Sequence
atgc intronic sequence ATGC exonic sequencegtaattttgatgcaacatgttgtgcgtcctttccactcaaaagttcctgatatgaaatcaatttttatttactacagGCAACTGCAGTTGTTAACTCAGGTTTACTGTTGATGGCTGTCATGGGACTAATGTTTCCTGCTGTCCTTCACTTCACGCATTCAGAAGTGAGGCAAGGAG
Basic information
species | Oryza sativa |
transcript | LOC_Os04g55940.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g55940.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G040017_T02 (Zea mays), 3'ss of exon 5
gtaattttgatgcaacatgttgtgcgtcctttccactcaaaagttcctgatat-gaaatcaatttttatttactacagGCAACTGCAGTTGTTAACTCAGGTTTACTGTTGATGGCTGTCATGGGACTAATGTTTCCTGCTGTCCTTCACTTCACGCATTCAGAAGTGAGGCAAGGAG
|| || || || || || | | ||| || | | |||||| || || ||| || | | ||| ||||||||||||||||| ||||||||||||||||||||||||||||||||| | ||||||||||| || ||||| ||||| |||||||||||| | ||||| |
gtgatgtttgtgtgactgtttttctcttcttcagtaacatgacattttgatattgagattaatattcaatcactgcagGCAACTGCAGTTGTCAACTCAGGTTTACTGTTGATGGCTGTCATGGGATTGATGTTTCCTGCCGTTCTTCATTTCACTCATTCAGAAGTGCGTCAAGGGG
upper sequence: LOC_Os04g55940.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G143356_T01 (Zea mays), 3'ss of exon 6
gtaattttgatgcaacatgttgtgcgtccttt--ccactcaaaagttcctgatatgaaatcaatttttatttactacagGCAACTGCAGTTGTTAACTCAGGTTTACTGTTGATGGCTGTCATGGGACTAATGTTTCCTGCTGTCCTTCACTTCACGCATTCAGAAGTGAGGCAAGGAG
|| | | ||| | || || || | | | | | || | ||| || ||| | | | || ||||||||||||| ||| ||||||||||||||||||||||||||||||||| | ||||||||||| || || || ||||| |||||||||||| |||||||||
gtgacaattatgtgattgtttttgtgttcatcagtaaggtgacattttttatagtgagattaatatccaatcacaccagGCAACTGCAGCTGTCAACTCAGGTTTACTGTTGATGGCTGTCATGGGATTGATGTTTCCTGCCGTTCTCCATTTCACTCATTCAGAAGTGCGGCAAGGAG
upper sequence: LOC_Os04g55940.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA13G44960.1 (Glycine max), 3'ss of exon 4
gtaattttgatgcaacatgttgtgcgtcctttccactcaaaagttcctgatatgaaatc--aatttttatttactacagGCAACTGCAGTTGTTAACTCAGGTTTACTGTTGATGGCTGTCATGGGACTAATGTTTCCTGCTGTCCTTCACTTCACGCATTCAGAAGTGAGGCAAGGAG
||| | | || || | || || | | | | || | || | | || | | ||| | ||||||| |||| ||||| || || || ||||| ||||||||||| |||||| || | ||||||||||| ||| |||| || || || ||||| |||||
gtacatatcat-caccccatt-catttctgcttcctcctgatgtcacagacttcacattgtagtccgcctttgcaacagGCAGCTGCTGTTGTCAATTCTGGGTTACTCTTGATGGCTGTAATGGGAATACTATTTCCTGCTGTGCTTTACTTTACTCACTCCGAAGTTCATCAAGGGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcgtcctttccactcaaaagttcctgatatgaaatcaatttttatttactacagGCAACTGCAGTTGTTAACTCAGGTTTACTGTTGATGGCTGTCATGGGACTAATGTTTCCTGCTGTCCTTCACTTCACGCATTCAGAAGTGAGGCAAGGAG
tcctgat putative branch site (score: 3)
tttttattt putative PPT
tgatatgaaatcaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattttgatgcaacatgttgtgcgtcctttccactcaaaagttcctgatatgaaatcaatttttatttactacagGCAACTGCAGTTGTTAACTCAGGTTTACTGTTGATGGCTGTCATGGGACTAATGTTTCCTGCTGTCCTTCACTTCACGCATTCAGAAGTGAGGCAAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG