Sequence
atgc intronic sequence ATGC exonic sequencegtatatgtcttgattatatcactcttttatgtatcctctttatctttgtttctttggaaaaaatataaatcgctaatgtccttgtagGTTAATGCACCTTCTCCAAGTAATGTCATTGTTGTATCAAATGCGATTATAAAATCAGAATCTTTGAGTGGCATAGGGCAACGAAGTATGGTGGAAAGTC
Basic information
species | Oryza sativa |
transcript | LOC_Os01g47256.3 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g47256.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM5G802854_T01 (Zea mays), 3'ss of exon 9
--------------gtatatgtcttgattatatcactcttttatgtatcctctttatctttgtttctttggaaaaaatataaatcgctaatgtccttgtagGTTAATGCACCTTCTCCAAGTAATGTCATTGTTGTATCAAATGCGATTATAAAATCAGAATCTTTGAGTGGCATAGGGCAACGAAGTATGGTGGAAAGTC
|| | || | | || || | | || || | | | | | | | | | | ||| || |||||| ||||| ||| | |||||| ||||||| ||||||||||||| ||||| | |||||||||||||| |||||| ||| || |||||| |||| ||
caagagaaaatgaactaattttccttgggaaatggagtttccaaactagccctaaatggtaatgtttcttgtgttttatttcttggtttgtgttct-gtagGTGAATGCTCCTGCAGCAAGTACTGTCATTCTTGTATCAAATGCAATTATGAGGTCAGAATCTTTGAGCGGCATAAAACAAAGAGCTATGGTAGAAAATC
upper sequence: LOC_Os01g47256.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G173989_T01 (Zea mays), 3'ss of exon 9
--------------------gtatatgtcttgattatatcactcttttatgtatcctctttatctttgtttctttggaaaaaatataaatcgctaatgtccttgtagGTTAATGCACCTTCTCCAAGTAATGTCATTGTTGTATCAAATGCGATTATAAAATCAGAATCTTTGAGTGGCATAGGGCAACGAAGTATGGTGGAAAGTC
| || | || |||| | | ||| ||| | | || | | | | | | | | | ||| || |||||| ||||| ||| | |||||| ||||||| ||||||||||||| || || | |||||||||||||| |||||| ||| || |||||| |||| ||
gtatgttctagcaactgtccattgatcattattttttatcccacctttttgttatttgtaaatggtaatgtttcctgtgttttatttcttggtttgtgttct-gtagGTGAATGCTCCTGCAGCAAGTACTGTCATTCTTGTATCAAATGCAATAATGAGGTCAGAATCTTTGAGCGGCATAAAACAAAGAGCTATGGTAGAAAATC
upper sequence: LOC_Os01g47256.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G540589_T01 (Zea mays), 3'ss of exon 7
--------------------gtatatgtcttgattatatcactcttttatgtatcctctttatctttgtttctttggaaaaaatataaatcgctaatgtccttgtagGTTAATGCACCTTCTCCAAGTAATGTCATTGTTGTATCAAATGCGATTATAAAATCAGAATCTTTGAGTGGCATAGGGCAACGAAGTATGGTGGAAAGTC
|| | || || | | | ||| | || || | |||||||| | | | | | | || | | |||||| ||||| ||| | |||||| ||||||| ||||||||||||| ||||| | ||||||||||||||||||||| ||| || |||||| |||| ||
gtatgttctagatactgtccacatggttttttatcccacctttttttgttagattgtcaacagtaatgtttcttgtgttgtatttct--tggtttatattat-gtagGTGAATGCTCCTGCGGCAAGTACTGTCATTCTTGTATCAAATGCAATTATGAGGTCAGAATCTTTGAGTGGCATAAAACAAAGAGCTATGGTAGAAAATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atcctctttatctttgtttctttggaaaaaatataaatcgctaatgtccttgtagGTTAATGCACCTTCTCCAAGTAATGTCATTGTTGTATCAAATGCGATTATAAAATCAGAATCTTTGAGTGGCATAGGGCAACGAAGTATGGTGGAAAGTC
cgctaat putative branch site (score: 3)
tgtcctt CT-rich tract
tttctttggaaaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatatgtcttgattatatcactcttttatgtatcctctttatctttgtttctttggaaaaaatataaatcgctaatgtccttgtagGTTAATGCACCTTCTCCAAGTAATGTCATTGTTGTATCAAATGCGATTATAAAATCAGAATCTTTGAGTGGCATAGGGCAACGAAGTATGGTGGAAAGTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA