Sequence
atgc intronic sequence ATGC exonic sequence...tgaggtttcctcctttactttttgaaattatcttgggttttaataccctactattccacgttttggagtctgcattgacaagacattatacctattgcagCAACTAGTCATATACGAGACATCTGCCTCTGAACTGGATATAATTCGAGATATTTCTCGAACCTTCCCTTCACATGTATTCTTCCAACAGAGACATGGAC
Basic information
species | Glycine max |
transcript | GLYMA13G07090.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G07090.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os08g31840.2 (Oryza sativa), 3'ss of exon 3
----------------------------------------------------------------------tgaggtttcctcctttact-ttttgaaattatcttgggttttaataccctactattccacgttttggagtctgcattgacaagacattatacctattg--cagCAACTAGTCATATACGAGACATCTGCCTCTGAACTGGATATAATTCGAGATATTTCTCGAACCTTCCCTTCACATGTATTCTTCCAACAGAGACATGGAC
| ||| || | | ||| |||||||| || | || | | | || | ||| | ||| || || | ||| ||| ||| |||||||||||||||||||| || ||| |||| |||||||| || || || || || || || |||||| | |||||||||||||||||||| |
gtacctataacaattgtgaaagaactgcttgccctgatttttgttgaatgttccctattattttttaactttctgttgtcttagtagttatttctaaattatca-ggatattgtcttaagagtcatacatatcttgtcaacattattacatttctatactattttttggacagACACTGGTCATATACGAGACATCTGCATCAGAATTGGAAATAATTCGTGACATATCACGTACTTTTCCATCACATATTTTCTTCCAACAGAGACATGGTC
upper sequence: GLYMA13G07090.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G15930.1 (Arabidopsis thaliana), 3'ss of exon 3
tgaggtttcctcctttactttttgaaattatcttgggttttaataccctactattccacgttttggagtctgca-ttgacaagacattatacct-attgcagCAACTAGTCATATACGAGACATCTGCCTCTGAACTGGATATAATTCGAGATATTTCTCGAACCTTCCCTTCACATGTATTCTTCCAACAGAGACATGGAC
| || || || ||| | | ||| || | | | | ||| | | || | | |||| | | | | ||| ||||||| || || || ||||| || || || ||||| ||||| ||||| ||||| ||||| || ||||| |||||||| |||||||| ||||||||||||
--gtaataacttattatctccttgtg--tgttttgttattcattttctttggcttcattgctggaaagaaaaaaacttacaattctctcgatttcattatagCAACTGGTGATTTATGAGACGTCGGCATCAGAACTCGATATCATTCGGGATATATCTCGTACTTTCCCGTCACATGTTTTCTTCCAGAAGAGACATGGAC
upper sequence: GLYMA13G07090.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv14s0083g00540.t01 (Vitis vinifera), 3'ss of exon 3
-----tgaggtttcctcctttactttttgaaattatcttgggttttaataccctactattccacgttttggagtctgcattgacaagacattatacctattgcagCAACTAGTCATATACGAGACATCTGCCTCTGAACTGGATATAATTCGAGATATTTCTCGAACCTTCCCTTCACATGTATTCTTCCAACAGAGACATGGAC
| | || || | | ||||| ||| | | | | | | || | | || | || ||| | | | | ||| | | |||||||| || ||||||||||||||||| || ||| ||||||||||||||||||||||||| |||||||| |||||||| |||||||| |||||||||||||
tttttcgtagatttctgatg-atcctttgatatt-tgggagttcctttcagatagattctcttcatattcttat-tgtgctgatgaaa-aatgtacttgtc-cagCAACTGGTAATATACGAGACATCTGCTTCAGAATTGGATATAATTCGAGATATTTCTCGTACCTTCCCATCACATGTTTTCTTCCAGCAGAGACATGGAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccctactattccacgttttggagtctgcattgacaagacattatacctattgcagCAACTAGTCATATACGAGACATCTGCCTCTGAACTGGATATAATTCGAGATATTTCTCGAACCTTCCCTTCACATGTATTCTTCCAACAGAGACATGGAC
cattgac putative branch site (score: 3)
acattata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgaggtttcctcctttactttttgaaattatcttgggttttaataccctactattccacgttttggagtctgcattgacaagacattatacctattgcagCAACTAGTCATATACGAGACATCTGCCTCTGAACTGGATATAATTCGAGATATTTCTCGAACCTTCCCTTCACATGTATTCTTCCAACAGAGACATGGAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - ttcctcc
- - - - - - - - - - - - - - - - - gggtttt
- - - - - - - - - - - - - - - - - - - - - - - - - - -ttccacg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gagtctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgacaag