Sequence
atgc intronic sequence ATGC exonic sequence...agcatttctcttttatatacacatatatgattcatgctaaagtactcaaagattaattatctggagtatacatatactaattttctggtttatgcaacagGTATCGGTGCTGGCCCCTAACATCCCCGCGATGTATGAGATGCATTTTGCAGTGCCCATGGCTGGTGCTGTTCTCAACACCATCAACACTCGTCTTGATG
Basic information
species | Glycine max |
transcript | GLYMA11G33110.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G33110.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G65890.1 (Arabidopsis thaliana), 3'ss of exon 1
-----------------------------------agcatttctcttttatatacacatatatgattcatgctaaagtactcaaagattaattatctggagtatacat-atactaattttctggt--ttatgcaac-agGTATCGGTGCTGGCCCCTAACATCCCCGCGATGTATGAGATGCATTTTGCAGTGCCCATGGCTGGTGCTGTTCTCAACACCATCAACACTCGTCTTGATG
| || || | ||| | || | ||| || || || | || || | | || | | |||||| | | || || | | ||||| ||||||| || | || || |||| || || |||||||||||||| ||||| || ||||||||||| ||||| || ||| | |||||||||||||| || |
gtatgtcacactatccttaccttattttttctctgaacagttttagtttttttagagatagtccgtttat-ctgagata---aacattcatttgtatagagtatctgtgactgtacttaacccataattatgtgtttagGTATCCGTTGTTGCTCCAAACACACCGGCCATGTATGAGATGCACTTTGCCGTTCCCATGGCTGGAGCTGTACTTAACCCTATCAACACTCGTCTAGACG
upper sequence: GLYMA11G33110.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G65880.1 (Arabidopsis thaliana), 3'ss of exon 1
-------agcatttctcttttatatacacatatatgattcatgctaaagtactcaaagattaattatctggagtatacatat-actaattttctggtttatgcaacagGTATCGGTGCTGGCCCCTAACATCCCCGCGATGTATGAGATGCATTTTGCAGTGCCCATGGCTGGTGCTGTTCTCAACACCATCAACACTCGTCTTGATG
|| || |||| | || || | || ||| | ||| || | | || || ||| | ||||| || || || ||||||| || |||| || |||| ||||| ||||||| ||||| ||||| || ||||||||||| ||||| || ||| | |||||||||||||| || |
ttgttagagatagtccgttttgtgtagggtataattaaacagattaa--cattcatttatacaaagtatgagacatgcatgtgactaacattgtgtatt------tagGTATCAGTTATGGCTCCAAACACACCCGCCTTGTATGAAATGCACTTTGCCGTTCCCATGGCTGGAGCTGTACTTAACCCTATCAACACTCGTCTAGACG
upper sequence: GLYMA11G33110.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv04s0079g00790.t01 (Vitis vinifera), 3'ss of exon 1
--------------agcatttctcttttatatacacatatatgattcatgctaaa-gtactc-----aaagattaattatctggagtatacatatactaattttctgg------tttatgcaacagGTATCGGTGCTGGCCCCTAACATCCCCGCGATGTATGAGATGCATTTTGCAGTGCCCATGGCTGGTGCTGTTCTCAACACCATCAACACTCGTCTTGATG
| | | | ||| | | ||||||| | | || | | | | | || || | ||| |||| ||| | | | ||| | |||||||| || ||||| || || || || || ||||| |||||||| ||||||||||||||| || ||||| ||||||||||| |||| | || ||||
gtaagtgtgttttttaaaggccacacatgtatctatttttatgatttaaggtagatacattttgtaggagggagaaagatgttacacataaatatttaaatctggttggtattctttcccctgcagGTATCAGTTCTGGCTCCAAATATTCCAGCCATGTACGAGATGCACTTTGCAGTGCCCATGTGCGGGGCTGTCCTCAACACCATTAACATCAGGCTAGATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcaaagattaattatctggagtatacatatactaattttctggtttatgcaacagGTATCGGTGCTGGCCCCTAACATCCCCGCGATGTATGAGATGCATTTTGCAGTGCCCATGGCTGGTGCTGTTCTCAACACCATCAACACTCGTCTTGATG
tactaat putative branch site (score: 1)
tatacatatactaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agcatttctcttttatatacacatatatgattcatgctaaagtactcaaagattaattatctggagtatacatatactaattttctggtttatgcaacagGTATCGGTGCTGGCCCCTAACATCCCCGCGATGTATGAGATGCATTTTGCAGTGCCCATGGCTGGTGCTGTTCTCAACACCATCAACACTCGTCTTGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
-gcatttc
- - - - - - - - atacaca
- - - - - - - - - - - - - - - -tcatgct
- - - - - - - - - - - - - - - - - - - - - -actcaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catatac