Sequence
atgc intronic sequence ATGC exonic sequencegttaaagcatgatttttgcattagctatatgttgttctattcattcagtttattccttgtcttactattttgtgcccttgctaatttgtcgtacagCCTCTGTTTCCTGGTGAGAGCGGAGTTGATCAGCTTGTTGAAATCATTAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G09840.2 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G09840.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA16G00400.1 (Glycine max), 3'ss of exon 7
---gttaaagcatgatttt--tgcattagctatatgttgttctattcattcagtttattccttgtcttactattttgtgcccttg----ctaatttgtcgtacagCCTCTGTTTCCTGGTGAGAGCGGAGTTGATCAGCTTGTTGAAATCATTAAG
|| ||| || || | | | | | || || ||| ||| || |||||| || ||| | | || || ||| | ||||| |||||||||| ||||| |||||||||||||| ||||||||||| |||
gtatttggtgcaagaaaaaaatgtgacaaatttttctcatttcatcatttc--tttgttttctgtctt-ctttttcattttcctgaagttgaagttgatttgcagCCCTTGTTTCCTGGAGAGAGTGGAGTTGATCAGCTAGTTGAAATCATCAAG
upper sequence: AT1G09840.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA12G28730.2 (Glycine max), 3'ss of exon 8
gttaaagcatgatttttgcattagctatatgttgttctattcattcagtttattccttgtctt--actattttgtgcccttgct--------aatttgtcgtacagCCTCTGTTTCCTGGTGAGAGCGGAGTTGATCAGCTTGTTGAAATCATTAAG
|| || || | | | | || | ||||| | ||| ||| || | || ||| || | || ||| | ||||| |||||||||| ||||| |||||||||||||| ||||||||||| |||
----gtatttggttctttaaaaaaatgtgacaaatttttctcatttcatcatttctctgttttctgtcttcttttgcattttcctgaagttcaagttgatttgcagCCCTTGTTTCCTGGAGAGAGTGGAGTTGATCAGCTAGTTGAAATCATCAAG
upper sequence: AT1G09840.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv12s0035g01060.t01 (Vitis vinifera), 3'ss of exon 7
gttaaagcatgatttttgcattagctatatgttgtt---ctattcattcagtttattccttgtcttactattttgtgcccttgctaat----ttgtcgtacagCCTCTGTTTCCTGGTGAGAGCGGAGTTGATCAGCTTGTTGAAATCATTAAG
|| | | || | || | || | | || | || | |||| ||| | ||||| | | |||| || | ||||||||| |||||||||| || |||||||||||||| || ||||| ||||| |||
---gtagtacactgttaatttcagatgtagttgacttgccttcgcttttcatcatttccaagtcctgttatttaggcttttatctaaccatcttctggtacagCCTTTGTTTCCTGGAGAAAGCGGAGTTGATCAACTAGTTGAGATCATCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cattcagtttattccttgtcttactattttgtgcccttgctaatttgtcgtacagCCTCTGTTTCCTGGTGAGAGCGGAGTTGATCAGCTTGTTGAAATCATTAAG
tgctaat putative branch site (score: 2)
ttactatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttaaagcatgatttttgcattagctatatgttgttctattcattcagtttattccttgtcttactattttgtgcccttgctaatttgtcgtacagCCTCTGTTTCCTGGTGAGAGCGGAGTTGATCAGCTTGTTGAAATCATTAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT