAGCAATTATACTCTAAAGCATGGAGATACAGGATTGATAATTGTCGGTGGCA
upper sequence: AT3G51050.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA01G37580.1 (Glycine max), 3'ss of exon 3
gtttttatcttcttcgttctttgtctaacgttctgcataaaagtttgtcttggttcagtagtattgattctccttttgcttacctttgttggtggaatgacagGAGGATTTCCCACATAATGCACACCATAGAGAGATAGCAATTTCGATAAGCAATTACACATTGAAGCATGGTGATACGGGTTTGGTTATTGTTGGTGGAC
|| | | ||| | | | | | | | | | |||| | | || || | || | | | |||||||||| ||||||||||| |||||||| || | ||||| || ||||||||||| || | |||||||| ||||| || || | ||||| |||||
----------------------gtatgatgttttagctgtac-tatatgatcctgttattatattaggt-tgagttcactaattctttaagtgattgttatagGAGGATTTTCCACATAATGCTCACCATAGGGAAGTTGCAATCTCTATAAGCAATTATACTCTAAAGCATGGAGATACAGGATTAATAATTGTCGGTGGCA
upper sequence: AT3G51050.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv04s0023g02750.t01 (Vitis vinifera), 3'ss of exon 3
--------gtttttatcttcttcgttctttgtctaacgttctgcataaa-agtttgtcttggttcagtagtattgattctccttttgcttacctttgttggtggaatgacagGAGGATTTCCCACATAATGCACACCATAGAGAGATAGCAATTTCGATAAGCAATTACACATTGAAGCATGGTGATACGGGTTTGGTTATTGTTGGTGGAC
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gtgccctattcattggttacaattttacttgtttatgccttttcatggataatgttgtattgcctggtagtgt--atcttatgtcctcatccattgcctcgtctt-caatagGAGGATTTTCCACATAATGCTCACCATAGGGAGATAGCAATCTCAATAAGCAATTATACCCTGAAGCATGGCGATGCAGGATTGGTAATTGTTGGGGGGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttggttcagtagtattgattctccttttgcttacctttgttggtggaatgacagGAGGATTTCCCACATAATGCACACCATAGAGAGATAGCAATTTCGATAAGCAATTACACATTGAAGCATGGTGATACGGGTTTGGTTATTGTTGGTGGAC
tgcttac putative branch site (score: 2)
tattgatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttttatcttcttcgttctttgtctaacgttctgcataaaagtttgtcttggttcagtagtattgattctccttttgcttacctttgttggtggaatgacagGAGGATTTCCCACATAATGCACACCATAGAGAGATAGCAATTTCGATAAGCAATTACACATTGAAGCATGGTGATACGGGTTTGGTTATTGTTGGTGGAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA