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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttatttgcataatctgtttgtattgttgttgttttgacgtatatctcgtgttcaaaataaatatatgcatttcattccctctttattaattgagagcagttttattttgaaatgattcacagGACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTTTCTATCACTAACAG

Basic information

species Oryza sativa
transcript LOC_Os01g09120.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g09120.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G176506_T04 (Zea mays), 3'ss of exon 2
gtgagttatttgcataatctgt---ttgtattgttgt-----tgttttgacgtatatctcgtgttcaaaataa-atatatgcatttcattccctctttattaattgagagcagttttattttgaaatgattcacagGACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTTTCTATCACTAACAG
|||||||||||||||| | |||   || | |||||||     ||| | | | ||| | | ||||| |||| |   ||| | || ||||| |   ||| |||| |  |  |     | |||||||| |||| |||||||||||| |||  |||||| ||||||| || || ||||||||||||||||||  |||| ||||||
gtgagttatttgcatattttgtccattattttgttgtctacttgtctcgtcttat-ttttgtgttgaaaacattgtatgtccaattcatgcgtgcttcattattaaactga----tcattttgaactgat-cacagGACTGACTCCCGCTTGCCTAACATGCCAATTATTTATGCTAGTGATGCTTTTACATCATTAACAG

upper sequence: LOC_Os01g09120.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G176506_T07 (Zea mays), 3'ss of exon 2
-------------------------gtgagttatttgcataatctgt---ttgtattgttgt-----tgttttgacgtatatctcgtgttcaaaataa-atatatgcatttcattccctctttattaattgagagcagttttattttgaaatgattcacagGACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTTTCTATCACTAACAG
                         |||||||||||||||| | |||   || | |||||||     ||| | | | ||| | | ||||| |||| |   ||| | || ||||| |   ||| |||| |  |  |     | |||||||| |||| |||||||||||| |||  |||||| ||||||| || || ||||||||||||||||||  |||| ||||||
gtagaatcaaacagagctttgtattgtgagttatttgcatattttgtccattattttgttgtctacttgtctcgtcttat-ttttgtgttgaaaacattgtatgtccaattcatgcgtgcttcattattaaactga----tcattttgaactgat-cacagGACTGACTCCCGCTTGCCTAACATGCCAATTATTTATGCTAGTGATGCTTTTACATCATTAACAG
















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|29660689|gb|CB656964.1|CB656964
EST:     AGTTCTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATT                         GACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
genomic: AGTTCTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATTgtgagttatt ... tgattcacagGACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
EST: gi|29660992|gb|CB657267.1|CB657267
EST:     AGTTCTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATT                         GACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
genomic: AGTTCTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATTgtgagttatt ... tgattcacagGACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
EST: gi|29640574|gb|CB645583.1|CB645583
EST:     AGTTCTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATT                         GACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
genomic: AGTTCTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATTgtgagttatt ... tgattcacagGACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
EST: gi|29680769|gb|CB677044.1|CB677044
EST:     AGTTCTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATT                         GACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
genomic: AGTTCTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATTgtgagttatt ... tgattcacagGACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
EST: gi|31818552|gb|CD645551.1|CD645551
EST:     AGTTCTTCATTAAATCTTTCTCTCGGTAGAATCAAACAAAGCTTTGTATT                         GACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
genomic: AGTTCTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATTgtgagttatt ... tgattcacagGACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
EST: gi|29662742|gb|CB659017.1|CB659017
EST:     AGTTCTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATT                         GACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
genomic: AGTTCTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATTgtgagttatt ... tgattcacagGACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
EST: gi|29657673|gb|CB653948.1|CB653948
EST:     AGTTCTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATT                         GACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
genomic: AGTTCTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATTgtgagttatt ... tgattcacagGACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
EST: gi|14571448|gb|BI118816.1|BI118816
EST:     AGTTCTTCATTAAATCTTTCTCTCGGTAGAATCAAACAAAGCTTTGTATT                         GACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
genomic: AGTTCTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATTgtgagttatt ... tgattcacagGACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
EST: gi|38474285|gb|CF958417.1|CF958417
EST:     AGTTCTTCATTAAATCTTTCTCTCGGTAGAATCAAACAAAGCTTTGTATT                         GACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
genomic: AGTTCTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATTgtgagttatt ... tgattcacagGACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
EST: gi|88228766|gb|CI228246.1|CI228246
EST:     CAAACAAAGCTTTGTATT                         GACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
genomic: CAAACAAAGCTTTGTATTgtgagttatt ... tgattcacagGACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
EST: gi|29660961|gb|CB657236.1|CB657236
EST:     AGTTCTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATT                         GACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
genomic: AGTTCTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATTgtgagttatt ... tgattcacagGACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
EST: gi|29655805|gb|CB652080.1|CB652080
EST:     AGTTGTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATT                         GGCTGACCCCCATTTGCCTGACATGCCGATCATGTATGGTAGTGATGCTTT
genomic: AGTTCTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATTgtgagttatt ... tgattcacagGACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT

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), 56 (downstream exon)
Score: 16

GTCTAGTGGTCTGCGGGAAGAGATGTGATTCTGTTGGCATCCCAGCACTCAGTTCTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATTgtgagttatt ... tgattcacagGACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTTTCTATCACTAACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catttcattccctctttattaattgagagcagttttattttgaaatgattcacagGACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTTTCTATCACTAACAG
                tattaat  putative branch site (score: 16)
                                ttttattttgaaatga  TA-rich tract