Sequence
atgc intronic sequence ATGC exonic sequencegtaagtattttcattatatcaaaaatacattgtcacatatgatttggttagacccttaattttcaggggtagtataactattcgatgtattacagGTCACAACCTTATTTCACTTGGATCGGCAAATGTATTTACTGGGATATCTTGCTAACCAAAGCCGTGTCTATCTTATTGACAAGCAATTTAA
Basic information
species | Oryza sativa |
transcript | LOC_Os02g11840.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g11840.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G141587_T02 (Zea mays), 3'ss of exon 15
gtaagtattttcattatatcaaaaatacattgtcacatatgatttg-gttagacccttaattttcaggg-------gtagtataactattcgat--------gtattacagGTCACAACCTTATTTCACTTGGATCGGCAAATGTATTTACTGGGATATCTTGCTAACCAAAGCCGTGTCTATCTTATTGACAAGCAATTTAA
|| ||| ||||||| | | ||||| |||| | |||| || |||||| | || || || | | ||||| ||| || || |||||||||||||| || |||||||||||||||| |||||||||| | ||||||||||| |||||||||||||||||||||||||| |||||||||||
gtgagttttttcatcac-ttaaaaagacatc-ctatatatctttcaagttagatcatttatggatagagtgctttcatgtcataaccatttcatattttcatgtgttacagGTCACAACTTTGTTTCACTTGGATCGGCCAATGTATTTATTAGGATATCTTGCAAACCAAAGCCGTGTCTATCTTATTGATAAGCAATTTAA
upper sequence: LOC_Os02g11840.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G141587_T05 (Zea mays), 3'ss of exon 15
---gtaagtattttcattatatcaaaaatacattgtcacatatgatttg-gttagacccttaattttcaggg-------gtagtataactattcgat--------gtattacagGTCACAACCTTATTTCACTTGGATCGGCAAATGTATTTACTGGGATATCTTGCTAACCAAAGCCGTGTCTATCTTATTGACAAGCAATTTAA
|| ||| ||||||| | | ||||| |||| | |||| || |||||| | || || || | | ||||| ||| || || |||||||||||||| || |||||||||||||||| |||||||||| | ||||||||||| |||||||||||||||||||||||||| |||||||||||
gaggtgagttttttcatcac-ttaaaaagacatc-ctatatatctttcaagttagatcatttatggatagagtgctttcatgtcataaccatttcatattttcatgtgttaCAGGTCACAACTTTGTTTCACTTGGATCGGCCAATGTATTTATTAGGATATCTTGCAAACCAAAGCCGTGTCTATCTTATTGATAAGCAATTTAA
upper sequence: LOC_Os02g11840.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G124886_T01 (Zea mays), 3'ss of exon 15
gtaagtattttcattatatcaaaaatacattgtcacatatgatttg-gttagacccttaattttcaggg-------gtagtataactattcgatgtattacagGTCACAACCTTATTTCACTTGGATCGGCAAATGTATTTACTGGGATATCTTGCTAACCAAAGCCGTGTCTATCTTATTGACAAGCAATTTAA
|| || |||| | | | ||||| |||| | | |||| || |||||| | || | | || | | ||||| ||| |||| |||||||| ||||||||||||||||||||||||| |||||||||||| ||||||||||| |||||||||||||||||||||||||| |||||||||||
gtgggt-tttttgtcac-ttaaaaagacatc-ttatatatctttcaagttagatcatttagtgatagagcgctttcatgtcataaccatttcatgtgttacagGTTACAACCTTATTTCACTTGGATCGGCCAATGTATTTACTAGGATATCTTGCAAACCAAAGCCGTGTCTATCTTATTGATAAGCAATTTAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatttggttagacccttaattttcaggggtagtataactattcgatgtattacagGTCACAACCTTATTTCACTTGGATCGGCAAATGTATTTACTGGGATATCTTGCTAACCAAAGCCGTGTCTATCTTATTGACAAGCAATTTAA
gtataac putative branch site (score: 3)
ttaattttca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtattttcattatatcaaaaatacattgtcacatatgatttggttagacccttaattttcaggggtagtataactattcgatgtattacagGTCACAACCTTATTTCACTTGGATCGGCAAATGTATTTACTGGGATATCTTGCTAACCAAAGCCGTGTCTATCTTATTGACAAGCAATTTAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA