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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcgccctgtccattctcaaagctcttcctcctccttgccgccatggctctgtgattgatctctctctctcgctggatgaatccttaccttgcagGTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAG

Basic information

species Oryza sativa
transcript LOC_Os01g52490.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g52490.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G151252_T03 (Zea mays), 3'ss of exon 1
gtgagcgccctgtccattctcaaagctcttcctcctccttgccgccatggctctgtgattgatctctctctctcgctggatgaat----------ccttac-cttgcagGTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAG----------------------------------------------------------
|| || | |  ||||||      | | | | |   || || ||  |   ||||   |  |  || |  |||||| ||  ||   |          ||| |  |||||||||||| ||||| ||||||||||||||  ||||||||||||||                                                          
gtaagtgac--gtccatcagaccaacaccttccaatcatt-ccatcggtgctccccgtctcgtccccatctctcactaaatctctgcctctcctccctcattcttgcagGTGCTTGAGGTTATCCACCCCGGCCGCGCCAACGTCTCCAAGGTGAGATATCGGCCCCGGTACTGTGTGCGCGGCTCATATGGCGGGAGCTTCTGGCCTG

upper sequence: LOC_Os01g52490.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G171426_T01 (Zea mays), 3'ss of exon 1
gtgagcgccctgtccattctcaaagctcttcctcctccttgccgccatggctctgtgattgatctctc-tctctcgctggatgaatccttacc-----------ttgcagGTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAG
|| || | |   |||||      | |   | |   ||||| ||| |   ||||   |  |  || | | |||||| ||  ||   | | | ||           ||||||||||| ||||||||||||||||||||  ||||||||||||||
gtaagtggc--atccatcagaccaacatcttccaatcctt-ccgtcgatgctccccgtctcgtcccccatctctcactaaatctttgcctgccctccctctgtcttgcagGTGCTTGAGGTGATCCACCCCGGCCGCGCCAACGTCTCCAAG

upper sequence: LOC_Os01g52490.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G151252_T01 (Zea mays), 3'ss of exon 1
gtgagcgccctgtccattctcaaagctcttcctcctccttgccgccatggctctgtgattgatctctctctctcgctggatgaat----------ccttac-cttgcagGTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAG
|| || | |  ||||||      | | | | |   || || ||  |   ||||   |  |  || |  |||||| ||  ||   |          ||| |  |||||||||||| ||||| ||||||||||||||  ||||||||||||||
gtaagtgac--gtccatcagaccaacaccttccaatcatt-ccatcggtgctccccgtctcgtccccatctctcactaaatctctgcctctcctccctcattcttgcagGTGCTTGAGGTTATCCACCCCGGCCGCGCCAACGTCTCCAAG

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|29685668|gb|CB681943.1|CB681943
EST:     TCCGCACCCGCAAGTTCATGACCAACCGCCTCCTCTCCCGCAAGCAATTC                         GTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAG
genomic: TCCGCACCCGCAAGTTCATGACCAACCGCCTCCTCTCCCGCAAGCAATTCgtgagcgccc ... taccttgcagGTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAG
EST: gi|66927289|gb|CX114137.1|CX114137
EST:     TCCGCACCCGCAAGTTCATGACCAACCGCCTCCTCTCCCGCAAGCAATTC                         GTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAG
genomic: TCCGCACCCGCAAGTTCATGACCAACCGCCTCCTCTCCCGCAAGCAATTCgtgagcgccc ... taccttgcagGTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAG
EST: gi|286327|gb|D15135.1|D15135
EST:     TCCGCACCCGCAAGTTCATGACCAACCGCCTCCTCTCCCGCAAGCAATTC                         GTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAG
genomic: TCCGCACCCGCAAGTTCATGACCAACCGCCTCCTCTCCCGCAAGCAATTCgtgagcgccc ... taccttgcagGTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAG
EST: gi|4716872|gb|AU057988.1|AU057988
EST:     TCCGCACCCGCAAGTTCATGACCAACCGCCTCCTCTCCCGCAAGCAATTC                         GTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAG
genomic: TCCGCACCCGCAAGTTCATGACCAACCGCCTCCTCTCCCGCAAGCAATTCgtgagcgccc ... taccttgcagGTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAG
EST: gi|38468914|gb|CF953045.1|CF953045
EST:     TCCGCACCCGCAAGTTCATGACCAACCGCCTCCTCTCCCGCAAGCAATTC                         GTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAG
genomic: TCCGCACCCGCAAGTTCATGACCAACCGCCTCCTCTCCCGCAAGCAATTCgtgagcgccc ... taccttgcagGTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAG
EST: gi|55436887|gb|CV731621.1|CV731621
EST:     TCCGCACCCGCAAGTTCATGACCAACCGCCTCCTCTCCCGCAAGCAATTC                         GTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAG
genomic: TCCGCACCCGCAAGTTCATGACCAACCGCCTCCTCTCCCGCAAGCAATTCgtgagcgccc ... taccttgcagGTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAG
EST: gi|29685667|gb|CB681942.1|CB681942
EST:     TCCGCACCCGCAAGTTCATGACCAACCGCCTCCTCTCCCGCAAGCAATTC                         GTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAG
genomic: TCCGCACCCGCAAGTTCATGACCAACCGCCTCCTCTCCCGCAAGCAATTCgtgagcgccc ... taccttgcagGTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAG
EST: gi|8857380|gb|AU094698.1|AU094698
EST:     TCCGCACCCGCAAGTTCATGACCAACCGCCTCCTCTCCCGCAAGCAATTC                         GTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAG
genomic: TCCGCACCCGCAAGTTCATGACCAACCGCCTCCTCTCCCGCAAGCAATTCgtgagcgccc ... taccttgcagGTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAG
EST: gi|4716870|gb|AU057986.1|AU057986
EST:     TCCGCACCCGCAAGTTCATGACCAACCGCCTCCTCTCCCGCAAGCAATTC                         GTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAG
genomic: TCCGCACCCGCAAGTTCATGACCAACCGCCTCCTCTCCCGCAAGCAATTCgtgagcgccc ... taccttgcagGTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAG
EST: gi|89167241|gb|CI252772.1|CI252772
EST:     CTCCCGCAAGCAATTC                         GTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAG
genomic: CTCCCGCAAGCAATTCgtgagcgccc ... taccttgcagGTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAG
EST: gi|29659093|gb|CB655368.1|CB655368
EST:     TCCGCACCCGCAAGTTCATGACCAACCGCCTCCTCTCCCGCAAGCAATTC                         GTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAG
genomic: TCCGCACCCGCAAGTTCATGACCAACCGCCTCCTCTCCCGCAAGCAATTCgtgagcgccc ... taccttgcagGTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAG

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: 72 (upstream exon), 73 (downstream exon)
Score: 94

GCGGCCAACTCCAGCCATGTCGGACTCCAAGGCCGCGGCGGCGGTCACCCTCCGCACCCGCAAGTTCATGACCAACCGCCTCCTCTCCCGCAAGCAATTCgtgagcgccc ... taccttgcagGTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccatggctctgtgattgatctctctctctcgctggatgaatccttaccttgcagGTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAG
                                         tccttac  putative branch site (score: 94)
                                         tccttacctt  CT-rich tract