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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttttacattaatttttgaagttctatccaaacaacttcttgtttgaacctttagccgcttctttctatgctaatattttgttactatgaacattgacagCGATGTCCACAACCTGAGAACTGAATCACTCAAGCAGCAGTACAATCTC

Basic information

species Oryza sativa
transcript LOC_Os01g37910.1
intron # 5
splice site 3'
intron type U2

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|58692028|gb|CK080715.1|CK080715
EST:     TGCTTGGATGGAAGACAG                         CGATGTCCACAACCTGAGAACTGAATCACTCAAGCAGCAGTACAATCTC
genomic: TGCTTGGATGGAAGACAGgtacttcatt ... acattgacagCGATGTCCACAACCTGAGAACTGAATCACTCAAGCAGCAGTACAATCTC
EST: gi|51946162|gb|CV152503.1|CV152503
EST:     ATGGAAGACAG                         CGATGTCCACAACCTGAGAACTGAATCACTCAAGCAGCAGTACAATCTC
genomic: ATGGAAGACAGgtacttcatt ... acattgacagCGATGTCCACAACCTGAGAACTGAATCACTCAAGCAGCAGTACAATCTC
EST: gi|58691139|gb|CK079826.1|CK079826
EST:     TACGACACATGCCTAGGGGACTTGTACAGCGTTGCTTGGATGGAAGACAG                         CGATGTCCACAAGCTGAGAACTGAATCACTCAAGCAGCAGT
genomic: TACGACACATGCCTAGGGGACTTGTACAGCGTTGCTTGGATGGAAGACAGgtacttcatt ... acattgacagCGATGTCCACAACCTGAGAACTGAATCACTCAAGCAGCAGT
EST: gi|4715544|gb|AU056660.1|AU056660
EST:     TACGACACATGCCTAGGGGACTTGTACAGCGTTGCTTGGATGGAAGACAG                         CGATGTCCACAACCTGAGAACTGAATCACTCAAGCAGCAGTACAATCTC
genomic: TACGACACATGCCTAGGGGACTTGTACAGCGTTGCTTGGATGGAAGACAGgtacttcatt ... acattgacagCGATGTCCACAACCTGAGAACTGAATCACTCAAGCAGCAGTACAATCTC
EST: gi|58592657|gb|CF990965.1|CF990965
EST:     TACGACACATGCCTAGGGGACTTGTACAGCGTTGCTTGGATGGAAGACAG                         CGATGTCCACAACCTGAGAACTGAATCAGGCAAGCAGCAGTACAATCTC
genomic: TACGACACATGCCTAGGGGACTTGTACAGCGTTGCTTGGATGGAAGACAGgtacttcatt ... acattgacagCGATGTCCACAACCTGAGAACTGAATCACTCAAGCAGCAGTACAATCTC
EST: gi|58692937|gb|CK081624.1|CK081624
EST:     TACGACACATGCCTAGGGGACTTGTACAGCGTTGCTTGGATGGAAGACAG                         CGATGTCCACAACCTGAGAACTGAATCACTCAAGCAGCAGTACAATCTC
genomic: TACGACACATGCCTAGGGGACTTGTACAGCGTTGCTTGGATGGAAGACAGgtacttcatt ... acattgacagCGATGTCCACAACCTGAGAACTGAATCACTCAAGCAGCAGTACAATCTC
EST: gi|58688098|gb|CK076785.1|CK076785
EST:     TACGACACATGCCTAGGGGACTTGTACAGCGTTGCTTGGATGGAAGACAG                         CGATGTCCACAACCTGAGAACTGAATCACTCAAGCAGCAGTACAATCTC
genomic: TACGACACATGCCTAGGGGACTTGTACAGCGTTGCTTGGATGGAAGACAGgtacttcatt ... acattgacagCGATGTCCACAACCTGAGAACTGAATCACTCAAGCAGCAGTACAATCTC
EST: gi|58692781|gb|CK081468.1|CK081468
EST:     GACACATGCCTA-GGGACTTGTACAGCGTTGCTTGGATGGAAGACAG                         CGATGTCCACAACCTGAGAACTGAATCACTCAAGCAGCAGTACAATCTC
genomic: GACACATGCCTAGGGGACTTGTACAGCGTTGCTTGGATGGAAGACAGgtacttcatt ... acattgacagCGATGTCCACAACCTGAGAACTGAATCACTCAAGCAGCAGTACAATCTC
EST: gi|58691202|gb|CK079889.1|CK079889
EST:     TACGACACATGCCTAGGGGACTTGTACAGCGTTGCTTGGATGGAAGACAG                         CGATGTCCACAACCTGAGAACTGAATCACTCAAGCAGCAGTACAATCTC
genomic: TACGACACATGCCTAGGGGACTTGTACAGCGTTGCTTGGATGGAAGACAGgtacttcatt ... acattgacagCGATGTCCACAACCTGAGAACTGAATCACTCAAGCAGCAGTACAATCTC
EST: gi|88387208|gb|CI580553.1|CI580553
EST:     TACGACACATGCCTAGGGGACTTGTACAGCGTTGCTTGGATGGAAGACAG                         CGATGTCCACAACCTGAGAACTGAATCACTCAAGCAGCAGTACAATCTC
genomic: TACGACACATGCCTAGGGGACTTGTACAGCGTTGCTTGGATGGAAGACAGgtacttcatt ... acattgacagCGATGTCCACAACCTGAGAACTGAATCACTCAAGCAGCAGTACAATCTC
EST: gi|163923567|gb|EG713308.1|EG713308
EST:     TACGACACATGCCTAGGGGACTTGTACAGCGTTGCTTGGATGGAAGACAG                         CGATGTCCACAACCTGAGAACTGAATCACTCAAGCAGCAGTACAATC
genomic: TACGACACATGCCTAGGGGACTTGTACAGCGTTGCTTGGATGGAAGACAGgtacttcatt ... acattgacagCGATGTCCACAACCTGAGAACTGAATCACTCAAGCAGCAGTACAATC
EST: gi|58690742|gb|CK079429.1|CK079429
EST:     TACGACACATGCCTAGGGGACTTGTACAGCGTTGCTTGGATGGAAGACAG                         CGATGTCCACAACCTGAGAACTGAATCACTCAAGCAGCAGTACAATCTC
genomic: TACGACACATGCCTAGGGGACTTGTACAGCGTTGCTTGGATGGAAGACAGgtacttcatt ... acattgacagCGATGTCCACAACCTGAGAACTGAATCACTCAAGCAGCAGTACAATCTC
EST: gi|58686800|gb|CK075487.1|CK075487
EST:     TACGACACATGCCTAGGGGACTTGTACAGCGTTGCTTGGATGGAAGACAG                         CGATGTCCACAACCTGAGAACTGAATCACTCAAGCAGCAGTACAATCTC
genomic: TACGACACATGCCTAGGGGACTTGTACAGCGTTGCTTGGATGGAAGACAGgtacttcatt ... acattgacagCGATGTCCACAACCTGAGAACTGAATCACTCAAGCAGCAGTACAATCTC

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: 75 (upstream exon), 50 (downstream exon)
Score: 305

GCAGCTGGGGAACATACTGCCCTGGGGAGTACCCGAGCCCACCTCCGGAGTACGACACATGCCTAGGGGACTTGTACAGCGTTGCTTGGATGGAAGACAGgtacttcatt ... acattgacagCGATGTCCACAACCTGAGAACTGAATCACTCAAGCAGCAGTACAATCTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaacctttagccgcttctttctatgctaatattttgttactatgaacattgacagCGATGTCCACAACCTGAGAACTGAATCACTCAAGCAGCAGTACAATCTC
                       tgctaat  putative branch site (score: 305)
                          taatattttgttacta  TA-rich tract