Sequence
atgc intronic sequence ATGC exonic sequence...acaaaataaatcctagaatgcatatgcacacacccacgtggaagttcttttatgttccccatacatatcccctgatgttgcttgcgcttgtgttgtgcagATTCGATAGAGATCTCAAGTGGCGAACCGGGGTGGAGATTGTTCCAATACAATGCACAAGCTCCAATAACTTCCAAGTCACTGAACCCGCTTTGCAGCAA
Basic information
species | Glycine max |
transcript | GLYMA11G04890.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G04890.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv00s0840g00010.t01 (Vitis vinifera), 3'ss of exon 3
------acaaaataaatcctagaatgcatatgc-acacacccacgtggaagttcttttatgttccccatacatatcccctgatgttgcttgcgcttgtg--ttgtgcagATTCGATAGAGATCTCAAGTGGCGAACCGGGGTGGAGATTGTTCCAATACAATGCACAAGCTCCAATAACTTCCAAGTCACTGAACCCGCTTTGCAGCAA
|| | | || | |||| ||| | | | || | ||| || | | | | | || | || || ||| | | |||||||| |||||||||||||||||||| ||||| || || ||||| || ||||| || | || || ||| |||||| | |||||| ||||| | | ||
gtaattaccttgctatttct-gtttgcaactgctataaagcctttaagttgtttattgctttacgcatgaaatgtagttaactgacttttttttttgcgattcttgcagATTTGATAGAGATCTCAAGTGGCGTACCGGAGTTGAAATTGTACCGATACAGTGTTCTAGTTCGAATGGCTTCCAGATTACTGAATCCGCTCTCGAAGAA
upper sequence: GLYMA11G04890.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv00s1437g00010.t01 (Vitis vinifera), 3'ss of exon 3
------acaaaataaatcctagaatgcatatgc-acacacccacgtggaagttcttt--tatgttccccatacata-tcccctgatgttgcttgcgcttgtgttgtgcagATTCGATAGAGATCTCAAGTGGCGAACCGGGGTGGAGATTGTTCCAATACAATGCACAAGCTCCAATAACTTCCAAGTCACTGAACCCGCTTTGCAGCAA
|| | | || | |||| ||| | | | || | ||| || | | | | | || | ||||| || ||||| || | |||||||| |||||||||||||||||||| ||||| || || ||||| || ||||| || | || || ||| |||||| | |||||| ||||| | | ||
gtaattaccttgctatttct-gtttgcaactgctataaagcctttaagtcgtttattgctttacgcatgaaatgtagttaactgattttttttgcgattct----tgcagATTTGATAGAGATCTCAAGTGGCGTACCGGAGTTGAAATTGTACCGATACAGTGTTCTAGTTCGAATGGCTTCCAGATTACTGAATCCGCTCTCGAAGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttttatgttccccatacatatcccctgatgttgcttgcgcttgtgttgtgcagATTCGATAGAGATCTCAAGTGGCGAACCGGGGTGGAGATTGTTCCAATACAATGCACAAGCTCCAATAACTTCCAAGTCACTGAACCCGCTTTGCAGCAA
ccctgat putative branch site (score: 4)
atacatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acaaaataaatcctagaatgcatatgcacacacccacgtggaagttcttttatgttccccatacatatcccctgatgttgcttgcgcttgtgttgtgcagATTCGATAGAGATCTCAAGTGGCGAACCGGGGTGGAGATTGTTCCAATACAATGCACAAGCTCCAATAACTTCCAAGTCACTGAACCCGCTTTGCAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- aaaataa
- - - - - - - -gaatgca
- - - - - - - - - - - - - -acacacc
- - - - - - - - - - - - - - - - - cacgtgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cccctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcttgc