Sequence
atgc intronic sequence ATGC exonic sequence...ttgttagagatagtccgttttgtgtagggtataattaaacagattaacattcatttatacaaagtatgagacatgcatgtgactaacattgtgtatttagGTATCAGTTATGGCTCCAAACACACCCGCCTTGTATGAAATGCACTTTGCCGTTCCCATGGCTGGAGCTGTACTTAACCCTATCAACACTCGTCTAGACG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G65880.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G65880.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA11G33110.1 (Glycine max), 3'ss of exon 1
ttgttagagatagtccgttttgtgtagggtataattaaacagattaa--cattcatttatacaaagtatgagacatgcatgtgactaacattgtgtatt------tagGTATCAGTTATGGCTCCAAACACACCCGCCTTGTATGAAATGCACTTTGCCGTTCCCATGGCTGGAGCTGTACTTAACCCTATCAACACTCGTCTAGACG
|| || |||| | || || | || ||| | ||| || | | || || ||| | ||||| || || || ||||||| || |||| || |||| ||||| ||||||| ||||| ||||| || ||||||||||| ||||| || ||| | |||||||||||||| || |
-------agcatttctcttttatatacacatatatgattcatgctaaagtactcaaagattaattatctggagtatacatat-actaattttctggtttatgcaacagGTATCGGTGCTGGCCCCTAACATCCCCGCGATGTATGAGATGCATTTTGCAGTGCCCATGGCTGGTGCTGTTCTCAACACCATCAACACTCGTCTTGATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aacattcatttatacaaagtatgagacatgcatgtgactaacattgtgtatttagGTATCAGTTATGGCTCCAAACACACCCGCCTTGTATGAAATGCACTTTGCCGTTCCCATGGCTGGAGCTGTACTTAACCCTATCAACACTCGTCTAGACG
gactaac putative branch site (score: 1)
atttatacaaagtat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgttagagatagtccgttttgtgtagggtataattaaacagattaacattcatttatacaaagtatgagacatgcatgtgactaacattgtgtatttagGTATCAGTTATGGCTCCAAACACACCCGCCTTGTATGAAATGCACTTTGCCGTTCCCATGGCTGGAGCTGTACTTAACCCTATCAACACTCGTCTAGACG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - gttttgt
- - - - - - - - - - - - - - - - - - aaacaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - atacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -actaaca