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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGAATCTGACCGGTGCATGCTTTATCATCAGGGATCTCCTTTCTGTAAAATAGTACGAGAGACCCTTGTTGAATTAGAGTTGCCACACTTGCTACACAGgtactcaataacgttacaccaatgacaaaattgctggatatgctgttagctatcatcagtgttttttcctgctgtaaaatcacaaccctgtatcacaaagccttgcaattgcaagcactacactcttggagtaactggtagctgaaaatttctgcag

Basic information

species Oryza sativa
transcript LOC_Os08g44400.3
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g44400.3 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G085000_T04 (Zea mays), 5'ss of exon 7
CAGAATCTGACCGGTGCATGCTTTATCATCAGGGATCTCCTTTCTGTAAAATAGTACGAGAGACCCTTGTTGAATTAGAGTTGCCACACTTGCTACACAGgtactcaata-acgtta----caccaatgacaaaattgctggatatgctgttagctatcatcagtgttttttcctgctgtaaaatcacaaccctgtatcacaaagccttgcaattgcaagcactacactcttggagtaactggtagctgaaaatt---tctgcag
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--------------------------------GGATCTCCCTTCTGTAGATTAGTACGAGAGACGCTTGTTGAGTTGGAATTGCCACATCTGCTACACAGgtatccaaaatactttaaaaccacaagtcaacgaatggcattataacagcgtggaagctgttgctaaacatcaccttagtagaattacacattagtttggtta---ttctggattgagatatgtgctcgacaagagtg-ttagtaactgaaaattattcctgcag

upper sequence: LOC_Os08g44400.3 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G022866_T01 (Zea mays), 5'ss of exon 9
CAGAATCTGACCGGTGCATGCTTTATCATCAGGGATCTCCTTTCTGTAAAATAGTACGAGAGACCCTTGTTGAATTAGAGTTGCCACACTTGCTACACAGgtactcaataacgtta------caccaatgacaaaattgct---ggatatgctgttagctatcatcagtgttttttcctgctgtaaaatcacaacc-ctgtatcacaaagccttgcaattgcaagcactacactcttggagtaactggtagctgaaaatttctgcag---
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--------------------------------GGATCTCCCTTCTGTAAATTAGTACGAGAGACGCTTGTCGAGTTGGAATTACCACATCTGCTACACAGgtatccaaaaatactttaaaaccacaagtcactgaatggcatcagaattcagaacagcctgcaagctgttgctaaacttaacctagtagaattaccactttagttcagttcttctggactgagatatgtgctctgcaagagtg-ttagtaactagaagttactcctgcag

upper sequence: LOC_Os08g44400.3 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM5G825090_T02 (Zea mays), 5'ss of exon 10
CAGAATCTGACCGGTGCATGCTTTATCATCAGGGATCTCCTTTCTGTAAAATAGTACGAGAGACCCTTGTTGAATTAGAGTTGCCACACTTGCTACACAGgtactcaata-acgtta----caccaatgacaaaattgct---ggatatgctgttagctatcatcagtgttttttcctgctgtaaaatcacaacc-ctgtatcacaaagccttgcaattgcaagcactacactcttggagtaactggtagctgaaaatttctgcag---
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--------------------------------GGATCTCCCTTCTGTAAATTAGTACGAGAGACACTTGTCGAGTTGGAATTGCCACATCTGCTACACAGgtatccaaaatactttaaaaccacaagtcactgaatggcatcagaattcagaacagcctgcaagctgttgctaaacttaacctagtagaattatcactttagttcagttcttctggactgagatatgtgctctgcaagagtg-ttagtaactagaagttactcctgcag

upper sequence: LOC_Os08g44400.3 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G085000_T02 (Zea mays), 5'ss of exon 9
CAGAATCTGACCGGTGCATGCTTTATCATC--AGGGATCTCCTTTCTGTAAAATAGTACGAGAGACCCTTGTTGAATTAGAGTTGCCACACTTGCTACACAGgtactcaata-acgtta----caccaatgacaaaattgctggatatgctgttagctatcatcagtgttttttcctgctgtaaaatcacaaccctgtatcacaaagccttgcaattgcaagcactacactcttggagtaactggtagctgaaaatt---tctgcag
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--GAGTCTGAATGGCTGATGATCTATTTTCTCAGGGATCTCCCTTCTGTAGATTAGTACGAGAGACGCTTGTTGAGTTGGAATTGCCACATCTGCTACACAGgtatccaaaatactttaaaaccacaagtcaacgaatggcattataacagcgtggaagctgttgctaaacatcaccttagtagaattacacattagtttggtta---ttctggattgagatatgtgctcgacaagagtg-ttagtaactgaaaattattcctgcag

Mapped 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|88473739|gb|CI411010.1|CI411010
EST:     ATAGTACGAGAGACCCTTGTTGAATTAGAGTTGCCACACTTGCTACACAG                         CTGTGCACGCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCAT
genomic: ATAGTACGAGAGACCCTTGTTGAATTAGAGTTGCCACACTTGCTACACAGgtactcaata ... atttctgcagCTGTGCACGCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCAT
EST: gi|88518244|gb|CI445898.1|CI445898
EST:     TAGTACGAGAGACCCTTGGTTGAATTAGAGTTNCCACACTTGCTACACAG                         CTGTGCA-GNCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCA
genomic: TAGTACGAGAGACCCTTG-TTGAATTAGAGTTGCCACACTTGCTACACAGgtactcaata ... atttctgcagCTGTGCACG-CGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 68 (upstream exon), 58 (downstream exon)
Score: 25

CAGAATCTGACCGGTGCATGCTTTATCATCAGGGATCTCCTTTCTGTAAAATAGTACGAGAGACCCTTGTTGAATTAGAGTTGCCACACTTGCTACACAGgtactcaata ... atttctgcagCTGTGCACGCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCATTTTCCAG




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