Sequence
atgc intronic sequence ATGC exonic sequence...ttaggactccctttgaattgctatcatcctaatcactttaggattttgataatgtggaatggttttgtgatccattttctcatcaactctctttgcacagGATACACTGATGAGACTCCTCGTGACTACCAGTGTAATCTCGGTCCAGATGGTAGACGTAGGGATGCTGATGAAAGGCCTGAGCTGTGTAGGGGAACTGT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G44340.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G44340.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA10G42720.1 (Glycine max), 3'ss of exon 7
ttaggactccctttgaattgctatcatcctaatcactttaggattttgataatgtggaatggttttgtgatcca----ttttctcatcaactctctttgcacagGATACACTGATGAGACTCCTCGTGACTACCAGTGTAATCTCGGTCCAGATGGTAGACGTAGGGATGCTGATGAAAGGCCTGAGCTGTGTAGGGGAACTGT
|| | || | | || | | || | |||||| | | | |||||||| | |||| | | | | ||||||| | |||||| ||||| || |||||||| || ||| | |||||||||||| | ||||| ||||||||||||||||||||||||||||| ||||| ||
ttttctcattgttctagcttctttatgagaggactgttcaatattttgcttctt----gtctttttgtgacataaaatttttgttgttgatatgtctgttacagGATTTAGTGATGAAACTCCACGGGACTACCACTGCAATTTAGGTCCAGATGGTCGGCGTAGAGATGCTGATGAAAGGCCTGAGCTGTGTAGAGGAACAGT
upper sequence: AT3G44340.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA20G24330.1 (Glycine max), 3'ss of exon 7
ttaggactccctttgaattgctatcatcctaatcactttaggattttgataatgtggaatggttttgtgatc--cattttctcatcaac-tctctttgc-acagGATACACTGATGAGACTCCTCGTGACTACCAGTGTAATCTCGGTCCAGATGGTAGACGTAGGGATGCTGATGAAAGGCCTGAGCTGTGTAGGGGAACTGT
|| | | | | | ||| || || | || | |||||| | | ||| | || || || |||||| | | | | | | || ||||||| | |||||| ||||| || |||||||| || ||| | |||||||||||| | ||||| |||||||||||||| |||||||||||||| ||||| ||
ttctcattattctagcttctttatgatag-gatta-ttcaatattttgct--tttggtctttttgtgacatgaacattttgttgttgatatatgtctgttacagGATTTAGTGATGAAACTCCACGGGACTACCACTGCAATTTAGGTCCAGATGGTCGGCGTAGAGATGCTGATGAAAGACCTGAGCTGTGTAGAGGAACGGT
upper sequence: AT3G44340.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv19s0014g05310.t01 (Vitis vinifera), 3'ss of exon 6
ttaggactccctttgaattgctatcatcctaat---cactttaggattttgat-aatgtggaatggttttgtgatcc-attttctcatcaactctctttgcacagGATACACTGATGAGACTCCTCGTGACTACCAGTGTAATCTCGGTCCAGATGGTAGACGTAGGGATGCTGATGAAAGGCCTGAGCTGTGTAGGGGAACTGT
||| ||| | | | |||| |||||| | | || | || | | |||| | || | | | | | ||||||| ||||| |||||||| || |||||||||||||| || ||| | || |||||||| || ||||| |||||||| |||||||||||||| ||||| ||||| ||
---ggatcattagaacatttccttgaaaataatttgcacttttagctcttactcaacagttattaaggttgtatttttatgatacctaccattttctttgc--agGATTTACTGATGAAACACCTCGTGACTACCATTGCAATTTGGGGCCAGATGGCAGGCGTAGAGATGCTGAGGAAAGGCCTGAGCTATGTAGAGGAACAGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgataatgtggaatggttttgtgatccattttctcatcaactctctttgcacagGATACACTGATGAGACTCCTCGTGACTACCAGTGTAATCTCGGTCCAGATGGTAGACGTAGGGATGCTGATGAAAGGCCTGAGCTGTGTAGGGGAACTGT
ttttgat putative branch site (score: 4)
ctctctttgc putative PPT
attttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttaggactccctttgaattgctatcatcctaatcactttaggattttgataatgtggaatggttttgtgatccattttctcatcaactctctttgcacagGATACACTGATGAGACTCCTCGTGACTACCAGTGTAATCTCGGTCCAGATGGTAGACGTAGGGATGCTGATGAAAGGCCTGAGCTGTGTAGGGGAACTGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - -atcctaa
- - - - - - - - - - - - - - - - - - - - -gattttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggttttg