Sequence
atgc intronic sequence ATGC exonic sequencegtgcctatttcatctctcatctgtacatctccctgtccctggggcctcctactaacctcctgcatttgcccttgcttttcagGTGATGGAACAGTTCCAATTATGCTATCACTTGGTATATTAACA
Basic information
species | Oryza sativa |
transcript | LOC_Os08g44400.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g44400.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM5G825090_T03 (Zea mays), 3'ss of exon 6
----------gtgcctatttcatctctcatctgtacatctcc-----ctgtccctggggcctcct-actaacctcctgcatttgcccttgcttttc--agGTGATGGAACAGTTCCAATTATGCTATCACTTGGTATATTAACA
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ccccttcctagaccccatttttggcactgggtatgccctcttaaagtttcttcctataatgaccttactgacctcactcacttatgcttgtttttcttagGCGATGGAACTGTTCCAATTATGCTATCACTTGGTCTGTTGACA
upper sequence: LOC_Os08g44400.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G085000_T03 (Zea mays), 3'ss of exon 5
gtgcctatttcatctctcatctgtacatctcc-ctgtccctggggcctcctactaacctcctgcatttgc-ccttgcttttcagGTGATGGAACAGTTCCAATTATGCTATCACTTGGTATATTAACA
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gtgtgtattcaacgtatcttctttttgtttctgctcttaaaggttgttccttttagtcacctttgtttgtgctttgtttttcagGTGATGGAAGTGTTCCAATTATGCTATCGCTTGGTCTGTTGACA
upper sequence: LOC_Os08g44400.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G085000_T05 (Zea mays), 3'ss of exon 3
gtgcctatttcatctctcatctgtacatctcc-ctgtccctggggcctcctactaacctcctgcatttgc-ccttgcttttcagGTGATGGAACAGTTCCAATTATGCTATCACTTGGTATATTAACA-------------------------------------------------
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gtgtgtattcaacgtatcttctttttgtttctgctcttaaaggttgttccttttagtcacctttgtttgtgctttgtttttcagGTGATGGAAGTGTTCCAATTATGCTATCGCTTGGTCTGTTGACAGTAAGTAAATAAGTACCAAGTAATTCAAAAGTATATGATATGTTTTAAC
upper sequence: LOC_Os08g44400.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G022866_T02 (Zea mays), 3'ss of exon 6
---------gtgcctattt----catctctcat---ctgtacatctccctgtccctggggcctcctactaacctcctgcatttgcccttgcttttc--agGTGATGGAACAGTTCCAATTATGCTATCACTTGGTATATTAACA
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cccttcctagaccccatttttggcactgggtatgccctcttaaagtttcttcctataagtgaccttactgacctcactcacttatgcttgtttttcttagGCGATGGAACTGTTCCAATTATGCTATCACTTGGTCTGTTGACAMapped 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|58590549|gb|CF988857.1|CF988857EST: TGCCATGTATGAATCTGATGCCATCATAAAATACCTGGCCGACAAATATG GTGATGGAACAGTTCCAATTATGCTATCACTTGGTATATTAACA
genomic: TGCCATGTATGAATCTGATGCCATCATAAAATACCTGGCCGACAAATATGgtgcctattt ... tgcttttcagGTGATGGAACAGTTCCAATTATGCTATCACTTGGTATATTAACA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctccctgtccctggggcctcctactaacctcctgcatttgcccttgcttttcagGTGATGGAACAGTTCCAATTATGCTATCACTTGGTATATTAACA
tactaac putative branch site (score: 0)
tttgcccttgcttttc putative PPT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgcctatttcatctctcatctgtacatctccctgtccctggggcctcctactaacctcctgcatttgcccttgcttttcagGTGATGGAACAGTTCCAATTATGCTATCACTTGGTATATTAACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA