Sequence
atgc intronic sequence ATGC exonic sequence...atcactagtaggctccactcaaaatgcttatttgacattgtagtgagtgatgagtgatgactgtcacttcctatgaattcacatgcgcatctttaaccagGGCTTGGGCAGAGGATGAAGCAAAGAAGGCCAGGGAGCATGCCAGGGCCCTTGAGGAAGCCCGGAACCAATGGGAGCGTCATGGAATCAAGGTTGTTGTT
Basic information
species | Oryza sativa |
transcript | LOC_Os03g64400.4 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g64400.4 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM5G869004_T01 (Zea mays), 3'ss of exon 1
atcactagtaggctccactcaaaatgctt---atttgacattgtagtgagtgatgagtgatgactgtcacttcctatgaattcac-atgcgcatc--tttaaccagGGCTTGGGCAGAGGATGAAGCAAAGAAGGCCAGGGAGCATGCCAGGGCCCTTGAGGAAGCCCGGAACCAATGGGAGCGTCATGGAATCAAGGTTGTTGTT
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--------------gcaagaagaattcttgacatctgagatttgatcattttgtgcatatta--tttcattgtgcatgatgttattgtgctctttaatttaaccagGGCTTGGGCAGAGGAGGAAGCCAAAAAGGCCCGGGAGCATGCACGCGCCCTTGAGGAGGCCCGGAACCAATGGGAGCGTCAAGGAATCAGAGTTGTTGTC
upper sequence: LOC_Os03g64400.4 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G077222_T01 (Zea mays), 3'ss of exon 9
atcactagtaggctccactcaaaatgctt---atttgacattgtagtgagtgatgagtgatgactgtcacttcctatgaattcac-atgcgcatc--tttaaccagGGCTTGGGCAGAGGATGAAGCAAAGAAGGCCAGGGAGCATGCCAGGGCCCTTGAGGAAGCCCGGAACCAATGGGAGCGTCATGGAATCAAGGTTGTTGTT
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--------------gcaagaagaattcttgacatctgagatt-tgatcatttttgtgcatattatttcattgtgcatgatgttattgtgctctttaacttaaccagGGCTTGGGCAGAGGAGGAAGCCAAAAAGGCCCGGGAGCATGCACGCGCCCTTGAGGAGGCCCGGAACCAATGGGAGCGTCAAGGAATCAGAGTTGTTGTC
upper sequence: LOC_Os03g64400.4 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G140874_T01 (Zea mays), 3'ss of exon 6
atcactagtaggctccactcaaaatgcttatttgacattgtagtgagtgatgagtgatgactgtcacttcctatgaattcac-atgcgcatc--tttaaccagGGCTTGGGCAGAGGATGAAGCAAAGAAGGCCAGGGAGCATGCCAGGGCCCTTGAGGAAGCCCGGAACCAATGGGAGCGTCATGGAATCAAGGTTGTTGTT
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-------gtaagaagaattcttgac----atttgagatttgatcattttgtgcatatta--tttcattgtgcatgatgttattgtgctctttatcttaaccagGGCTTGGGCAGAGGAGGAAGCCAAAAAGGCCCGGGAGCATGCACGCGCCCTTGAGGAGGCCCAGAACCAATGGGAGCATCAAGGAATCAGAGTTGTTGTCMapped 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|10109136|gb|AU063166.2|AU063166EST: CTTGAAGTTGAGAGGAAGGCTTTATCAATGGCCCG GGCTT-GGNANGAGGATGAAGCAAAGAAGGCCAGGGAGCATGCCAGGGCCC
genomic: CTTGAAGTTGAGAGGAAGGCTTTATCAATGGCCCGgtaacaattc ... ctttaaccagGGCTTGGGCA-GAGGATGAAGCAAAGAAGGCCAGGGAGCATGCCAGGGCCC
EST:
gi|218483304|gb|FG967001.1|FG967001EST: CAGCTTCAATATGAACTTGAAGTTGAGAGGAAGGCTTTATCAATGGCCCG GGCTTGGGCAGAGGATGAAGCAAAGAAGGCCAGGGAGCATGCCAGGGCCCT
genomic: CAGCTTCAATATGAACTTGAAGTTGAGAGGAAGGCTTTATCAATGGCCCGgtaacaattc ... ctttaaccagGGCTTGGGCAGAGGATGAAGCAAAGAAGGCCAGGGAGCATGCCAGGGCCCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtgatgagtgatgactgtcacttcctatgaattcacatgcgcatctttaaccagGGCTTGGGCAGAGGATGAAGCAAAGAAGGCCAGGGAGCATGCCAGGGCCCTTGAGGAAGCCCGGAACCAATGGGAGCGTCATGGAATCAAGGTTGTTGTT
catcttt CT-rich tract
tatgaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atcactagtaggctccactcaaaatgcttatttgacattgtagtgagtgatgagtgatgactgtcacttcctatgaattcacatgcgcatctttaaccagGGCTTGGGCAGAGGATGAAGCAAAGAAGGCCAGGGAGCATGCCAGGGCCCTTGAGGAAGCCCGGAACCAATGGGAGCGTCATGGAATCAAGGTTGTTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - -gctccac
- - - - - - - - - - - aatgctt
- - - - - - - - - - - - - - - - - - - - - - - gtgatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - atgactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgcgc