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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcactcaagatataaccataaccacatttctctccactcccttgttatgtcaatttgttaatgataacattcaatgcagTGTGCGACTGCTGATCCTGATGGCCGCAAGAGAGCTCTTCTCATTGGAGGGGGTATAGCTAACTTCACCGACGTCGGGGCCACATTTAGCGGCATCATTC

Basic information

species Oryza sativa
transcript LOC_Os11g47330.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g47330.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G107082_T01 (Zea mays), 3'ss of exon 8
------------------------gtaagcactcaagatataaccataaccacatt-tctctccactcccttgttatgtcaatttgttaatgataacattcaatgcagTGTGCGACTGCTGATCCTGATGGCCGCAAGAGAGCTCTTCTCATTGGAGGGGGTATAGCTAACTTCACCGACGTCGGGGCCACATTTAGCGGCATCATTC
                               |||   |    ||| ||    |||  |||        |  ||||| |   || || |||  |||  ||| |||| ||||||| ||||||||||||||||||||||||||||| |||||||||||||| || |||||||||||||| || || |   ||||||| |  |||||||| |
gtaagcaaacattgtaaccttgtcaatgctgctcttaactccaccttaggaccatcatctggttgggacaatgttaggatcatctgctaaccatacaattaaatgtagTGTGCAACTGCTGATCCTGATGGCCGCAAGAGAGCCCTTCTCATTGGAGGTGGCATAGCTAACTTCACTGATGTTGCTACCACATTCAATGGCATCATCC

upper sequence: LOC_Os11g47330.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv14s0060g00550.t01 (Vitis vinifera), 3'ss of exon 9
--------------------gtaagcactcaagatataa--ccataaccacatttctctccactcccttgttatgtcaatttgttaatgataacattcaatgcagTGTGCGACTGCTGATCCTGATGGCCGCAAGAGAGCTCTTCTCATTGGAGGGGGTATAGCTAACTTCACCGACGTCGGGGCCACATTTAGCGGCATCATTC
                    | |  |  |   |   | |   | |    | | ||  || |      |  || |      ||||  |  |  | | ||  | |||||||| |||||||| ||||||||||| |||||||| |||||||||||||||||||| ||||||||||| || || |  ||||| || |  || ||  | |
gtaagaaattatgaactttggcataccttttgggcttcagctctttgttaaaatttgctgcttaaaataattttcatttgttgtggaacaatatactctttacagTGTGCTACTGCTGACCCTGATGGCCGTAAGAGAGCCCTTCTCATTGGAGGGGGTATTGCTAACTTCACTGATGTTGCTGCCACTTTCAATGGGATTGTCC
















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|87026947|gb|CI259600.1|CI259600
EST:     GTGCTCCCAATGAGGAGGAGGTTCTGCAGTATGCTAGAGTAGTACTTAAT                         TGTGCGACTGCTGATCCTGATGGCCGCAAGAGAGCTCTTCTCATTGGAGGG
genomic: GTGCTCCCAATGAGGAGGAGGTTCTGCAGTATGCTAGAGTAGTACTTGATgtaagcactc ... ttcaatgcagTGTGCGACTGCTGATCCTGATGGCCGCAAGAGAGCTCTTCTCATTGGAGGG
EST: gi|89167861|gb|CI021560.1|CI021560
EST:     GTGCTCCCAATGAGGAGGAGGTTCTGCAGTATGCTAGAGTAGTACTTGAT                         TGTGCGACTGCTGATCCTGATGGCCGCAAGAGAGCTCTTCTCATTGGAGGG
genomic: GTGCTCCCAATGAGGAGGAGGTTCTGCAGTATGCTAGAGTAGTACTTGATgtaagcactc ... ttcaatgcagTGTGCGACTGCTGATCCTGATGGCCGCAAGAGAGCTCTTCTCATTGGAGGG
EST: gi|86434803|gb|CI106036.1|CI106036
EST:     AGGAGGTTCTGCAGTATGCTAGAGTAGTACTTGAT                         TGTGCGACTGCTGATCCTGATGGCCGCAAGAGAGCTCTTCTCATTGGAGGG
genomic: AGGAGGTTCTGCAGTATGCTAGAGTAGTACTTGATgtaagcactc ... ttcaatgcagTGTGCGACTGCTGATCCTGATGGCCGCAAGAGAGCTCTTCTCATTGGAGGG
EST: gi|88993356|gb|CI257784.1|CI257784
EST:     GTGCTCCCAATGAGGAGGAGTTTCTGCAGTATGCTAGAGTAGTACTTAAT                         TGTGCGACTGCTGATCCTGATGGCCGCAAGAGAGCTCTTCTCATTGGAGGG
genomic: GTGCTCCCAATGAGGAGGAGGTTCTGCAGTATGCTAGAGTAGTACTTGATgtaagcactc ... ttcaatgcagTGTGCGACTGCTGATCCTGATGGCCGCAAGAGAGCTCTTCTCATTGGAGGG
EST: gi|89173357|gb|CI041250.1|CI041250
EST:     AGTAGTACTTGAT                         TGTGCGACTGCTGATCCTGATGGCCGCAAGAGAGCTCTTCTCATTGGAGGG
genomic: AGTAGTACTTGATgtaagcactc ... ttcaatgcagTGTGCGACTGCTGATCCTGATGGCCGCAAGAGAGCTCTTCTCATTGGAGGG
EST: gi|29623682|gb|CB628693.1|CB628693
EST:     GTGCTCCCAATGAGGAGGAGGTTCTGCAGTATGCTAGAGTAGTACTTGAT                         TGTGCGACTGCTGATCCTGATGGCCGCAAGAGAGCTCTTCTCATTGGAGGG
genomic: GTGCTCCCAATGAGGAGGAGGTTCTGCAGTATGCTAGAGTAGTACTTGATgtaagcactc ... ttcaatgcagTGTGCGACTGCTGATCCTGATGGCCGCAAGAGAGCTCTTCTCATTGGAGGG
EST: gi|89195503|gb|CI051616.1|CI051616
EST:     CCCAATGAGGAGGAGGTTCTGCAGTATGCTAGAGTAGTACTTGAT                         TGTGCGACTGCTGATCCTGATGGCCGCAAGAGAGCTCTTCTCATTGGAGGG
genomic: CCCAATGAGGAGGAGGTTCTGCAGTATGCTAGAGTAGTACTTGATgtaagcactc ... ttcaatgcagTGTGCGACTGCTGATCCTGATGGCCGCAAGAGAGCTCTTCTCATTGGAGGG
EST: gi|86418647|gb|CI053448.1|CI053448
EST:     CAGTATGCTAGAGTAGTACTTGAT                         TGTGCGACTGCTGATCCTGATGGCCGCAAGAGAGCTCTTCTCATTGGAGGG
genomic: CAGTATGCTAGAGTAGTACTTGATgtaagcactc ... ttcaatgcagTGTGCGACTGCTGATCCTGATGGCCGCAAGAGAGCTCTTCTCATTGGAGGG
EST: gi|89185634|gb|CI047503.1|CI047503
EST:     CTAGAGTAGTACTTGAT                         TGTGCGACTGCTGATCCTGATGGCCGCAAGAGAGCTCTTCTCATTGGAGGG
genomic: CTAGAGTAGTACTTGATgtaagcactc ... ttcaatgcagTGTGCGACTGCTGATCCTGATGGCCGCAAGAGAGCTCTTCTCATTGGAGGG
EST: gi|29687148|gb|CB683423.1|CB683423
EST:     GTGCTCCCAATGAGGAGGAGGTTCTGCAGTATGCTAGAGTAGTACTTGAT                         TGTGCGACTGCTGATCCTGATGGCCGCAAGAGAGCTCTTCTCATTGGAGGG
genomic: GTGCTCCCAATGAGGAGGAGGTTCTGCAGTATGCTAGAGTAGTACTTGATgtaagcactc ... ttcaatgcagTGTGCGACTGCTGATCCTGATGGCCGCAAGAGAGCTCTTCTCATTGGAGGG
EST: gi|88976891|gb|CI257587.1|CI257587
EST:     GTGCTCCCAATGAGGAGGAGGTTCTGCAGTATGCTAGAGTAGTACTTGAT                         TGTGCGACTGCTGATCCTGATGGCCGCAAGAGAGCTCTTCTCATTGGAGGG
genomic: GTGCTCCCAATGAGGAGGAGGTTCTGCAGTATGCTAGAGTAGTACTTGATgtaagcactc ... ttcaatgcagTGTGCGACTGCTGATCCTGATGGCCGCAAGAGAGCTCTTCTCATTGGAGGG
EST: gi|88993379|gb|CI257807.1|CI257807
EST:     GTGCTCCCAATGAGGAGGAGGTTCTGCAGTATGCTAGAGTAGTACTTAAT                         TGTGCGACTGCTGATCCTGATGGCCGCAAGAGAGCTCTTCTCATTGGAGGG
genomic: GTGCTCCCAATGAGGAGGAGGTTCTGCAGTATGCTAGAGTAGTACTTGATgtaagcactc ... ttcaatgcagTGTGCGACTGCTGATCCTGATGGCCGCAAGAGAGCTCTTCTCATTGGAGGG
EST: gi|88988022|gb|CI018065.1|CI018065
EST:     GTGCTCCCAACGAGGAGGAGGTTCTGCAGTATGCTAGAGTAGTACTTGAT                         TGTGCGACTGCTGATCCTGATGGCCGCAAGAGAGCTCTTCTCATTGGAGGG
genomic: GTGCTCCCAATGAGGAGGAGGTTCTGCAGTATGCTAGAGTAGTACTTGATgtaagcactc ... ttcaatgcagTGTGCGACTGCTGATCCTGATGGCCGCAAGAGAGCTCTTCTCATTGGAGGG
EST: gi|29667083|gb|CB663358.1|CB663358
EST:     GTGCTCCCAATGAGGAGGAGGTTCTGCAGTATGCTAGAGTAGTACTTGAT                         TGTGCGACTGCTGATCCTGATGGCCGCAAGAGAGCTCTTCTCATTGGAGGG
genomic: GTGCTCCCAATGAGGAGGAGGTTCTGCAGTATGCTAGAGTAGTACTTGATgtaagcactc ... ttcaatgcagTGTGCGACTGCTGATCCTGATGGCCGCAAGAGAGCTCTTCTCATTGGAGGG
EST: gi|88994381|gb|CI117335.1|CI117335
EST:     GAGGAGGTTCTCCAGTATGCTAGAGTAGTACTTGAT                         TGTGCGACTGCTGATCCTGATGTCCGCAAGAGAGCTCTTCTCATTGGAGGG
genomic: GAGGAGGTTCTGCAGTATGCTAGAGTAGTACTTGATgtaagcactc ... ttcaatgcagTGTGCGACTGCTGATCCTGATGGCCGCAAGAGAGCTCTTCTCATTGGAGGG
EST: gi|27920666|gb|CB096474.1|CB096474
EST:     GTGCTCCCAATGAGGAGGAGGTTCTGCAGTATGCTAGAGTAGTACTTGAT                         TGTGCGACTGCTGATCCTGATGGCCGCAAGAGAGCTCTTCTCATTGGAGGG
genomic: GTGCTCCCAATGAGGAGGAGGTTCTGCAGTATGCTAGAGTAGTACTTGATgtaagcactc ... ttcaatgcagTGTGCGACTGCTGATCCTGATGGCCGCAAGAGAGCTCTTCTCATTGGAGGG

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: 73 (upstream exon), 70 (downstream exon)
Score: 33

CGGAGATTTGGGATATGCTTCAGAATTAGGAAACTATGCAGAGTATAGCGGTGCTCCCAATGAGGAGGAGGTTCTGCAGTATGCTAGAGTAGTACTTGATgtaagcactc ... ttcaatgcagTGTGCGACTGCTGATCCTGATGGCCGCAAGAGAGCTCTTCTCATTGGAGGGGGTATAGCTAACTTCACCGACGTCGGGGCCACATTTAGCGGCATCATTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catttctctccactcccttgttatgtcaatttgttaatgataacattcaatgcagTGTGCGACTGCTGATCCTGATGGCCGCAAGAGAGCTCTTCTCATTGGAGGGGGTATAGCTAACTTCACCGACGTCGGGGCCACATTTAGCGGCATCATTC
                                     tgataac  putative branch site (score: 33)
                           aatttgttaatgataa  TA-rich tract