Sequence
atgc intronic sequence ATGC exonic sequencegtaggtagcagatgctggcctcagataaatcacattcaagtagctgcatatgaatacaagtacctgttgacatgtaatttgatggaatatgagttgattgttaaaagccatggtgaaatataaataaatatattgtttttcagGGGCTGGGCAAAACATTACAAACAATATCTTTGTTAGGCTACTTACATGAGTTCAGAGGAATAACAGGCCCTCATATGGTGGTTGCTCCAAAATCTACTC
Basic information
species | Glycine max |
transcript | GLYMA17G02640.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 5
lower sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 5
gtaggtagcagatgctggcctcagataaatcacattcaagta-gctgcatatgaatacaagtacctgttgacatgtaatttgatggaatatgagttgattgttaaaagccatggtgaaatataaataaatatattgtttttcagGGGCTGGGCAAAACATTACAAACAATATCTTTGTTAGGCTACTTACATGAGTTCAGAGGAATAACAGGCCCTCATATGGTGGTTGCTCCAAAATCTACTC
||| ||| ||| || | | || | ||| || | || | || |||| | ||| || ||| | | || | || |||| || || |||||| | ||||| || || ||| | ||||| | |||||||||||||| ||||| || ||||| ||||||||||| || || || || |
---------------------------------------gtatgctacatgtg----ttaatcttgattaagatgatcttctactctattttgttt---tgtttggcactttggctttgaatgcatactttt-ttataatttagGGACTTGGGAAAACACTTCAAACTATTTCATTGCTGGGCTATCTGCATGAGTTCAGAGGTATAACTGGTCCTCACATGGTGGTTGCGCCGAAGTCCACCC
upper sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaggtagcagatgctggcctcagataaatcacattcaagtagctgcatatgaatacaagtacctgttgacatgtaatttgatggaatatgagttgattgttaaaagccatggtgaaatataaataaatatatt-gtttttcagGGGCTGGGCAAAACATTACAAACAATATCTTTGTTAGGCTACTTACATGAGTTCAGAGGAATAACAGGCCCTCATATGGTGGTTGCTCCAAAATCTACTC
| | | | || | || || | ||| |||| ||| | | || | | | | | | || | | | | | || | | |||| ||||| || || | ||||| || |||||||| | ||| | ||||||| ||| ||||| | |||||||||||||| |||||||||||||| || |
---------------------------------------------gtaaaccacta--attatct--tagcatataataagat---ttttcagctctctaatgttatctgatgctaatctttattgtttttgttcatggtctagGGTCTGGGGAAGACGCTTCAAACCATTTCTTTGTTGGCTTACCTGCATGAGTACAGGGGAATTAATGGCCCTCATATGGTAGTTGCTCCAAAATCAACCC
upper sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 5
gtaggtagcagatgctggcctcagataaatcacattcaagtagctgcatatgaatacaagtacctgttgacatgtaatttgatggaatatgagttgattgttaaaagccatggtgaaat-ataaataaatatattgtttttcagGGGCTGGGCAAAACATTACAAACAATATCTTTGTTAGGCTACTTACATGAGTTCAGAGGAATAACAGGCCCTCATATGGTGGTTGCTCCAAAATCTACTC
| | | | || || | || || | ||| ||| || ||| | || || | | | || | | | | || | ||| ||||| ||||| |||||||| ||||| || ||||| || || || | |||||||| ||||||||||| || || || ||||| ||||| |||||||| ||||
-----------------------------------------tgatttttttttctataa-catctctt-atgtgttgttttatataat-caatttacttttgatcaatcagaatatactgacaacttggtattcctaccaccagGGTCTGGGTAAAACATTGCAAACCATTTCTTTATTGGGTTATCTGCATGAGTTTAGAGGAATAACTGGTCCCCACATGGTTGTTGCCCCAAAATCGACTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgagttgattgttaaaagccatggtgaaatataaataaatatattgtttttcagGGGCTGGGCAAAACATTACAAACAATATCTTTGTTAGGCTACTTACATGAGTTCAGAGGAATAACAGGCCCTCATATGGTGGTTGCTCCAAAATCTACTC
agttgat putative branch site (score: 5)
ttgtttttc putative PPT
atggtgaaatataaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaggtagcagatgctggcctcagataaatcacattcaagtagctgcatatgaatacaagtacctgttgacatgtaatttgatggaatatgagttgattgttaaaagccatggtgaaatataaataaatatattgtttttcagGGGCTGGGCAAAACATTACAAACAATATCTTTGTTAGGCTACTTACATGAGTTCAGAGGAATAACAGGCCCTCATATGGTGGTTGCTCCAAAATCTACTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG