Sequence
atgc intronic sequence ATGC exonic sequenceCGCAGAACCACTTCTATCAGACCTTCCCAGTGTGAAACGTCCTGAAGAGCCAAAATCAGTGTATGTAGGAGGGGATTATCATTGCCAAGCAGATTCTACAgtgagttggcctcttctattatcattctcaagggctcaagtctgtcttcacagttacttttcttgttcctaatgtattttttgttag
Basic information
species | Oryza sativa |
transcript | LOC_Os05g44916.2 |
intron # | 4 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g44916.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G068336_T01 (Zea mays), 5'ss of exon 5
CGCAGAACCACTTCTATCAGACCTTCCCAGTGTGAAACGTCCTGAAGAGCCAAAATCAGTGTATGTAGGAGGGGATTATCATTGCCAAGCAGATTCTACAgtgagttggcctc-ttctattatcattctcaagggctcaagtctgtcttcacagttacttttcttgttcctaatgtattttttgttag------
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TGTAGAACCACTTTTGTCTGACCTTCCGTGCGTGAAACGTCCTGAAGAGCCAAAATCTGTGTACGTGGGAGGCGACTATCGCTGCCAAGCAGATTCTCAAgtgagttgttggcattgcattattattcttgaggggttatgaatg-------atttacttcaattatgcttaaaatgggattcattggaaacag
upper sequence: LOC_Os05g44916.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G005036_T01 (Zea mays), 5'ss of exon 5
CGCAGAACCACTTCTATCAGACCTTCCCAGTGTGAAACGTCCTGAAGAGCCAAAATCAGTGTATGTAGGAGGGGATTATCATTGCCAAGCAGATTCTACAgtgagttggcctc-ttctattatcattctcaagggctcaagtctgtcttcacagtt-acttttcttgttcctaatgtattttttgttag------
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TGTAGAACCACTTCTGTCTGACCTTCCGTGCGTGAAACGTCCTGAAGAGCCAAAATCTGTGTACGTGGGAGGAGACTATCGCTGCCAAGCAGATTCTCCAgtgagttgttggcattgcattattaatttattattcttgaggggttatgaatgatttacttcaattatgcttaaaattggattcattggaaacag
upper sequence: LOC_Os05g44916.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv09s0002g03200.t01 (Vitis vinifera), 5'ss of exon 5
CGCAGAACCACTTCTATCAGACCTTCCCAGTGTGAAACGTCCTGAAGAGCCAAAATCAGTGTATGTAGGAGGGGATTATCATTGCCAAGCAGATTCTACAgtgagttggcctcttctattatcattctcaagggctcaagtctgtcttcacagttacttttcttgttc--ctaatgtattttttgttag-----
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TGCAGAGCCACTTGTTTCTTATCTTCCCAGTGTGCCCCGTCCAGAAGAGCCAAAATCTGTTTATGTTGGAGGGGATTATCGTTGTCAGGCTGATTCAGGGgtgtgt--atctctaattgttcacatctagtggtttcatgtctgattgatctgttgattttgtttctcatctgtttaattcgttttgagtacag
upper sequence: LOC_Os05g44916.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv10s0003g03230.t01 (Vitis vinifera), 5'ss of exon 4
CGCAGAACCACTTCTATCAGACCTTCCCAGTGTGAAACGTCCTGAAGAGCCAAAATCAGTGTATGTAGGAGGGGATTATCATTGCCAAGCAGATTCTACAgtgagttggcctcttctattatcattctcaagggctcaagtctgtcttcacagttacttttcttgttc--ctaatgtattttttgttag-----
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TGCAGAGCCACTTGTTTCTGATCTTCCCAGTGTGCCCCGTCCAGAAGAGCCAAAATTTGTTTATGTTGGAGGGGATTATCGTTGTCAGGCTTATTCAGGGgtgtgt--atctctaattgttcacttctagtggtttcatgtctgattgatctgttgattttgtttttcatctgtttaattcgttttgagtacag
upper sequence: LOC_Os05g44916.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv11s0016g02870.t01 (Vitis vinifera), 5'ss of exon 5
CGCAGAACCACTTCTATCAGACCTTCCCAGTGTGAAACGTCCTGAAGAGCCAAAATCAGTGTATGTAGGAGGGGATTATCATTGCCAAGCAGATTCTACAgtgagt----tggcctcttctattatcattctcaagggctcaagtctgtcttcacagttacttttcttgttcctaatgtattttttgttag
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TGCAGAACCACTTCTCTCTGACCTACCCAGTGTTCCTCGTCCTGAGGAACCTAAATCTGTGTATGTTGGAGGTGATTATCGCTGTCAAGCTGACTCAGGGgtgtgtataataaatgttctgtttaaaaatattctttgttcaa-tgtgcattaccaattaataac--tgttatttctttcttatatgccagMapped 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|286522|gb|D15329.1|D15329EST: CAAAATCAGTGTATGTAGGAGGGGATTATCATTGCCAAGCAGATTCTACA AGTACACACATTGCACTTGCCTTTGAGGTTCCAGGTGGCTGGCGTCAAGAG
genomic: CAAAATCAGTGTATGTAGGAGGGGATTATCATTGCCAAGCAGATTCTACAgtgagttggc ... tttttgttagAGTACACACATTGCACTTGCCTTTGAGGTTCCAGGTGGCTGGCGTCAAGAG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CGCAGAACCACTTCTATCAGACCTTCCCAGTGTGAAACGTCCTGAAGAGCCAAAATCAGTGTATGTAGGAGGGGATTATCATTGCCAAGCAGATTCTACAgtgagttggcctcttctattatcattctcaagggctcaagtctgtcttcacagttacttttcttgttcctaatgtattttttgttag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT