Sequence
atgc intronic sequence ATGC exonic sequence...ggattggagcttatgttaatattgctattgcatgtcattttccatcaacaaggcttttagtgtgatgtagcttaccatgtaatccatcatatgctggcagGTCAAGCATTTTTGATGCAAAGGCTGGAATTTCATTGAACAACAACTTTGTGAAACTTGTCTCTTGGTATGACAATGAGTGGGGCTACAG
Basic information
species | Glycine max |
transcript | GLYMA19G22780.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G22780.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os04g40950.1 (Oryza sativa), 3'ss of exon 10
ggattggagcttatgttaatattgctattgcatgtcattttccatcaacaaggcttttagtgtgatgtagcttaccatgtaatccatcatatgctggcagGTCAAGCATTTTTGATGCAAAGGCTGGAATTTCATTGAACAACAACTTTGTGAAACTTGTCTCTTGGTATGACAATGAGTGGGGCTACAG
|| | || || || | || | || || | | || | ||| | | | | || | |||||||||||| |||||||||||||| || ||| | | || |||||||||| || ||||| |||||||||||||| || ||||| |||||
--------------gtggagat--ctgtttaaattcgtcttgtatttg---gatactcggttactcgaagcccctgacctcttttgctctgtg-taacagGTCAAGCATCTTTGATGCAAAGGCCGGTATTGCTCTCAATGACAACTTTGTTAAGCTTGTGTCTTGGTATGACAACGAATGGGGATACAG
upper sequence: GLYMA19G22780.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os04g40950.3 (Oryza sativa), 3'ss of exon 10
ggattggagcttatgttaatattgctattgcatgtcattttccatcaacaaggcttttagtgtgatgtagcttaccatgtaatccatcatatgctggcagGTCAAGCATTTTTGATGCAAAGGCTGGAATTTCATTGAACAACAACTTTGTGAAACTTGTCTCTTGGTATGACAATGAGTGGGGCTACAG----------
|| | || || || | || | || || | | || | ||| | | | | || | |||||||||||| |||||||||||||| || ||| | | || |||||||||| || ||||| |||||||||||||| || ||||| |||||
--------------gtggagat--ctgtttaaattcgtcttgtatttg---gatactcggttactcgaagcccctgacctcttttgctctgtg-taacagGTCAAGCATCTTTGATGCAAAGGCCGGTATTGCTCTCAATGACAACTTTGTTAAGCTTGTGTCTTGGTATGACAACGAATGGGGATACAGGTAATCATTT
upper sequence: GLYMA19G22780.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G071630_T01 (Zea mays), 3'ss of exon 10
------------------------------------------------------ggattggagcttatgttaatattgctattgcatgtc---attttccatcaacaaggcttttagt---gtgatgtagcttaccatgtaatc-catcatatgctggcagGTCAAGCATTTTTGATGCAAAGGCTGGAATTTCATTGAACAACAACTTTGTGAAACTTGTCTCTTGGTATGACAATGAGTGGGGCTACAG
|| | | || || | ||| || | | | ||| | || | || ||| | || || | || | | |||||| ||||| |||||||| |||||||| ||| | |||||| |||||||||||| ||||| || ||||| ||||| |||||||| |||||
gtgtgtgcttatatatatatatatatatatatatatatatatatatatatatatatatatatacattccctactactaatatctaatcgctcagtagttaatcgccggggacctcaggttactgacaatgtttttttcgtggttgtctctttcaatcacagGTCTAGCATCTTTGATGCGAAGGCTGGCATTGCCTTGAACGGCAACTTTGTGAAGCTTGTGTCCTGGTACGACAACGAGTGGGGATACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caacaaggcttttagtgtgatgtagcttaccatgtaatccatcatatgctggcagGTCAAGCATTTTTGATGCAAAGGCTGGAATTTCATTGAACAACAACTTTGTGAAACTTGTCTCTTGGTATGACAATGAGTGGGGCTACAG
agcttac putative branch site (score: 3)
ttttagt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggattggagcttatgttaatattgctattgcatgtcattttccatcaacaaggcttttagtgtgatgtagcttaccatgtaatccatcatatgctggcagGTCAAGCATTTTTGATGCAAAGGCTGGAATTTCATTGAACAACAACTTTGTGAAACTTGTCTCTTGGTATGACAATGAGTGGGGCTACAG
- - - - gcttatg
- - - - - - - - - - - tgctatt
- - - - - - - - - - - - - - -gcatgtc
- - - - - - - - - - - - - - - - - - - - -ccatcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccatgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccatcat