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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattatgctcacctccgaatcgaattaattcccccgtttgattactgctggtgcttcgcgtcctgatctgattgatgtttttttttctgatttttttggtgaattttctggtggtgtttttggggacgcagGCAAGATTAAGATCGGAATCAACG

Basic information

species Oryza sativa
transcript LOC_Os08g03290.3
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g03290.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G046804_T02 (Zea mays), 3'ss of exon 1
gtaattatgctcacctccgaatcgaattaattccc-ccgtttgattactgctggtgcttcgcgtcctgatctgattgatgtttttttttctgatt-tttttggtgaattttctgg-----tggtgtttttggggacgcagGCAAGATTAAGATCGGAATCAACG
        | |   |||    ||     ||||  | |    || |     ||  |||  || |  |  ||||||   | ||   || | |||| | ||||| |||  ||||  ||     | |   || |  ||| ||||||||||||||||||||||||||||
--------gtttctctctctctctctacaattatcactacctgctgctccctcatgcaccgtgctcaaatctgaccaaagtgggttctgctgactgttttttgtgtttttttggggtctctcgatcttctctggatgcagGCAAGATTAAGATCGGAATCAACG

upper sequence: LOC_Os08g03290.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G180625_T03 (Zea mays), 3'ss of exon 1
gtaattatgctcacctccgaatcgaattaattcccccgtttgattactgctggtgcttcgcgtcctgatctgattgatgtttttttttctgatttttttggtgaattttctggtggtgtttttggggacgcagGCAAGATTAAGATCGGAATCAACG
             |  | |   ||   | |  | |   |  ||  |  ||    | |||||   || |  |       ||||||||||||               ||||||||  |  ||  |||  ||||||||||||| ||||||||||||||||
-------------ctcctgctccgtgctcagactcagatccgaccaaagc---ggtttcgctgactaaattctccttcgtttttttttct---------------ttttctggacggattcctgg--acgcagGCAAGATCAAGATCGGAATCAACG

upper sequence: LOC_Os08g03290.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G046804_T06 (Zea mays), 3'ss of exon 1
gtaattatgctcacctccgaatcgaattaattccc-ccgtttgattactgctggtgcttcgcgtcctgatctgattgatgtttttttttctgatt-tttttggtgaattttctgg-----tggtgtttttggggacgcagGCAAGATTAAGATCGGAATCAACG
    |   | |   |||    ||     ||||  | |    || |     ||  |||  || |  |  ||||||   | ||   || | |||| | ||||| |||  ||||  ||     | |   || |  ||| ||||||||||||||||||||||||||||
---gtcgggtttctctctctctctctacaattatcactacctgctgctccctcatgcaccgtgctcaaatctgaccaaagtgggttctgctgactgttttttgtgtttttttggggtctctcgatcttctctggatgcagGCAAGATTAAGATCGGAATCAACG

upper sequence: LOC_Os08g03290.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G046804_T05 (Zea mays), 3'ss of exon 1
----------------------gtaattatgctcacctccgaatcgaattaattccc-ccgtttgattactgctggtgcttcgcgtcctgatctgattgatgtttttttttctgatt-tttttggtgaattttctgg-----tggtgtttttggggacgcagGCAAGATTAAGATCGGAATCAACG----------------------------------------------------------------------------
                          |   | |   |||    ||     ||||  | |    || |     ||  |||  || |  |  ||||||   | ||   || | |||| | ||||| |||  ||||  ||     | |   || |  ||| ||||||||||||||||||||||||||||                                                                            
gtaattcctcgctcccggattcagcgtcgggtttctctctctctctctacaattatcactacctgctgctccctcatgcaccgtgctcaaatctgaccaaagtgggttctgctgactgttttttgtgtttttttggggtctctcgatcttctctggatgcagGCAAGATTAAGATCGGAATCAACGGTGAGTTTGTCCCCTCTCCCCATGCTACGCTATTTCTCCTCCTCGAGCTGGTTCGGTCCGATCTGAGTTGCGCCTT

upper sequence: LOC_Os08g03290.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G046804_T08 (Zea mays), 3'ss of exon 1
gtaattatgctcacctccgaatcgaattaattcccccgtttgattactgctggtgcttcgcgtcctgatctgattgatgtttttttttctgatt-tttttggtgaattttctgg-----tggtgtttttggggacgcagGCAAGATTAAGATCGGAATCAACG
                                   |    || |     ||  |||  || |  |  ||||||   | ||   || | |||| | ||||| |||  ||||  ||     | |   || |  ||| ||||||||||||||||||||||||||||
-----------------------------------ctacctgctgctccctcatgcaccgtgctcaaatctgaccaaagtgggttctgctgactgttttttgtgtttttttggggtctctcgatcttctctggatGCAGGCAAGATTAAGATCGGAATCAACG

upper sequence: LOC_Os08g03290.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G046804_T01 (Zea mays), 3'ss of exon 1
----------------------gtaattatgctcacctccgaatcgaattaattccc-ccgtttgattactgctggtgcttcgcgtcctgatctgattgatgtttttttttctgatt-tttttggtgaattttctgg-----tggtgtttttggggacgcagGCAAGATTAAGATCGGAATCAACG
                          |   | |   |||    ||     ||||  | |    || |     ||  |||  || |  |  ||||||   | ||   || | |||| | ||||| |||  ||||  ||     | |   || |  ||| ||||||||||||||||||||||||||||
gtaattcctcgctcccggattcagcgtcgggtttctctctctctctctacaattatcactacctgctgctccctcatgcaccgtgctcaaatctgaccaaagtgggttctgctgactgttttttgtgtttttttggggtctctcgatcttctctggatgcagGCAAGATTAAGATCGGAATCAACG

upper sequence: LOC_Os08g03290.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G180625_T01 (Zea mays), 3'ss of exon 1
---------------------------gtaattatgctcacctccgaat-cgaattaattcccccgtttgattactgctggtgcttcg---cgtcc----tgatctgattgatgtttttttttctgatttttttggtgaattttctggtggtgtttttggggacgcagGCAAGATTAAGATCGGAATCAACG----------------------------------------------------------------------------
                           |       | |  ||    | | | | |   | | |||   || |   ||||    ||  |   || ||     | | |   |||     || |   |  |||||||  |   ||||||||  |  ||  |||  ||||||||||||| ||||||||||||||||                                                                            
gtaactcctcgctcccggccggcccccgcgtcggggttttccatttactactactcgctgctccctcctgctccgtgctcagactcagatccgaccaaagcggtttcgctgactaaattctccttcgttttttt--ttctttttctggacggattcctgg--acgcagGCAAGATCAAGATCGGAATCAACGGTGAGTCTGTACCCCCAACACAAACTCGTTCTTCCTGCTCGGTTCGTTGGGTCTGGACTCTGGAGTGATCTGAGTG

upper sequence: LOC_Os08g03290.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G180625_T02 (Zea mays), 3'ss of exon 1
---------------------------gtaattatgctcacctccgaat-cgaattaattcccccgtttgattactgctggtgcttcg---cgtcc----tgatctgattgatgtttttttttctgatttttttggtgaattttctggtggtgtttttggggacgcagGCAAGATTAAGATCGGAATCAACG
                           |       | |  ||    | | | | |   | | |||   || |   ||||    ||  |   || ||     | | |   |||     || |   |  |||||||  |   ||||||||  |  ||  |||  ||||||||||||| ||||||||||||||||
gtaactcctcgctcccggccggcccccgcgtcggggttttccatttactactactcgctgctccctcctgctccgtgctcagactcagatccgaccaaagcggtttcgctgactaaattctccttcgttttttt--ttctttttctggacggattcctgg--acgcagGCAAGATCAAGATCGGAATCAACG

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|29612744|gb|CB617757.1|CB617757
EST:     TCTAATCTCAAGTCTCTGTCTCGTCGTCCTCGCATCTCCACTCGCCATGG                         GCAAGATTAAGATCGGAATCAACG
genomic: TCTAATCTCAAGTCTCTGTCTCGTCGTCCTCGCATCTCCACTCGCCATGGgtaattatgc ... ggggacgcagGCAAGATTAAGATCGGAATCAACG
EST: gi|58689109|gb|CK077796.1|CK077796
EST:     TCAAGTCTCTGTCTCGTCGTCCTCGCATCTCCACTCGCCATGG                         GCAAGATTAAGATCGGAATCAACG
genomic: TCAAGTCTCTGTCTCGTCGTCCTCGCATCTCCACTCGCCATGGgtaattatgc ... ggggacgcagGCAAGATTAAGATCGGAATCAACG
EST: gi|29612772|gb|CB617785.1|CB617785
EST:     TCTAATCTCAAGTCTCTGTCTCGTCGTCCTCGCATCTCCACTCGCCATGG                         GCAAGATTAAGATCGGAATCAACG
genomic: TCTAATCTCAAGTCTCTGTCTCGTCGTCCTCGCATCTCCACTCGCCATGGgtaattatgc ... ggggacgcagGCAAGATTAAGATCGGAATCAACG
EST: gi|58692398|gb|CK081085.1|CK081085
EST:     TCTAATCTCAAGTCTCTGTCTCGTCGTCCTCGCATCTCCACTCGCCATGG                         GCAAGATTAAGATCGGAATCAACG
genomic: TCTAATCTCAAGTCTCTGTCTCGTCGTCCTCGCATCTCCACTCGCCATGGgtaattatgc ... ggggacgcagGCAAGATTAAGATCGGAATCAACG
EST: gi|29612742|gb|CB617755.1|CB617755
EST:     TCTAATCTCAAGTCTCTGTCTCGTCGTCCTCGCATCTCCACTCGCCATGG                         GCAAGATTAAGATCGGAATCAACG
genomic: TCTAATCTCAAGTCTCTGTCTCGTCGTCCTCGCATCTCCACTCGCCATGGgtaattatgc ... ggggacgcagGCAAGATTAAGATCGGAATCAACG
EST: gi|58598058|gb|CK008586.1|CK008586
EST:     TCTAATCTCAAGTCTCTGTCTCGTCGTCCTCGCATCTCCACTCGCCATGG                         GCAAGATTAAGATCGGAATCAACG
genomic: TCTAATCTCAAGTCTCTGTCTCGTCGTCCTCGCATCTCCACTCGCCATGGgtaattatgc ... ggggacgcagGCAAGATTAAGATCGGAATCAACG
EST: gi|5003435|gb|AU068584.1|AU068584
EST:     TCTAATCTCAAGTCTCTGTCTCGTCGTCCTCGCATCTCCACTCGCCATGG                         GCAAGATTAAGATCGGGAATCAACG
genomic: TCTAATCTCAAGTCTCTGTCTCGTCGTCCTCGCATCTCCACTCGCCATGGgtaattatgc ... ggggacgcagGCAAGATTAAGATCGG-AATCAACG
EST: gi|29617660|gb|CB622672.1|CB622672
EST:     TCTAATCTCCCTTAAGTGTCTCGTCGTCCTCGCATCTCCACTCGCCATGG                         GCAAGATTAAGATCGGAATCAACG
genomic: TCTAATCTCAAGTCTCTGTCTCGTCGTCCTCGCATCTCCACTCGCCATGGgtaattatgc ... ggggacgcagGCAAGATTAAGATCGGAATCAACG
EST: gi|88693521|gb|CI737096.1|CI737096
EST:     TCTAATCTCAAGTCTCTGTCTCGTCGTCCTCGCATCTCCACTCGCCATGG                         GCAAGATTAAGATCGGAATCAANG
genomic: TCTAATCTCAAGTCTCTGTCTCGTCGTCCTCGCATCTCCACTCGCCATGGgtaattatgc ... ggggacgcagGCAAGATTAAGATCGGAATCAACG
EST: gi|33690134|gb|CF318373.1|CF318373
EST:     TCTAATCTCAAGTCTCTGTCTCGTCGTCCTCGCATCTCCACTCGCCATGG                         GCAAAATTAAGATCGGAATCAACG
genomic: TCTAATCTCAAGTCTCTGTCTCGTCGTCCTCGCATCTCCACTCGCCATGGgtaattatgc ... ggggacgcagGCAAGATTAAGATCGGAATCAACG
EST: gi|29612746|gb|CB617759.1|CB617759
EST:     TCTAATCTCAAGTCTCTGTCTCGTCGTCCTCGCATCTCCACTCGCCATGG                         GCAAGATTAAGATCGGAATCAACG
genomic: TCTAATCTCAAGTCTCTGTCTCGTCGTCCTCGCATCTCCACTCGCCATGGgtaattatgc ... ggggacgcagGCAAGATTAAGATCGGAATCAACG

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), 24 (downstream exon)
Score: 1258

TAAACCCTCTCCACCTCTCCATATCCGGCTTCCAGACGCTTCTCTCCTCCTCTAATCTCAAGTCTCTGTCTCGTCGTCCTCGCATCTCCACTCGCCATGGgtaattatgc ... ggggacgcagGCAAGATTAAGATCGGAATCAACG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttttttttctgatttttttggtgaattttctggtggtgtttttggggacgcagGCAAGATTAAGATCGGAATCAACG
        ttctgat  putative branch site (score: 1258)
     tttttctgattttttt  TA-rich tract