Sequence
atgc intronic sequence ATGC exonic sequencegtttcatttcttaccacctcaattggacactgaagctctgttagtttagttagtttttagatatctgaatgaatatcctgtagGTTGCGCTTAAATTTGAGCACCGAAGCAGTAAAGGATGTAACTATGGCCCTCCATACGAGTGGCAGGTTTACCA
Basic information
species | Oryza sativa |
transcript | LOC_Os03g57940.3 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g57940.3 (Oryza sativa), 3'ss of exon 3
lower sequence: EDO97462 (Chlamydomonas reinhardtii), 3'ss of exon 2
gtttcatttcttaccacctcaattggacactgaagctctgttagtttagttagttt-ttagatatctgaatgaatatcctgtagGTTGCGCTTAAATTTGAGCACCGAAGCAGTAAAGGATGTAACTATGGCCCTCCATACGAGTGGCAGGTTTACCA
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--------gtcagcaagattgtttgaaccctg--gttttgctagtccacgaaactaatcagctctttg---------cgcgcagGTGGCTTTAAAATTTGAGCACCGCAGCAGTAAAGGCTGCAACTATGGGCCCCCCTACGAGTGGTCCGTGTACAA
upper sequence: LOC_Os03g57940.3 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ38433 (Selaginella moellendorffii), 3'ss of exon 2
gtttcatttcttaccacctcaattggacactgaagctctgttagtttagttagtttttagatatctgaatgaatatcctgt-agGTTGCGCTTAAATTTGAGCACCGAAGCAGTAAAGGATGTAACTATGGCCCTCCATACGAGTGGCAGGTTTACCA
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-------------gtagactgttcgaagattt--gctcagttggattggctcttttctcagcggctgatcaaagatgttgtcagGTTGCTTTGAAGTTTGAACACAGAAGCAGTAAAGGATGCAACTATGGGCCTCCGTATGAGTGGCAAGTTTACAC
upper sequence: LOC_Os03g57940.3 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 2
gtttcatttcttaccacctcaattggacactgaagctctgttagtttagttagtttttagatatctgaatgaatatcctgt-agGTTGCGCTTAAATTTGAGCACCGAAGCAGTAAAGGATGTAACTATGGCCCTCCATACGAGTGGCAGGTTTACCA
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-------------gtagactgttcgaagattt--tctcagttggatt-gctcttttctcagcggctgatcaaagatgttgtcagGTTGCTTTGAAGTTTGAACACAGAAGCAGTAAAGGATGCAACTATGGGCCTCCGTATGAGTGGCAAGTTTACACMapped 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|58609402|gb|CK037435.1|CK037435EST: GTCGAAGAGTATCTGGTGGAGGTTCTCGCACGGGTCCAGATGCGCAAGAG GTTGCGCTTAAATTTGAGCACCGAAGCAGTAAAGGATGTAACTATGGCCCT
genomic: GTCGAAGAGTATCTGGTGGAGGTTCTCGCACGGGTCCAGATGCGCAAGAGgtttcatttc ... tatcctgtagGTTGCGCTTAAATTTGAGCACCGAAGCAGTAAAGGATGTAACTATGGCCCT
EST:
gi|29616079|gb|CB621091.1|CB621091EST: GTCGAAGAGTATCTGGTGGAGGTTCTCGCACGGGTCCAGATGCGCAAGAG GTTGCGCTTAAATTTGAGCACCGAAGCAGTAAAGGATGTAACTATGGCCCT
genomic: GTCGAAGAGTATCTGGTGGAGGTTCTCGCACGGGTCCAGATGCGCAAGAGgtttcatttc ... tatcctgtagGTTGCGCTTAAATTTGAGCACCGAAGCAGTAAAGGATGTAACTATGGCCCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actgaagctctgttagtttagttagtttttagatatctgaatgaatatcctgtagGTTGCGCTTAAATTTGAGCACCGAAGCAGTAAAGGATGTAACTATGGCCCTCCATACGAGTGGCAGGTTTACCA
tttagttagttttta 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 |
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttcatttcttaccacctcaattggacactgaagctctgttagtttagttagtttttagatatctgaatgaatatcctgtagGTTGCGCTTAAATTTGAGCACCGAAGCAGTAAAGGATGTAACTATGGCCCTCCATACGAGTGGCAGGTTTACCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG