Sequence
atgc intronic sequence ATGC exonic sequencegtaggtgaaatacgaacatgtcaatacattaccttgtctttctcaaaaacctttttttgatttggttttaccttttcatagCACAAGGAAAGAGAATTCATGTTGAAGTTTTCGGCAATTGAGATTTATAATGAATCTGTCAGGGACCTCCTTAGTCCAGACTGTACTCCTCTCAGACTTC
Basic information
species | Glycine max |
transcript | GLYMA01G37340.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G37340.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os08g43400.4 (Oryza sativa), 3'ss of exon 3
gtaggtgaaatacgaacatgtcaatacattaccttgtctttctcaaaaacctttttttgatttggttttaccttttcatagCACAAGGAAAGAGAATTCATGTTGAAGTTTTCGGCAATTGAGATTTATAATGAATCTGTCAGGGACCTCCTTAGTCCAGACTGTACTCCTCTCAGACTTC
|| ||| ||| |||||| | | |||| || || | | |||| | | | | || | | || | |||| |||||||||||||| |||| ||||||||||| ||||| || |||||| |||| ||||||||||| || | ||| || || ||||||||||
gtgtgtgcaatgtgaacat-----tgctttactttacctctg-cgaaaatttatccgtctcattgtgtgccattgctacagCATCCTGAAAGAGAATTCATTTTGAGATTTTCGGCAATAGAGATATACAATGAAGCTGTGAGGGACCTCCTGAGCCACGACACCACACCCCTCAGACTTC
upper sequence: GLYMA01G37340.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G51150.2 (Arabidopsis thaliana), 3'ss of exon 5
---------------gtaggtgaaatacgaacatgtcaatacattaccttgtcttt-ctcaaaaaccttt---ttttgatttggtt-ttaccttttcatagCACAAGGAAAGAGAATTCATGTTGAAGTTTTCGGCAATTGAGATTTATAATGAATCTGTCAGGGACCTCCTTAGTCCAGACTGTACTCCTCTCAGACTTC
|| | || | | ||||| | || ||| ||| | |||| | || || |||| ||||||| |||||||||||||| ||||||| || || || ||||| |||||||| ||||| || |||||| | ||| ||||| || ||| |||||| |||
gtaaagttaacaatatcagagtcttcatagtaatcttaccgcattatttccaattcattcagtaactgtcgccttttaaaaaaattatttgttttttgcagCACAATGAAAGAGAATTCATTCTGAAGTTCTCAGCCATGGAGATCTATAATGAGTCTGTAAGAGACCTCTTGAGTACAGACATTAGTCCACTCAGAGTTC
upper sequence: GLYMA01G37340.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv04s0023g03060.t01 (Vitis vinifera), 3'ss of exon 3
gtaggtgaaatacgaacatgtcaatacattaccttgtctt---tctcaaaaacctttttttgatttggtt----------ttaccttttcatagCACAAGGAAAGAGAATTCATGTTGAAGTTTTCGGCAATTGAGATTTATAATGAATCTGTCAGGGACCTCCTTAGTCCAGACTGTACTCCTCTCAGACTTC
||| ||| || | || ||| | || ||| || | || || ||| |||| | ||| || |||||||||||||||||||| | |||||||| || || || |||||||| |||||||||||||| ||||| || || |||| | |||| || ||||||
gtaatcaaaacaccactatatcatcccctttcctctctttcagttccataatttcccatttcctttgatgaaaaaaattgttatacatttgtagCACAAGGAAAGAGAATTTCTTTTGAAGTTCTCTGCTATGGAGATTTACAATGAATCTGTCAGAGACCTTCTCAGCTCAGATACTGCTCCGCTTCGACTTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cattaccttgtctttctcaaaaacctttttttgatttggttttaccttttcatagCACAAGGAAAGAGAATTCATGTTGAAGTTTTCGGCAATTGAGATTTATAATGAATCTGTCAGGGACCTCCTTAGTCCAGACTGTACTCCTCTCAGACTTC
ttttgat putative branch site (score: 4)
ttttaccttttcat putative PPT
aaaaaccttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaggtgaaatacgaacatgtcaatacattaccttgtctttctcaaaaacctttttttgatttggttttaccttttcatagCACAAGGAAAGAGAATTCATGTTGAAGTTTTCGGCAATTGAGATTTATAATGAATCTGTCAGGGACCTCCTTAGTCCAGACTGTACTCCTCTCAGACTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC