Sequence
atgc intronic sequence ATGC exonic sequence...ttttcaactgtgcaacatcaatatttaatgctttttagttcaactattattgctcttgtaacttgtgaatcataacactcacctttttattgttgagcagGATCTTGGTTGGTCTTCCATCTGTTGAGAACAGGGAAATGATCTTGAAGACTCTTTTGGCTAAAGAAAAACATGAAAACTTAGACTTCAAAGAGCTGGCA
Basic information
species | Glycine max |
transcript | GLYMA16G29290.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G29290.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv16s0050g01840.t01 (Vitis vinifera), 3'ss of exon 12
---------------------------------ttttcaactgtgcaacatcaatatttaatgctttttagttcaactattattgctcttgtaact----tgtgaatcataacactcacctttttattgttgagcagGATCTTGGTTGGTCTTCCATCTGTTGAGAACAGGGAAATGATCTTGAAGACTCTTTTGGCTAAAGAAAAACATGAAAACTTAGACTTCAAAGAGCTGGCA
|||||| | | | | || | | | || | || || || ||| || | ||| | | ||| | | | || ||| ||| || |||||||||| |||||||| |||| ||| || |||||| |||||||||| |||||||||||| || || | | ||||| || ||||| |||
gtagatttgcatattgtgttacactcagcatcattttcatcgttttactctgaagctatggagaaggatatattaaagatagatgaatgtgtcaccatgctttgagtaggcaaactaatggtatctgtgatgaacagAATTATGGTTGGTCTACCATCTGTGGAGAGCAGAGAGATGATCCTGAAGACTCTCTTGGCTAAAGAACAAGCCGAGGATCTTGACTTTAAGGAGCTTGCA
upper sequence: GLYMA16G29290.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv16s0050g01850.t01 (Vitis vinifera), 3'ss of exon 13
---ttttcaactgtgcaacatcaatatttaatgctttttagttcaactattattgctcttgtaacttgtgaatcataacactcacctttttat-tgttgagcagGATCTTGGTTGGTCTTCCATCTGTTGAGAACAGGGAAATGATCTTGAAGACTCTTTTGGCTAAAGAAAAACATGAAAACTTAGACTTCAAAGAGCTGGCA
|| | | | || ||||| | ||||| | | | | | ||| | ||||| | | | | ||| || ||| ||| || |||||||||| |||||||| |||| |||||| ||||||||||||||||| |||| ||||||||| || | | ||||| || ||||| |||
atcttctgtgttatcaaatcaaaatatcagaaatgttttaagtagataagcgt-gtcactgtgcttc---aatcagacaaactaatggtctatatgatgaacagAATTATGGTTGGTCTACCATCTGTGGAGAGCAGGGAGATGATCTTGAAGACTCTCCTGGCAAAAGAAAAAGCAGAGGATCTTGACTTTAAGGAGCTTGCA
upper sequence: GLYMA16G29290.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv16s0050g01830.t01 (Vitis vinifera), 3'ss of exon 11
---------------------------------------------------ttttcaactgt-gcaacatca-atatttaatgctttttagttcaactattattgctcttgtaacttgtgaatcataacactcacctttttattgttgagcagGATCTTGGTTGGTCTTCCATCTGTTGAGAACAGGGAAATGATCTTGAAGACTCTTTTGGCTAAAGAAAAACATGAAAACTTAGACTTCAAAGAGCTGGCA
||| |||| || | || || | | | | | | || | || | | || | | ||| | | | || ||| ||| || |||||||||| |||||||| |||| |||||| ||||| ||||||||||| ||||| ||||||||| || | | ||||| || ||||| |||
gtagatttgcatattgtgtcacactcggcatcattttcatcgttttaccgcatttaaactaaagccgtgttgtatggagaaggatatattgaagatagatgaatgtgtcaccatgcttcgagtaggcaaactaatggtatctgtgatgaacagAATTATGGTTGGTCTACCATCTGTGGAGAGCAGGGAGATGATATTGAAGACTCTCTTGGCAAAAGAAAAAGCAGAGGATCTTGACTTTAAGGAGCTTGCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attattgctcttgtaacttgtgaatcataacactcacctttttattgttgagcagGATCTTGGTTGGTCTTCCATCTGTTGAGAACAGGGAAATGATCTTGAAGACTCTTTTGGCTAAAGAAAAACATGAAAACTTAGACTTCAAAGAGCTGGCA
cactcac putative branch site (score: 2)
ctcacctttttatt CT-rich tract
tttttattgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttttcaactgtgcaacatcaatatttaatgctttttagttcaactattattgctcttgtaacttgtgaatcataacactcacctttttattgttgagcagGATCTTGGTTGGTCTTCCATCTGTTGAGAACAGGGAAATGATCTTGAAGACTCTTTTGGCTAAAGAAAAACATGAAAACTTAGACTTCAAAGAGCTGGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - actgtgc
- - - - - - - - - - - - ttaatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acttgtg