Sequence
atgc intronic sequence ATGC exonic sequencegttcttttattttctttgctttaatctgtatccatgaaacaattggtgttatatagttttttttttaatatttactatttttagGTACTGGAAATTAATCTTGTGACCTTTCCAAATGTTGCTGATGCTATATTGGCCAATGGCATGTTTAGTCATTATGACCGTCCACGGATTGCTCAGCTTT
Basic information
species | Glycine max |
transcript | GLYMA02G39360.1 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 16
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 16
--------------------------gttctttta--ttttctttgct---ttaatctgta---tccatgaaacaattggtgttatatagttttttttttaatattt--actatttttagGTACTGGAAATTAATCTTGTGACCTTTCCAAATGTTGCTGATGCTATATTGGCCAATGGCATGTTTAGTCATTATGACCGTCCACGGATTGCTCAGCTTT
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gttagcagttttttcccaataagttcggccttttacctttgcattgccatgttgctcagtggcttcttttacctttatactgttgtgttgctcagtagtttctgtttgaattgattgtagGTTTTGGAGATCAACTTGGTCACTTACCCAAATGTTGCTGATGCCATCCTTGCTAATGGTATGTTCAGTCATTATGATCGCCCTCGTGTTGCTCAGCTTT
upper sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 16
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 16
----------------------------------------gttcttttattttctttgctttaatctgtatccatgaaacaattggtgttatatagttttttttttaatattt--actatttttagGTACTGGAAATTAATCTTGTGACCTTTCCAAATGTTGCTGATGCTATATTGGCCAATGGCATGTTTAGTCATTATGACCGTCCACGGATTGCTCAGCTTT
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gttagcagttttttcccaataagttaggccttttgcctttgcattgccatgttgctcagtggcttcttttacctttatactgttgtgtttgtgttgctcagtagtttctgtttgaattggttgtagGTTTTGGAGATCAACTTGGTCACTTACCCAAATGTTGCTGATGCCATCCTTGCTAATGGTATGTTCAGTCATTATGATCGCCCTCGTGTTGCTCAGCTTT
upper sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 16
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 14
------gttcttttattttctttgctttaatctgtatccatgaaacaat-tggtgttatatagttttttttttaatattt--actatttt-tagGTACTGGAAATTAATCTTGTGACCTTTCCAAATGTTGCTGATGCTATATTGGCCAATGGCATGTTTAGTCATTATGACCGTCCACGGATTGCTCAGCTTT
|| || || || | | | | | || | | | || || | | | | | | | || | | | || ||||| |||| || || | ||||| | ||||||||||| ||||| || | || ||||| ||||| ||||||||||||||||| || ||||||||||| |
gttagtatttgattgttcatttcaatatgaacatttgccttagacctgcatgctgcttaactactcaatgtcttctgcttggattgtcttgtagGTTTTGGAGATCAACTTAGTGACTTACCCAAATGTTGCAGATGCCATTCTTGCGAATGGTATGTTCAGTCATTATGACCGTCCTCGTATTGCTCAGCTCT
upper sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 16
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 16
gttcttttattttctttgctttaatctgtatccatgaaacaattggtgttatatagttttttttttaatatttactatttttagGTACTGGAAATTAATCTTGTGACCTTTCCAAATGTTGCTGATGCTATATTGGCCAATGGCATGTTTAGTCATTATGACCGTCCACGGATTGCTCAGCTTT
|| | |||||| ||| | | ||| | | || | | ||| | || | |||| | | || | || |||| ||||||| ||||| || || ||||||||||| || ||||||||||| || ||||| ||||||||||| ||||| || ||||| ||||| ||||| |
gtcgatctatttttttttcctaaatgaatttttatatagtttctttagttctg----cttcctaataat-tctgctctattcagGTTTTGGAAATCAATCTGGTTACATTTCCAAATGTCGCAGATGCTATATTAGCTAATGGTATGTTTAGTCACTATGATCGCCCACGTATTGCACAGCTCT
upper sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 16
lower sequence: PP1S270_53V6.1 (Physcomitrella patens), 3'ss of exon 16
gttcttttattttctttgctt-taatctgtatccatgaaacaattggtgttatatagttttttttttaatatttac-tatttttagGTACTGGAAATTAATCTTGTGACCTTTCCAAATGTTGCTGATGCTATATTGGCCAATGGCATGTTTAGTCATTATGACCGTCCACGGATTGCTCAGCTTT
|| | | | |||| | | | || | || || || | | | || | | || | | | ||| || ||||| |||||||| || |||||||| || || ||||| || ||| | |||||||| || | |||||||||||||| || |||||||||||||
gtaaaaatttaaatctagcttctcagttacatttgctgattttttatgattccttaactcatgctgtactttccacgtgtatacagGCTCTCGAAATCAATCTTGTCACTTTTCCAAACGTCGCAGATGCGATTTTGACTAATGGCATCTTCAAACATTATGACCGTCCTCGAATTGCTCAGCTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atccatgaaacaattggtgttatatagttttttttttaatatttactatttttagGTACTGGAAATTAATCTTGTGACCTTTCCAAATGTTGCTGATGCTATATTGGCCAATGGCATGTTTAGTCATTATGACCGTCCACGGATTGCTCAGCTTT
ttttaat putative branch site (score: 3)
ctattttt putative PPT
tgttatatagtttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcttttattttctttgctttaatctgtatccatgaaacaattggtgttatatagttttttttttaatatttactatttttagGTACTGGAAATTAATCTTGTGACCTTTCCAAATGTTGCTGATGCTATATTGGCCAATGGCATGTTTAGTCATTATGACCGTCCACGGATTGCTCAGCTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT