Sequence
atgc intronic sequence ATGC exonic sequenceTTCTTGGCTACTGTTTCACATGAGATCAGAACTCCAATGAATGGTGTTCTAGgttagtccactgccttcgtttcaaaataattgttgttttaggctttggcatcaactctaacttacttctatgagcattaatattttggtttcgccttgat...
Basic information
species | Oryza sativa |
transcript | LOC_Os01g69920.2 |
intron # | 5 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g69920.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G423456_T02 (Zea mays), 5'ss of exon 6
TTCTTGGCTACTGTTTCACATGAGATCAGAACTCCAATGAATGGTGTTCTAGgttagtccactgccttcgtttcaaaataattgttgttttaggctttggcatcaactctaacttacttctatgagcattaatattttggtttcgccttgat
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TTCTTGGCTACTGTTTCTCATGAGATCAGAACTCCAATGAATGGTGTTCTAGgtgaggttctagtc--catctaaactgtacaataatcttaattgtta--attagagtgaaaggagatatgatgtttccgattttgcag------------
upper sequence: LOC_Os01g69920.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G471529_T01 (Zea mays), 5'ss of exon 6
TTCTTGGCTACTGTTTCACATGAGATCAGAACTCCAATGAATGGTGTTCTAGgttag--tccactgccttcg--tttcaaaataattgttgttttaggctttggcatcaactctaacttacttctatgagcattaatattttggtttcgccttgat
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TTCTTGGCTACTGTTTCTCATGAGATCAGAACTCCAATGAATGGTGTCCTAGgtgaggttctaatgtatctaaattgtacaataattttcattgttaattagggcgaaaggagatatgaatgtttccaatttttgcag------------------
upper sequence: LOC_Os01g69920.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA08G11060.2 (Glycine max), 5'ss of exon 7
TTCTTGGCTACTGTTTCACATGAGATCAGAACTCCAATGAATGGTGTTCTAGgttagt---ccactgccttcgtttcaaaataat-tgttgttttaggctttggcat--caactctaacttacttctatgagcattaatattttggtttcgccttgat------
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TTTCTTGCTACTGTTTCCCATGAGATCAGAACACCAATGAATGGTGTTTTGGgtgagttgtcttctgtctacggcttagtctattatccaatttttatctatattatttccacagaaaagaagagcttcttcagccatgaccctgctctaaattggattttcag
upper sequence: LOC_Os01g69920.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA05G28070.1 (Glycine max), 5'ss of exon 6
TTCTTGGCTACTGTTTCACATGAGATCAGAACTCCAATGAATGGTGTTCTAGgttagtccactgccttcgtttcaaaataattgttgttttaggctttggcatcaactctaacttacttctatgagcattaatattttggtttcgccttgat-----------------------
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TTTCTTGCTACTGTTTCCCATGAAATCAGAACACCAATGAATGGTGTTTTAGgtgagttgtcttctgtc--tatggtttagtcgattatccaatttttaatttttaa-ctatatacattccacaaaaaagaagagcttc-ttcagccatgaccctgctctaaattggattttcag
upper sequence: LOC_Os01g69920.2 (Oryza sativa), 5'ss of exon 5
lower sequence: AT1G27320.1 (Arabidopsis thaliana), 5'ss of exon 6
TTCTTGGCTACTGTTTCACATGAGATCAGAACTCCAATGAATGGTGTTCTAGgttagtcc----actgccttcgtttcaaaataattgttgttttaggctttggcatcaactct----aacttacttctatgagcattaatattttggtttcgccttgat------
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TTCCTTGCCACTGTTTCACATGAAATCAGAACTCCAATGAATGGTGTTCTAGgtgagtatcgaaatggccactatgttgcctccttctctcacctatgcccatgaatattttctgaagaacaaacttaaccaaatattctcatgttgactttgatctggggtgtag
upper sequence: LOC_Os01g69920.2 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv01s0010g03780.t01 (Vitis vinifera), 5'ss of exon 6
TTCTTGGCTACTGTTTCACATGAGATCAGAACTCCAATGAATGGTGTTCTAGgttagtccact-gccttcgtttcaaaataatt---gttgttttaggctttggcatcaactctaac------ttacttctatgagcatt---aatattttggtttcgccttgat---------------------
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TTCCTTGCCACTGTTTCTCATGAGATCAGAACCCCAATGAATGGTGTTCTCGgtgagttttcttaaatttatgctctattcacttcagtcatgtctagatatcgcctcacctttgatcagaaataaattatgggaacactgaaaagattttggagccatgacagtctaaatatgttcatcttgcag
upper sequence: LOC_Os01g69920.2 (Oryza sativa), 5'ss of exon 5
lower sequence: PP1S50_141V6.1 (Physcomitrella patens), 5'ss of exon 7
TTCTTGGCTACTGTTTCACATGAGATCAGAACTCCAATGAATGGTGTTCTAGgttagtccactgccttcgtttcaaaataattgttgttttaggctttggcatcaactctaactt-acttctatgagcattaatattttggtttcgccttgat-------
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TTCTTGGCAACTGTGTCTCACGAGATTCGGACTCCAATGAATGGTGTTCTAGgttagtataatatatccac-----aacacttga-atttcatactttgttatt---tctaagtagaattgtgcgcatattgtctgcttatgtacatctctgtgatgcagMapped 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|29630153|gb|CB635162.1|CB635162EST: CTTGGCTACTGTTTCACATGAGATCAGAACTCCAATGAATGGTGTTCTAG GGATGCTCCAAATGCTCATGGATACTGATTTGGA
genomic: CTTGGCTACTGTTTCACATGAGATCAGAACTCCAATGAATGGTGTTCTAGgttagtccac ... tccttttcagGGATGCTCCAAATGCTCATGGATACTGATTTGGA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TTCTTGGCTACTGTTTCACATGAGATCAGAACTCCAATGAATGGTGTTCTAGgttagtccactgccttcgtttcaaaataattgttgttttaggctttggcatcaactctaacttacttctatgagcattaatattttggtttcgccttgat
- - - - - - - - - - GAGATC
- - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaataa