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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACACATCATTGAGCCCGGATGGTAAACTTGTTGCTATTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAAgtaagcagaaagcaacgctcagcgattaacttccaaatactgacctcacatttcagaaaaagaaaagctcatggctgtttgtttctcgcagacag

Basic information

species Oryza sativa
transcript LOC_Os08g38880.3
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g38880.3 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G113726_T02 (Zea mays), 5'ss of exon 8
CACACATCATTGAGCCCGGATGGTAAACTTGTTGCTATTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAAgtaagcagaaagcaacgctcagcgattaacttccaaatactgacctcacatttcagaaaaagaaaagctcatggctgtttgttt-ctcgcagacag
|| ||||| |||||||| ||||||||||||| ||||||||| |||||||  ||||| |||||| |  | ||  ||||||||||||| |||||| ||| |||  || |||  | | | |||            | | ||   |  ||| | |    | ||   |    | || |||||||    
CATACATCGTTGAGCCCAGATGGTAAACTTGCTGCTATTGTGGGGGACAGTCCTGATGGACTTCTGATTGACGCTAATTCAGGAAAGgtaagcggaacgcagtgcacagtaactgatttct---------ttttatat---aataaatgcacgattgatatatacaagcttgctcgcag----

upper sequence: LOC_Os08g38880.3 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G113726_T04 (Zea mays), 5'ss of exon 8
-------------CACACATCATTGAGCCCGGATGGTAAACTTGTTGCTATTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAAgtaagcagaaagcaacgctcagcgattaacttccaaatactgacctcacatttcagaaaaagaaaagctcatggctgtttgttt-ctcgcagacag
             || ||||| |||||||| ||||||||||||| ||||||||| |||||||  ||||| |||||| |  | ||  ||||||||||||| |||||| ||| |||  || |||  | | | |||            | | ||   |  ||| | |    | ||   |    | || |||||||    
TAATTTTCTGCAGCATACATCGTTGAGCCCAGATGGTAAACTTGCTGCTATTGTGGGGGACAGTCCTGATGGACTTCTGATTGACGCTAATTCAGGAAAGgtaagcggaacgcagtgcacagtaactgatttct---------ttttatat---aataaatgcacgattgatatatacaagcttgctcgcag----

upper sequence: LOC_Os08g38880.3 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA17G00740.3 (Glycine max), 5'ss of exon 9
CACACATCATTGAGCCCGGATGGTAAACTTGTTGCTATTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAAgtaagcagaaagcaacgctcagcgat-taacttccaaatactgacctcacatttcagaaaaagaaaagct-catggctgtttgtttctcgcagacag
|| || ||||||||||||||||| ||||| ||||  |||||||| |||||||| |||||  |  |||| ||| || |  | ||||| ||  |           | |  | | |  || ||||  ||     | |    | |  | |||  |  |      |   | || |||  | | ||    
CATACTTCATTGAGCCCGGATGGGAAACTGGTTGTGATTGTTGGAGACAACCCAGAAGGGATACTAGTGGATTCTCAAACTGGAAAGgtg-gtgttctcttttggtttgtgttacaaattccgtatg----cattgtgtctgggtaaattatgaataatttaaattttggttctttgtag----

upper sequence: LOC_Os08g38880.3 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA15G12980.1 (Glycine max), 5'ss of exon 10
CACACATCATTGAGCCCGGATGGTAAACTTGTTGCTATTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAAgtaagcagaaagcaacgctcagcg--attaacttccaaatactgacctc-------acatttcagaaaaaga-aaagctcatggctgtttgtttctcgca-gacag---------------------------------------
|| || ||||||||||| ||||| ||||| |||| ||||||||| ||| |||| |||||  |  | || ||| || |  ||||||| ||  |||           ||      ||    | |    |    |  ||       ||  |   |||   ||  | | |   || ||  |||  |  |   || |                                        
CATACTTCATTGAGCCCTGATGGGAAACTAGTTGTTATTGTTGGAGACTACCCAGAAGGGTTACTGGTGGATTCTCAAACAGGAAAGgttggcatgttctgtttgtctatatcataggttcctggctgtatatttctctaaggactctcttgaatgggatgagggtggggggtggatgtgccaagtgtgagaaattgtgaatgtctaattttaattttgattgtctttgtag

upper sequence: LOC_Os08g38880.3 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA07G40060.1 (Glycine max), 5'ss of exon 9
CACACATCATTGAGCCCGGATGGTAAACTTGTTGCTATTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAAgtaa-gcagaaagcaacgctcagcgattaacttc-caaatactgacctcacatttcagaaaaagaaaagctcatggctgtttgtttctcgcagacag
||||| ||||||||||| ||||| ||||| ||||  |||||||| |||||||| |||||  |  |||| ||| || |  | ||||| ||   | |    |      |  |  |  || | |  |  |||||    ||  |   | |  | ||| |  |  |   | || |||  | | ||    
CACACTTCATTGAGCCCAGATGGGAAACTGGTTGTGATTGTTGGAGACAACCCAGAAGGGATACTAGTGGATTCTCAAACTGGAAAGgtggtgtactctgttgatttgtgttacaaattccataggtactgtttgcaggt---aaattatgaataatt--taaattttggttctttgtag----

upper sequence: LOC_Os08g38880.3 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA15G12970.1 (Glycine max), 5'ss of exon 6
CACACATCATTGAGCCCGGATGGTAAACTTGTTGCTATTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAAgtaagcagaaagcaacgctcagcg--attaacttccaaatactgacctc-------acatttcagaaaaaga-aaagctcatggctgtttgtttctcgca-gacag---------------------------------------
|| || ||||||||||| ||||| ||||| |||| ||||||||| ||| |||| |||||  |  | || ||| || |  ||||||| ||  |||           ||      ||    | |    |    |  ||       ||  |   |||   ||  | | |   || ||  |||  |  |   || |                                        
CATACTTCATTGAGCCCTGATGGGAAACTAGTTGTTATTGTTGGAGACTACCCAGAAGGGTTACTGGTGGATTCTCAAACAGGAAAGgttggcatgttctgtttgtctatatcataggttcctggctgtatatttctcttaggactctcttgaatgggatgagggtggggggtggatgtgccaagtgtgagaagttgtgaatgtctaattttaattttgattgtctttgtag

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|29677554|gb|CB673829.1|CB673829
EST:     TTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAAACA                       
genomic: TTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGG--AAA-Agtaagcagaa ... tcgcagac
EST: gi|29677554|gb|CB673829.1|CB673829
EST:     TTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAAACA                       
genomic: TTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGG--AAA-Agtaagcagaa ... tcgcagac
EST: gi|88267006|gb|CI378941.1|CI378941
EST:     TTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAA                         TTCATGAACTCCGCGGTCATCTGGACTACTCTTTCGCGTCAGCGTGGAACC
genomic: TTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAAgtaagcagaa ... tcgcagacagTTCATGAACTCCGCGGTCATCTGGACTACTCTTTCGCGTCAGCGTGGAACC
EST: gi|6984506|gb|AU082482.1|AU082482
EST:     TGAAGGACTTATAGTCGATACTAATTCAGGAAAANCA                       
genomic: TGAAGGACTTATAGTCGATACTAATTCAGG-AAA--Agtaagcagaa ... tcgcagac
EST: gi|6984506|gb|AU082482.1|AU082482
EST:     TGAAGGACTTATAGTCGATACTAATTCAGGAAAANCA                       
genomic: TGAAGGACTTATAGTCGATACTAATTCAGG-AAA--Agtaagcagaa ... tcgcagac
EST: gi|218498616|gb|FG945329.1|FG945329
EST:     TTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAA                         A
genomic: TTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAAgtaagcagaa ... tcgcagacag-
EST: gi|218498616|gb|FG945329.1|FG945329
EST:     TTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAA                         A
genomic: TTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAAgtaagcagaa ... tcgcagacag-
EST: gi|218498616|gb|FG945329.1|FG945329
EST:     TTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAA                         A
genomic: TTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAAgtaagcagaa ... tcgcagacag-
EST: gi|218498616|gb|FG945329.1|FG945329
EST:     TTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAA                         A
genomic: TTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAAgtaagcagaa ... tcgcagacag-
EST: gi|218498616|gb|FG945329.1|FG945329
EST:     TTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAA                         A
genomic: TTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAAgtaagcagaa ... tcgcagacag-
EST: gi|88272502|gb|CI386357.1|CI386357
EST:     TTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAAACA                       
genomic: TTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGG--AAA-Agtaagcagaa ... tcgcagac
EST: gi|88272502|gb|CI386357.1|CI386357
EST:     TTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAAACA                       
genomic: TTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGG--AAA-Agtaagcagaa ... tcgcagac
EST: gi|29640281|gb|CB645290.1|CB645290
EST:     TTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAAACA                       
genomic: TTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGG--AAA-Agtaagcagaa ... tcgcagac
EST: gi|29640281|gb|CB645290.1|CB645290
EST:     TTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAAACA                       
genomic: TTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGG--AAA-Agtaagcagaa ... tcgcagac
EST: gi|86499824|gb|CI142457.1|CI142457
EST:     AGTCGATACTAATTCAGGAAAAACA                       
genomic: AGTCGATACTAATTCAGG--AAA-Agtaagcagaa ... tcgcagac
EST: gi|86499824|gb|CI142457.1|CI142457
EST:     AGTCGATACTAATTCAGGAAAAACA                       
genomic: AGTCGATACTAATTCAGG--AAA-Agtaagcagaa ... tcgcagac
EST: gi|38477499|gb|CF961632.1|CF961632
EST:     TTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAA                         A
genomic: TTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAAgtaagcagaa ... tcgcagacag-
EST: gi|38477499|gb|CF961632.1|CF961632
EST:     TTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAA                         A
genomic: TTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAAgtaagcagaa ... tcgcagacag-
EST: gi|38477499|gb|CF961632.1|CF961632
EST:     TTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAA                         A
genomic: TTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAAgtaagcagaa ... tcgcagacag-
EST: gi|38477499|gb|CF961632.1|CF961632
EST:     TTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAA                         A
genomic: TTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAAgtaagcagaa ... tcgcagacag-
EST: gi|38477499|gb|CF961632.1|CF961632
EST:     TTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAA                         A
genomic: TTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAAgtaagcagaa ... tcgcagacag-
EST: gi|29669309|gb|CB665584.1|CB665584
EST:     TTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAAACA                       
genomic: TTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGG--AAA-Agtaagcagaa ... tcgcagac
EST: gi|29669309|gb|CB665584.1|CB665584
EST:     TTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAAACA                       
genomic: TTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGG--AAA-Agtaagcagaa ... tcgcagac
EST: gi|88271495|gb|CI387548.1|CI387548
EST:     TTGTTGGGGACAACCCTGAA-GACTTATAGTCGATACTAATTCAGGAAAAACA                       
genomic: TTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGG--AAA-Agtaagcagaa ... tcgcagac
EST: gi|88271495|gb|CI387548.1|CI387548
EST:     TTGTTGGGGACAACCCTGAA-GACTTATAGTCGATACTAATTCAGGAAAAACA                       
genomic: TTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGG--AAA-Agtaagcagaa ... tcgcagac
EST: gi|29621086|gb|CB626097.1|CB626097
EST:     TTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAAACA                       
genomic: TTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGG--AAA-Agtaagcagaa ... tcgcagac
EST: gi|29621086|gb|CB626097.1|CB626097
EST:     TTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAAACA                       
genomic: TTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGG--AAA-Agtaagcagaa ... tcgcagac
EST: gi|218505284|gb|FG952914.1|FG952914
EST:     CAACCCTGAAAGGACTTATAGTCGATACTAATTCAGGAAAAACA                       
genomic: CAACCCTG-AAGGACTTATAGTCGATACTAATTCAGG--AAA-Agtaagcagaa ... tcgcagac
EST: gi|218505284|gb|FG952914.1|FG952914
EST:     CAACCCTGAAAGGACTTATAGTCGATACTAATTCAGGAAAAACA                       
genomic: CAACCCTG-AAGGACTTATAGTCGATACTAATTCAGG--AAA-Agtaagcagaa ... tcgcagac

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: 58 (upstream exon), 18 (downstream exon)
Score: 2

CACACATCATTGAGCCCGGATGGTAAACTTGTTGCTATTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAAgtaagcagaa ... tcgcagacagTTCATGAACTCCGCGGTCATCTGGACTACTCTTTCGCGTCAGCGTGGAACCCAGATGGCCGGACATTCGCGACTGGTAACCAAGACAAGACATGCAGGAT




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACACATCATTGAGCCCGGATGGTAAACTTGTTGCTATTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAAgtaagcagaaagcaacgctcagcgattaacttccaaatactgacctcacatttcagaaaaagaaaagctcatggctgtttgtttctcgcagacag

- - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG