Sequence
atgc intronic sequence ATGC exonic sequence...gtgttaaatgttatcttgaaaatataaattgaatttatcatctttgtatagtttattccttcatttacataaattaataggaggattgcctgtgtcacagGGAGATCGTACTCTTGCTGATTACATGAAAGATCGCAACTTTCCTTCAAACTTGGAATCTGTGATGTTTGGACGTGTCTTGCAAGGAGTAGACTCTTCGA
Basic information
species | Glycine max |
transcript | GLYMA16G34620.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G34620.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G01920.1 (Arabidopsis thaliana), 3'ss of exon 2
gtgttaaatgttatcttgaaaatataaattgaatttatcatctttgtatagtttattccttcatttacataaattaataggaggattgcctgtgtcacagGGAGATCGTACTCTTGCTGATTACATGAAAGATCGCAACTTTCCTTCAAACTTGGAATCTGTGATGTTTGGACGTGTCTTGCAAGGAGTAGACTCTTCGA
||| |||| | | || ||| || | | |||||| | | | | || ||| | | || | | ||||||||| ||| ||| |||||||||||||||||||| | ||||||||| || ||||| || | |||||||| || || | |||||||| || ||| ||
-------gtgtggtcttc------ttacttacccttacaatgaatctgctgtttatagttgcgatgatgatgatgaatgaaatgttttctt---caacagGGAGACCGTGATCTCGCTGATTACATGAAAGATCGGAGCTTTCCTTCTAATTTGGAGTCCATCATGTTTGGGCGCGTTCTCCAAGGAGTCGAGTCTGTGA
upper sequence: GLYMA16G34620.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv08s0058g01450.t01 (Vitis vinifera), 3'ss of exon 2
---gtgttaaatgttatcttgaaaatataaattgaatttatcatctttgtatagtttattccttcatttacataaattaataggaggattgcct--gtgtcacagGGAGATCGTACTCTTGCTGATTACATGAAAGATCGCAACTTTCCTTCAAACTTGGAATCTGTGATGTTTGGACGTGTCTTGCAAGGAGTAGACTCTTCGA
|||||| ||| |||| | | | || | | || |||| |||| || | ||| | | | | | | || || |||| |||||||||| | ||||| || |||||||||||||| ||||| |||| ||||||||| ||| |||||||| ||||||||||||||| ||| ||
cctttgttaa--gttgacttgtttgtgtgatatgcaagaag-attggtgtacagtt-atagatgcata-aaaggcagcaccaactgctttctctctgtgtgacagGGAGATAGAGACCTTGCAGACTACATGAAAGATCGTAACTTCCCTTTAAACTTGGAGTCTACTATGTTTGGGCGTGTCTTGCAAGGACTAGGTTCAATTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtatagtttattccttcatttacataaattaataggaggattgcctgtgtcacagGGAGATCGTACTCTTGCTGATTACATGAAAGATCGCAACTTTCCTTCAAACTTGGAATCTGTGATGTTTGGACGTGTCTTGCAAGGAGTAGACTCTTCGA
aattaat putative branch site (score: 3)
tttattccttcattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgttaaatgttatcttgaaaatataaattgaatttatcatctttgtatagtttattccttcatttacataaattaataggaggattgcctgtgtcacagGGAGATCGTACTCTTGCTGATTACATGAAAGATCGCAACTTTCCTTCAAACTTGGAATCTGTGATGTTTGGACGTGTCTTGCAAGGAGTAGACTCTTCGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - -aaatataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gattgcc