Sequence
atgc intronic sequence ATGC exonic sequencegtatatgtcttaattatatcactcttttatgtatcctcttatctttgtttctttggaaaaatataaatcgttaatgtccttgtagGTTAATGCACCTTCTCCAAGTAATGTCATTGTTGTATCAAATGCGATTATAAAATCAGAATCTTTGAGTGGCATAGGGCAACGAAGTATGGTGGAAAGTC
Basic information
species | Oryza sativa |
transcript | LOC_Os01g66730.2 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g66730.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM5G802854_T01 (Zea mays), 3'ss of exon 9
---------------gtatatgtcttaattatatcactcttttatgtatcctcttatctttgtttctttggaaaaatataaatcg-ttaatgtccttgtagGTTAATGCACCTTCTCCAAGTAATGTCATTGTTGTATCAAATGCGATTATAAAATCAGAATCTTTGAGTGGCATAGGGCAACGAAGTATGGTGGAAAGTC
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caagagaaaatgaactaattttccttgggaaatggagtttccaaactagccctaaatggtaatgtttcttgtgttttatttcttggtttgtgttct-gtagGTGAATGCTCCTGCAGCAAGTACTGTCATTCTTGTATCAAATGCAATTATGAGGTCAGAATCTTTGAGCGGCATAAAACAAAGAGCTATGGTAGAAAATC
upper sequence: LOC_Os01g66730.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G173989_T01 (Zea mays), 3'ss of exon 9
----------------------gtatatgtcttaattatatcactcttttatgtatcctcttatctttgtttctttggaaaaatataaatcg-ttaatgtccttgtagGTTAATGCACCTTCTCCAAGTAATGTCATTGTTGTATCAAATGCGATTATAAAATCAGAATCTTTGAGTGGCATAGGGCAACGAAGTATGGTGGAAAGTC
|| | || |||| ||| |||| | ||| || | | | | | ||| | | || ||| || |||||| ||||| ||| | |||||| ||||||| ||||||||||||| || || | |||||||||||||| |||||| ||| || |||||| |||| ||
gtatgttctagcaactgtccattgatcattattttttatcccacctttttgt-tatttgtaaatggtaatgtttcctgtgttttatttcttggtttgtgttct-gtagGTGAATGCTCCTGCAGCAAGTACTGTCATTCTTGTATCAAATGCAATAATGAGGTCAGAATCTTTGAGCGGCATAAAACAAAGAGCTATGGTAGAAAATC
upper sequence: LOC_Os01g66730.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G540589_T01 (Zea mays), 3'ss of exon 7
--------------------gtatatgtcttaattatatcactcttttatgtatcctct-tatctttgtttctttggaaaaatataaatcgttaatgtccttgtagGTTAATGCACCTTCTCCAAGTAATGTCATTGTTGTATCAAATGCGATTATAAAATCAGAATCTTTGAGTGGCATAGGGCAACGAAGTATGGTGGAAAGTC
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gtatgttctagatactgtccacatggttttttatcccacctttttttgttagattgtcaacagtaatgtttcttgtgttgtat-ttcttggtttatattat-gtagGTGAATGCTCCTGCGGCAAGTACTGTCATTCTTGTATCAAATGCAATTATGAGGTCAGAATCTTTGAGTGGCATAAAACAAAGAGCTATGGTAGAAAATCMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|88480729|gb|CI418000.1|CI418000EST: CTTTCATTTGAGATTGCTGTTGGCCTGAATGGCCGAGTCTGG GTTAATGCACCTTCTCCAAGTAATGTCATTGTTGTATCAAATGCGATTATA
genomic: CTTTCATTTGAGATTGCTGTTGGCCTGAATGGCCGAGTCTGGgtatatgtct ... gtccttgtagGTTAATGCACCTTCTCCAAGTAATGTCATTGTTGTATCAAATGCGATTATA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtatcctcttatctttgtttctttggaaaaatataaatcgttaatgtccttgtagGTTAATGCACCTTCTCCAAGTAATGTCATTGTTGTATCAAATGCGATTATAAAATCAGAATCTTTGAGTGGCATAGGGCAACGAAGTATGGTGGAAAGTC
cgttaat putative branch site (score: 4)
tgtcctt CT-rich tract
tttctttggaaaaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatatgtcttaattatatcactcttttatgtatcctcttatctttgtttctttggaaaaatataaatcgttaatgtccttgtagGTTAATGCACCTTCTCCAAGTAATGTCATTGTTGTATCAAATGCGATTATAAAATCAGAATCTTTGAGTGGCATAGGGCAACGAAGTATGGTGGAAAGTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA