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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttaccactgttttactatttctcttttaaccacccccctcccccgccccccagtttcctcatgtagcttacatccatttatatcaatgaaatggtctaccttctcacgtaaaaaaaaaacataatactttcatcctcagGTGTTCAATGAATTCAATGCTAGGAAGCCCGATGAGCTGAACATATTCAAGGGCATTACTGGGAACCATCTCTTTATGGCCATTGTTGCCATAACAGTTG

Basic information

species Oryza sativa
transcript LOC_Os04g51610.1
intron # 30
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 30
lower sequence: GRMZM2G140328_T03 (Zea mays), 3'ss of exon 30
gtgagttaccactgttttactatttctcttttaaccacccccctcccccgccccccagtttcctcatgtagcttacatccatttatatcaatgaaatggtctaccttctcacgtaaaaaaaaaacataatactttcatcctcagGTGTTCAATGAATTCAATGCTAGGAAGCCCGATGAGCTGAACATATTCAAGGGCATTACTGGGAACCATCTCTTTATGGCCATTGTTGCCATAACAGTTG
             ||| | |  |||  |||||    |             |  ||   ||  || |||  |||  |     |||||| |||  ||            || || |            ||||  | || | || |||||||||| ||||||||| |  | || || ||||||||||| ||||||||||||||| | ||||||||||| ||||| | |||  | || ||||||||||
-------------gttctgcgttttagcttttgcttagaaaagatgttt-ctgcctttttgtctaatgcggctc-cggagctttata-caacaaacgcagtagtggcctgacatg---------tgtaattttgtc-ttcttagGTGTTCAACGAATTCAATTCGCGTAAACCAGATGAGCTGAATATATTCAAGGGCATTTCAGGGAACCATCTGTTTATTGGCATCATAGCTATAACAGTTG

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 30
lower sequence: GRMZM2G391042_T01 (Zea mays), 3'ss of exon 30
gtgagttaccactgttttactatttctcttttaaccacccccctcccccgccccccagtttcctcatgtagcttacatccatttatatcaatgaaatggtctaccttctcacgtaaaaaaaaaacataatactttcatcctcagGTGTTCAATGAATTCAATGCTAGGAAGCCCGATGAGCTGAACATATTCAAGGGCATTACTGGGAACCATCTCTTTATGGCCATTGTTGCCATAACAGTTG
    ||| |  |  ||   || ||   ||| |||             | |||      ||  ||  |||| ||  |     |||||| |||  ||            || || |    |          |  ||   |  | |||||||||| ||||||||| |  | || || ||||||||||| ||||||||||||||| | ||||||||||| ||||| | |||  | |  ||||||||| 
----gtt-ctgcgtttcagcttttatgcttataaaagaagt----ttctgccttttttttgtctattgtaactc-cggggctttata-caacaaatgcagtagtggcctgacatgtgca----------tttttgtcttgttagGTGTTCAACGAATTCAATTCACGTAAACCAGATGAGCTGAATATATTCAAGGGCATTTCAGGGAACCATCTTTTTATTGGCATCATAGTAATAACAGTTA
















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|86514508|gb|CI157141.1|CI157141
EST:     CAGACAAAGTCAAAAATACCTTCATATTCAATACATTTGTTCTCTGTCAG                         GTGTTCAATGAATTCAATGCTAGGAAGCCCGATGAGCTGAACATATTCAAG
genomic: CAGACAAAGTCAAAAATACCTTCATATTCAATACATTTGTTCTCTGTCAGgtgagttacc ... tcatcctcagGTGTTCAATGAATTCAATGCTAGGAAGCCCGATGAGCTGAACATATTCAAG
EST: gi|25806928|gb|CA762889.1|CA762889
EST:     CAGACAAAGTCAAAAATACCTTCATATTCAATACATTTGTTCTCTGTCAG                         GTGTTCAATGAATTCAATGCTAGGAAGCCCGATGAGCTGAACATATTCAAG
genomic: CAGACAAAGTCAAAAATACCTTCATATTCAATACATTTGTTCTCTGTCAGgtgagttacc ... tcatcctcagGTGTTCAATGAATTCAATGCTAGGAAGCCCGATGAGCTGAACATATTCAAG
EST: gi|29685708|gb|CB681983.1|CB681983
EST:     CAGACAAAGTCAAAAATACCTTCATATTCAATACATTTGTTCTCTGTCAG                         GTGTTCAATGAATTCAATGCTAGGAAGCCCGATGAGCTGAACATATTCAAG
genomic: CAGACAAAGTCAAAAATACCTTCATATTCAATACATTTGTTCTCTGTCAGgtgagttacc ... tcatcctcagGTGTTCAATGAATTCAATGCTAGGAAGCCCGATGAGCTGAACATATTCAAG
EST: gi|86520016|gb|CI160222.1|CI160222
EST:     CAGACAAAGTCAAAAATACCTTCATATTCAATACATTTGTTCTCTGTCAG                         GTGTTCAATGAATTCAATGCTAGGAAGCCCGATGAGCTGAACATATTCAAG
genomic: CAGACAAAGTCAAAAATACCTTCATATTCAATACATTTGTTCTCTGTCAGgtgagttacc ... tcatcctcagGTGTTCAATGAATTCAATGCTAGGAAGCCCGATGAGCTGAACATATTCAAG
EST: gi|87027607|gb|CI272372.1|CI272372
EST:     CAGACAAAGTCAAAAATACCTTCATATTCAATACATTTGTTCTCTGTCAG                         GTGTTCAATGAATTCAATGCTAGGAAGCCCGATGAGCTGGACATATTCAAG
genomic: CAGACAAAGTCAAAAATACCTTCATATTCAATACATTTGTTCTCTGTCAGgtgagttacc ... tcatcctcagGTGTTCAATGAATTCAATGCTAGGAAGCCCGATGAGCTGAACATATTCAAG
EST: gi|86518067|gb|CI158273.1|CI158273
EST:     CAGACAAAGTCAAGAATACCTTCATATTCAATACATTTGTTCTCTGTCAG                         GTGTTCAATGAATTCAATGCTAGGAAGCCCGATGAGCTGAACATATTCAAG
genomic: CAGACAAAGTCAAAAATACCTTCATATTCAATACATTTGTTCTCTGTCAGgtgagttacc ... tcatcctcagGTGTTCAATGAATTCAATGCTAGGAAGCCCGATGAGCTGAACATATTCAAG
EST: gi|87008601|gb|CI315059.1|CI315059
EST:     CAGACAAAGTCAAAAATACCTTCATATTCAATACATTTGTTCTCTGTCAG                         GTGTTCAATGAATTCAATGCTAGGAAGCCCGATGAGCTGAACATATTCAAG
genomic: CAGACAAAGTCAAAAATACCTTCATATTCAATACATTTGTTCTCTGTCAGgtgagttacc ... tcatcctcagGTGTTCAATGAATTCAATGCTAGGAAGCCCGATGAGCTGAACATATTCAAG
EST: gi|88906188|gb|CI375260.1|CI375260
EST:     GTTCTCTGTCAG                         GTGTTCAATGAATTCGATGGTAGGAAGCCCGATGAGCTGAACATATTCAAG
genomic: GTTCTCTGTCAGgtgagttacc ... tcatcctcagGTGTTCAATGAATTCAATGCTAGGAAGCCCGATGAGCTGAACATATTCAAG
EST: gi|29679578|gb|CB675853.1|CB675853
EST:     CAGACAAAGTCAAAAATACCTTCATATTCAATACATTTGTTCTCTGTCAG                         GTGTTCAATGAATTCAATGCTAGGAAGCCCGATGAGCTGAACATATTCAAG
genomic: CAGACAAAGTCAAAAATACCTTCATATTCAATACATTTGTTCTCTGTCAGgtgagttacc ... tcatcctcagGTGTTCAATGAATTCAATGCTAGGAAGCCCGATGAGCTGAACATATTCAAG
EST: gi|89165805|gb|CI102895.1|CI102895
EST:     CAGACAAAGTCAAAAATACCTTCATATTCAATACATTTGTTCTCTGTCAG                         GTGTTCAATGAATTCAATGCTAGGAAGCCCGATGAGCTGAACATATTCAAG
genomic: CAGACAAAGTCAAAAATACCTTCATATTCAATACATTTGTTCTCTGTCAGgtgagttacc ... tcatcctcagGTGTTCAATGAATTCAATGCTAGGAAGCCCGATGAGCTGAACATATTCAAG
EST: gi|29667908|gb|CB664183.1|CB664183
EST:     CAGACAAAGTCAAAAATACCTTCATATTCAATACATTTGTTCTCTGTCAG                         GTGTTCAATGAATTCAATGCTAGGAAGCCCGATGAGCTGAACATATTCAAG
genomic: CAGACAAAGTCAAAAATACCTTCATATTCAATACATTTGTTCTCTGTCAGgtgagttacc ... tcatcctcagGTGTTCAATGAATTCAATGCTAGGAAGCCCGATGAGCTGAACATATTCAAG
EST: gi|218500877|gb|FG965670.1|FG965670
EST:     CAGACAAAGTCAAGAATAACTTCATATTCAATACATTTGTTCTCTGTCAG                         GTGTTCAATGAATTCAATGCTAGGAAGCCCGATGAGCTGAACATATTCA
genomic: CAGACAAAGTCAAAAATACCTTCATATTCAATACATTTGTTCTCTGTCAGgtgagttacc ... tcatcctcagGTGTTCAATGAATTCAATGCTAGGAAGCCCGATGAGCTGAACATATTCA
EST: gi|86858245|gb|CI271129.1|CI271129
EST:     CAGACAAAGTCAAAAATACCTTCATATTCAATACATTTGTTCTCTGTCAG                         GTGTTCAATGAATTCAATGCTAGGAAGCCCGATGAGCTGAACATATTCAAG
genomic: CAGACAAAGTCAAAAATACCTTCATATTCAATACATTTGTTCTCTGTCAGgtgagttacc ... tcatcctcagGTGTTCAATGAATTCAATGCTAGGAAGCCCGATGAGCTGAACATATTCAAG
EST: gi|29688806|gb|CB685081.1|CB685081
EST:     CAGACAAAGTCAAAAATACCTTCATATTCAATACATTTGTTCTCTGTCAG                         GTGTTCAATGAATTCAATGCTAGGAAGCCCGATGAGCTGAACATATTCAAG
genomic: CAGACAAAGTCAAAAATACCTTCATATTCAATACATTTGTTCTCTGTCAGgtgagttacc ... tcatcctcagGTGTTCAATGAATTCAATGCTAGGAAGCCCGATGAGCTGAACATATTCAAG

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: 51 (upstream exon), 60 (downstream exon)
Score: 21

CTTTAGGGGCACAAGCCTTTTGCAGCTAAAAAACGACAACCAGGCACATGCAGACAAAGTCAAAAATACCTTCATATTCAATACATTTGTTCTCTGTCAGgtgagttacc ... tcatcctcagGTGTTCAATGAATTCAATGCTAGGAAGCCCGATGAGCTGAACATATTCAAGGGCATTACTGGGAACCATCTCTTTATGGCCATTGTTGCCATAACAGTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgaaatggtctaccttctcacgtaaaaaaaaaacataatactttcatcctcagGTGTTCAATGAATTCAATGCTAGGAAGCCCGATGAGCTGAACATATTCAAGGGCATTACTGGGAACCATCTCTTTATGGCCATTGTTGCCATAACAGTTG
                ttctcac  putative branch site (score: 21)
                                          ctttcatcctc  putative PPT
                        taaaaaaaaaacataa  TA-rich tract