Sequence
atgc intronic sequence ATGC exonic sequencegtaatagtctttactttctctctcactcttatatagatagttatttcggctactaattggtggttttcatttcgcttttagGTATGCAAATGTGAAGACACCTGAACGTCATGTGAGGACTCGACTTTACTTCACATCT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G01310.2 |
intron # | 27 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G01310.2 (Arabidopsis thaliana), 3'ss of exon 27
lower sequence: GLYMA19G02260.1 (Glycine max), 3'ss of exon 24
gtaatagtctttactttctctctcactcttatatagatagttatttcggctactaattggtggttttcatttcgcttttagGTATGCAAATGTGAAGACACCTGAACGTCATGTGAGGACTCGACTTTACTTCACATCT
| | | ||| | || || | | |||| | ||||| || | ||| || |||||||||||||||||||||||||| || |||||| | || || || |||||||||||
---gtgaataacaggtcctcatctgattttctaca--ttattatgatctgttctaatc-----ttattgttttgcacc-agGTATGCAAATGTGAAGACACCTGAGCGCCATGTGCGAACACGCCTCTACTTCACATCA
upper sequence: AT3G01310.2 (Arabidopsis thaliana), 3'ss of exon 27
lower sequence: GLYMA13G05060.1 (Glycine max), 3'ss of exon 40
gtaatagtctttactttctctctcactcttatatagatagttatttcggctactaattggtggttttcatttcgcttttagGTATGCAAATGTGAAGACACCTGAACGTCATGTGAGGACTCGACTTTACTTCACATCT
| | | | ||| | || || | | |||| | ||||| || | ||| || |||||||||||||||||||||||||| || |||||| | || || || |||||||||||
---gtgaacatcgggtcctcatctgattttctaca--ttattatgatctattctaatc-----ttattgttttgcacc-agGTATGCAAATGTGAAGACACCTGAGCGCCATGTGCGAACACGCCTCTACTTCACATCA
upper sequence: AT3G01310.2 (Arabidopsis thaliana), 3'ss of exon 27
lower sequence: GLYMA09G37610.1 (Glycine max), 3'ss of exon 24
gtaatagtctttactttctctctcactcttatatagatagttatttcggctactaattggtggttttcatttcgcttttagGTATGCAAATGTGAAGACACCTGAACGTCATGTGAGGACTCGACTTTACTTCACATCT
|| ||| | | | | || | || || | | || | ||||| | || || | | | | |||||||||||||| |||||||| ||||| |||||| | || || || |||||||||||
---gtaaatattatgtctttgttt--tattgtgtacattatcacttgcatt-ctaatacttttttatcgtc-cacctccagGTATGCAAATGTAAAGACACCAGAACGCCATGTGCGAACACGCCTATACTTCACATCA
upper sequence: AT3G01310.2 (Arabidopsis thaliana), 3'ss of exon 27
lower sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 26
------gtaatagtctttactttctctctcactcttatatagat-agttatttcggctactaattggtggttttcatttcgcttttagGTATGCAAATGTGAAGACACCTGAACGTCATGTGAGGACTCGACTTTACTTCACATCT
| | | | | | ||| | || | || | | | |||||| || ||| | || | |||| | | ||||||||||||||||||||||| ||||| |||||| | || || || || || |||||
gtgaatacatgaaccacttaagtttgtcttagtcctgtacacctcaattattta---tattaagatttccttgttatttt-caatcagGTATGCAAATGTGAAGACACCAGAACGCCATGTGCGCACACGCCTCTATTTTACATCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttatatagatagttatttcggctactaattggtggttttcatttcgcttttagGTATGCAAATGTGAAGACACCTGAACGTCATGTGAGGACTCGACTTTACTTCACATCT
tactaat putative branch site (score: 1)
ttttcatttcgctttt putative PPT
tatagatagttattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatagtctttactttctctctcactcttatatagatagttatttcggctactaattggtggttttcatttcgcttttagGTATGCAAATGTGAAGACACCTGAACGTCATGTGAGGACTCGACTTTACTTCACATCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA