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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtcataatggtcgcaacaagtaccgtccttctttttttaactagtagcaggcagatcttgtcacacatggacaatgatataacatttgtatttacacttagagagtcccttttttttttaacttgctttattttttttaactctgaaccagGGTGCATGCATTGGTTTGTATTTTATAAACAGACCTGAGTGGATCATAGTTGATCATGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACA

Basic information

species Oryza sativa
transcript LOC_Os11g04980.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g04980.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA10G39540.1 (Glycine max), 3'ss of exon 5
gtgagtcataatggtcgcaacaagtaccgtccttctttttttaactagtagcaggcagatcttgtcacacatggacaatgatataacatttgtatttacacttagagagtccctttttttt-ttaacttgctttattttttttaactctgaaccagGGTGCATGCATTGGTTTGTATTTTATAAACAGACCTGAGTGGATCATAGTTGATCATGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACA
                                               ||    |  ||||  |      |||||   ||    ||  |||| |||||    ||| | |||  | | |     ||   || | |  |  ||||||           |||  |  | ||||| ||||||||||| ||||||||||||||| |||| ||||||||||| ||  |  |||| ||||| || || ||||| || ||||| |
-----------------------------------------------gtgaatgctagattgtagt-ttcatggttgat----tattattt-tattt---tttacaaagtatcatgtaaccattggtttacatgctcattttta-----------gGGCTCCAGTATTGGGTTGTATTTTATTAACAGACCTGAGTGGCTCATTGTTGATCATGCTTGCTCTTCATACTCATTTGTATCAGTGCCTCTGTATGATA

upper sequence: LOC_Os11g04980.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA20G28200.1 (Glycine max), 3'ss of exon 5
gtgagtcataatggtcgcaacaagtaccgtccttctttttttaactagtagcaggcagatcttgtcacacatggacaatgatataacatttgtatttacacttagagagtcccttttttttttaacttgctttattttttttaactctgaaccagGGTGCATGCATTGGTTTGTATTTTATAAACAGACCTGAGTGGATCATAGTTGATCATGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACA
                                               ||    |  ||||  |      |||||   || ||     ||||  ||||    ||| | |||  | | |     |   ||    | || |||||           ||||  |  | ||||| ||||||||||| ||||||||||||||| |||| ||||||||||| ||  | ||||| ||||| || || ||||| || ||||| |
-----------------------------------------------gtgaatgctagattgtagt-ttcatggctgatcat----tattt-cattt---tttacaaagtatcatgtaaccattggtttacatgttcttttt----------tagGGCTCCAGTATTGGGTTGTATTTTATTAACAGACCTGAGTGGCTCATTGTTGATCATGCTTGCTCTGCATACTCATTTGTATCAGTGCCTCTGTATGATA

upper sequence: LOC_Os11g04980.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT5G27600.1 (Arabidopsis thaliana), 3'ss of exon 5
gtgagtcataatggtcgcaacaagtaccgtccttctttttttaactagtagcaggcagatcttgtcacacatggacaatgatataacatttgtatttacacttagagagtcccttttttttttaacttgctttattttttttaactctgaaccagGGTGCATGCATTGGTTTGTATTTTATAAACAGACCTGAGTGGATCATAGTTGATCATGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACA
                                                                      |||    |   ||       ||||   | |||||   ||      || || | ||       | | ||  || |   || | ||||| |  ||| ||||  | |||||||| |||||||| |||||| |  | || |||||||| ||||||||||||||||| || ||||| ||  | ||||| |
--------------------------------------------------------------------gtatgtttcactctactttgaatgta---aaacttatgcagctatggttcttgtaaagaaaaagtttcttcatttaa--tggaacagGGAGATTGCGTTGGACTCTATTTTATTAACAGACCAGAGTGGTTGGTTGTGGATCATGCTTGTGCAGCATATTCATTTGTCTCTGTTCCTTTATATGATA

upper sequence: LOC_Os11g04980.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv05s0020g03080.t01 (Vitis vinifera), 3'ss of exon 5
---------------------------------------gtg-agtcataatggtcgcaacaagtaccgtccttctttttttaactagta--gcaggcagatcttgtcacacatggacaatgatataacatttgtatttacacttagagagtcccttttttttttaacttgctttattttttttaactctgaaccagGGTGCATGCATTGGTTTGTATTTTATAAACAGACCTGAGTGGATCATAGTTGATCATGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACA
                                        || | || ||||  |         |        | ||||| |||   ||   |     | ||||  ||| | ||   |||    ||    | |  |  |    |||   | |   |||  |||||   ||  |  ||||| |||||  ||| | |||||  | ||  ||||  | |||||||| ||||||||||||||| |||| ||||||||||||||  | |||| |||||  || || || ||  | |||||||
gtgagttgtccaaattctaaattaagtttgaacattgtcatgcactcttaattttgttcttggattggacttatgtttttctaaaatgttttgtgaaaacatctactca-agattttcaaatccattctttcttaacatttggttatccattgattttcctttttttttttttaaattttctttaatgctgtaacagGGATCTTGTGTTGGCCTATATTTTATCAACAGACCTGAGTGGCTCATTGTTGATCATGCCTGCTCTGCATTTTCATATGTATCAGTTCCTTTATATGACA

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|33676001|gb|CF304240.1|CF304240
EST:     CAAACAGGACTGCAATAGGTTCTGGTCTTATTTATCATGGAATACCTGAA                         GGTGCATGCATTGGTTTGTATTTTATAAACAGACCTGAGTGGATCATAGTT
genomic: CAAACAGGACTGCAATAGGTTCTGGTCTTATTTATCATGGAATACCTGAAgtgagtcata ... tctgaaccagGGTGCATGCATTGGTTTGTATTTTATAAACAGACCTGAGTGGATCATAGTT
EST: gi|58696224|gb|CK084911.1|CK084911
EST:     CAAACAGGACTGCAATAGGTTCTGGTCTTATTTATCATGGAATACCTGAA                         GGTGCATGCATTGGTTTGTATTTTATAAACAGACCTGAGTGGATCATAGTT
genomic: CAAACAGGACTGCAATAGGTTCTGGTCTTATTTATCATGGAATACCTGAAgtgagtcata ... tctgaaccagGGTGCATGCATTGGTTTGTATTTTATAAACAGACCTGAGTGGATCATAGTT
EST: gi|58690407|gb|CK079094.1|CK079094
EST:     CAAACAGGACTGCAATAGGTTCTGGTCTTATTTATCATGGAATACCTGAA                         GGTGCATGCATTGGTTTGTATTTTATAAACAGACCTGAGTGGATCATAGTT
genomic: CAAACAGGACTGCAATAGGTTCTGGTCTTATTTATCATGGAATACCTGAAgtgagtcata ... tctgaaccagGGTGCATGCATTGGTTTGTATTTTATAAACAGACCTGAGTGGATCATAGTT
EST: gi|58611948|gb|CK039660.1|CK039660
EST:     CAAACAGGACTGCAATAGGTTCTGGTCTTATTTATCATGGAATACCTGAA                         GGTGCATGCATTGGTTTGTATTTTATAAACAGACCTGAGTGGATCATAGTT
genomic: CAAACAGGACTGCAATAGGTTCTGGTCTTATTTATCATGGAATACCTGAAgtgagtcata ... tctgaaccagGGTGCATGCATTGGTTTGTATTTTATAAACAGACCTGAGTGGATCATAGTT
EST: gi|33675052|gb|CF303291.1|CF303291
EST:     CAAACAGGACTGCAATAGGTTCTGGTCTTATTTATCATGGAATACCTGAA                         GGTGCATGCATTGGTTTGTATTTTATAAACAGACCTGAGTGGATCATAGTT
genomic: CAAACAGGACTGCAATAGGTTCTGGTCTTATTTATCATGGAATACCTGAAgtgagtcata ... tctgaaccagGGTGCATGCATTGGTTTGTATTTTATAAACAGACCTGAGTGGATCATAGTT
EST: gi|58692164|gb|CK080851.1|CK080851
EST:     CAAACAGGACTGCAATAGGTTCTGGTCTTATTTATCATGGAATACCTGAA                         GGTGCATGCATTGGTTTGTATTTTATAAACAGACCTGAGTGGATCATAGTT
genomic: CAAACAGGACTGCAATAGGTTCTGGTCTTATTTATCATGGAATACCTGAAgtgagtcata ... tctgaaccagGGTGCATGCATTGGTTTGTATTTTATAAACAGACCTGAGTGGATCATAGTT

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: 66 (upstream exon), 50 (downstream exon)
Score: 10

CTACAAATGGATGACATATGGAGAAGCTAGTACAAACAGGACTGCAATAGGTTCTGGTCTTATTTATCATGGAATACCTGAAgtgagtcata ... tctgaaccagGGTGCATGCATTGGTTTGTATTTTATAAACAGACCTGAGTGGATCATAGTTGATCATGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttagagagtcccttttttttttaacttgctttattttttttaactctgaaccagGGTGCATGCATTGGTTTGTATTTTATAAACAGACCTGAGTGGATCATAGTTGATCATGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACA
                                      ttttaac  putative branch site (score: 10)
                                  ttttttttaactct  CT-rich tract
             ttttttttttaacttg  TA-rich tract