Sequence
atgc intronic sequence ATGC exonic sequence...gggatcttttggcaatatagaaattttttcaattgccttattttctgcctgtttatgacatgaatgcagcattctcacatttattttgtcttttatctagGGTTTTGTGGAGGACCAATTTGGCTTAGGTTTAATTGCTAGGGCAGTTGAGGAGGGGATAGCAGTAATCAAACCAACTGGAATTATGATCTTTAACATGG
Basic information
species | Glycine max |
transcript | GLYMA12G28490.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G28490.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os05g01470.1 (Oryza sativa), 3'ss of exon 4
gggatcttttggcaatatagaaattttttcaattgccttattttc-tgcctgtttatgacatgaatgcagca-ttctcacatt----tattttgtcttttatctagGGTTTTGTGGAGGACCAATTTGGCTTAGGTTTAATTGCTAGGGCAGTTGAGGAGGGGATAGCAGTAATCAAACCAACTGGAATTATGATCTTTAACATGG
| ||| || || | || ||| || ||| | || | || ||| || || | | || | | || ||| |||||||||| ||||||||||||||| | || || |||||| |||| ||||| || |||||| |||| || || || | || |||||||| ||||||||||
------taggaccaaggcgtgaacttctacacttgatagatcttcatattctttaaccccagtaatccactgcttgttatcttagtgcacaccttattgcatccagGGTTTTGTTGAGGACCAATTTGGCCTTGGGTTGATTGCTCGGGCTGTTGAAGAAGGGATATCAGTCATAAAGCCTATGGGTATTATGATATTTAACATGG
upper sequence: GLYMA12G28490.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G49810.1 (Arabidopsis thaliana), 3'ss of exon 4
gggatcttttggcaatatagaaattttttcaattgccttattttctgcctgtttatgaca-tgaatgcagcattctcac---atttattttgtcttt-tatctagGGTTTTGTGGAGGACCAATTTGGCTTAGGTTTAATTGCTAGGGCAGTTGAGGAGGGGATAGCAGTAATCAAACCAACTGGAATTATGATCTTTAACATGG
| || | || | | | | || | | | | ||| | | | || |||| | | || | ||||| | ||| |||||||||| || || || |||||||||||||| ||||| || |||||||| || || ||| | || |||||||| | || |||||||| ||||||||||
----ttaatttactcta-aaaggtgtaaatgatagaccaggtactggaaactttgttaaagtggatgctctacctgtgcctgatgaaatttgtatccatattcagGGTTTTGTTGAAGATCAGTTTGGCTTAGGTTTGATTGCCAGAGCAGTTGAAGAAGGAATATCTGTCATCAAACCTGCAGGGATTATGATATTTAACATGG
upper sequence: GLYMA12G28490.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv12s0035g01920.t01 (Vitis vinifera), 3'ss of exon 5
gggatcttttggcaatatagaaatttttt-caattgccttattttctgcctgtttatgacatgaatgcagcattctcacatttatt--ttgtcttttatctagGGTTTTGTGGAGGACCAATTTGGCTTAGGTTTAATTGCTAGGGCAGTTGAGGAGGGGATAGCAGTAATCAAACCAACTGGAATTATGATCTTTAACATGG
| || || || | || || |||| | || || || || || | | | |||| | ||| | | || | | ||||||||||| ||||| || ||||| || ||| |||||||||| ||||||||||| || ||||| || |||||||||| || ||||||||||| || ||||
---tccaaagggaaaaattgttatccattacaatgggtttgttgcctttcttcttctttttcctctctctctctctctcttttcacaatctttttctctatagGGTTTTGTCGAGGATCAGTTTGGATTGGGTCTAATTGCTAGAGCAGTTGAGGAAGGAATAGCTGTCATCAAACCAATGGGCATTATGATCTTCAATATGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcctgtttatgacatgaatgcagcattctcacatttattttgtcttttatctagGGTTTTGTGGAGGACCAATTTGGCTTAGGTTTAATTGCTAGGGCAGTTGAGGAGGGGATAGCAGTAATCAAACCAACTGGAATTATGATCTTTAACATGG
ttctcac putative branch site (score: 2)
tttattttgtctttt CT-rich tract
atttattttgtctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gggatcttttggcaatatagaaattttttcaattgccttattttctgcctgtttatgacatgaatgcagcattctcacatttattttgtcttttatctagGGTTTTGTGGAGGACCAATTTGGCTTAGGTTTAATTGCTAGGGCAGTTGAGGAGGGGATAGCAGTAATCAAACCAACTGGAATTATGATCTTTAACATGG
- - -cttttgg
- - - - - - - - - - - - - - - - -tgcctta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcattct