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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAAGATTAAGATCGGAATCAACGgtgagtttgctatctgaattactacgagtttgtgctgtgctgggtgtggtttcgttggatttgtggtgatttgagtgggggttttttgtgtgtttgggattgtgattttgttcag

Basic information

species Oryza sativa
transcript LOC_Os08g03290.3
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g03290.3 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G046804_T02 (Zea mays), 5'ss of exon 2
GCAAGATTAAGATCGGAATCAACGgtgagtttgctatctgaat---tactacgagtttgtgctgtgctgggtgtggtttcgttggatttgtggtga---tttgagtgggggttttttgtgtgtttgggattgtgattttgttcag
|||||||||||||||||||||||||||||||||    ||       | |||||   ||   |      | |  |||||  ||  ||| || | ||    ||      | |  |   |  | ||  | |   | |  |  | ||||
GCAAGATTAAGATCGGAATCAACGgtgagtttgtcccctctccccatgctacgctatttctcctcctcgagc-tggttcggtccgatctgagttgcgccttctctctgcgactgcgtccgcgtccgcgtccgcg--tccgctcag

upper sequence: LOC_Os08g03290.3 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G046804_T08 (Zea mays), 5'ss of exon 2
----GCAAGATTAAGATCGGAATCAACGgtgagtttgctatctgaat---tactacgagtttgtgctgtgctgggtgtggtttcgttggatttgtggtga---tttgagtgggggttttttgtgtgtttgggattgtgattttgttcag
    |||||||||||||||||||||||||||||||||    ||       | |||||   ||   |      | |  |||||  ||  ||| || | ||    ||      | |  |   |  | ||  | |   | |  |  | ||||
GCAGGCAAGATTAAGATCGGAATCAACGgtgagtttgtcccctctccccatgctacgctatttctcctcctcgagc-tggttcggtccgatctgagttgcgccttctctctgcgactgcgtccgcgtccgcgtccgcg--tccgctcag

upper sequence: LOC_Os08g03290.3 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G046804_T03 (Zea mays), 5'ss of exon 2
----------------------------------------------------------------------------GCAAGATTAAGATCGGAATCAACGgtgagtttgctatctgaat---tactacgagtttgtgctgtgctgggtgtggtttcgttggatttgtggtga---tttgagtgggggttttttgtgtgtttgggattgtgattttgttcag
                                                                            |||||||||||||||||||||||||||||||||    ||       | |||||   ||   |      | |  |||||  ||  ||| || | ||    ||      | |  |   |  | ||  | |   | |  |  | ||||
TCAAATCTGACCAAAGTGGGTTCTGCTGACTGTTTTTTGTGTTTTTTTGGGGTCTCTCGATCTTCTCTGGATGCAGGCAAGATTAAGATCGGAATCAACGgtgagtttgtcccctctccccatgctacgctatttctcctcctcgagc-tggttcggtccgatctgagttgcgccttctctctgcgactgcgtccgcgtccgcgtccgcg--tccgctcag

upper sequence: LOC_Os08g03290.3 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G180625_T02 (Zea mays), 5'ss of exon 2
GCAAGATTAAGATCGGAATCAACGgtgagtttgctatctgaattactacgagtttgtgctgtgctgggtgtggtttcgttggatttgtggtgatttgagtgggggttttttgtgtgtttgggattgtgattttgttcag
||||||| |||||||||||||||||||||| ||    |  ||     ||  |||  | |||  | |   || |  || | |  | ||  ||||| |||||||||  | |  | |  |  | | |               
GCAAGATCAAGATCGGAATCAACGgtgagtctgtacccccaacacaaactcgttcttcctgctcggttcgttgggtc-tggactctggagtgatctgagtggggtctctgcgcgcctgcgtgctcag------------

upper sequence: LOC_Os08g03290.3 (Oryza sativa), 5'ss of exon 2
lower sequence: AT3G04120.1 (Arabidopsis thaliana), 5'ss of exon 2
------GCAAGATTAAGATCGGAATCAACGgtgagtttgctatctgaattactacgagtttgtgctgtgctgggtgtggtttcgttggatttgtggtgatttgagtgggggttttttgtgtgtttgggattgtgattttgttcag
        ||||||| ||||||||||||||||||||||   |||    ||      | || | | | ||   | | |  | |   | ||| |      || ||| ||  | ||| |  | |  || |                  
CTGACAAGAAGATTAGGATCGGAATCAACGgtgagtttcgaatcgattttgt----aattcgggtt-tgtatgttctcatgtatctagatcta---gaatctgactgttgatttctgttatcgttag------------------

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:     GGCAAGATTAAGATCGGAATCAACG                         GTTTCGGAAGGATCGGGAGGCTCGTGGCCAGGGTGGCCCTCCAGAGCGAGG
genomic: GGCAAGATTAAGATCGGAATCAACGgtgagtttgc ... ttttgttcagGTTTCGGAAGGATCGGGAGGCTCGTGGCCAGGGTGGCCCTCCAGAGCGAGG
EST: gi|58689109|gb|CK077796.1|CK077796
EST:     GGCAAGATTAAGATCGGAATCAACG                         GTTTCGGAAGGATCGGGAGGCTCGTGGCCAGTGTGGGCCTCCAGAGCGAGG
genomic: GGCAAGATTAAGATCGGAATCAACGgtgagtttgc ... ttttgttcagGTTTCGGAAGGATCGGGAGGCTCGTGGCCAGGGTGGCCCTCCAGAGCGAGG
EST: gi|29612772|gb|CB617785.1|CB617785
EST:     GGCAAGATTAAGATCGGAATCAACG                         GTTTCGGAAGGATCGGGAGGCTCGTGGCCAGGGTGGCCCTCCAGAGCGAGG
genomic: GGCAAGATTAAGATCGGAATCAACGgtgagtttgc ... ttttgttcagGTTTCGGAAGGATCGGGAGGCTCGTGGCCAGGGTGGCCCTCCAGAGCGAGG
EST: gi|58692398|gb|CK081085.1|CK081085
EST:     GGCAAGATTAAGATCGGAATCAACG                         GTTTCGGAAGGATCGGGAGGCTCGTGGCCA
genomic: GGCAAGATTAAGATCGGAATCAACGgtgagtttgc ... ttttgttcagGTTTCGGAAGGATCGGGAGGCTCGTGGCCA
EST: gi|29612742|gb|CB617755.1|CB617755
EST:     GGCAAGATTAAGATCGGAATCAACG                         GTTTCGGAAGGATCGGGAGGCTCGTGGCCAGGGTGGCCCTCCAGAGCGAGG
genomic: GGCAAGATTAAGATCGGAATCAACGgtgagtttgc ... ttttgttcagGTTTCGGAAGGATCGGGAGGCTCGTGGCCAGGGTGGCCCTCCAGAGCGAGG
EST: gi|58598058|gb|CK008586.1|CK008586
EST:     GGCAAGATTAAGATCGGAATCAACG                         GTTTCGGAAGGATCGGGAGGCTCGTGGC
genomic: GGCAAGATTAAGATCGGAATCAACGgtgagtttgc ... ttttgttcagGTTTCGGAAGGATCGGGAGGCTCGTGGC
EST: gi|5003435|gb|AU068584.1|AU068584
EST:     GCAAGATTAAGATCGGGAATCAACG                         GTTTCGGNAGGATCGGGAGGCTCGTGGC
genomic: GCAAGATTAAGATCGG-AATCAACGgtgagtttgc ... ttttgttcagGTTTCGGAAGGATCGGGAGGCTCGTGGC
EST: gi|29617660|gb|CB622672.1|CB622672
EST:     GGCAAGATTAAGATCGGAATCAACG                         GTTTCGGAAGGATCGGGAGGCTCGTGGCCAGGGTGGCCCTCCAGAGCGAGG
genomic: GGCAAGATTAAGATCGGAATCAACGgtgagtttgc ... ttttgttcagGTTTCGGAAGGATCGGGAGGCTCGTGGCCAGGGTGGCCCTCCAGAGCGAGG
EST: gi|88693521|gb|CI737096.1|CI737096
EST:     GGCAAGATTAAGATCGGAATCAANG                         GTTTCGGAAGGATCGGGAGGCTCGTGGCCAGGGTGGCCCTCCAGAGCGAGG
genomic: GGCAAGATTAAGATCGGAATCAACGgtgagtttgc ... ttttgttcagGTTTCGGAAGGATCGGGAGGCTCGTGGCCAGGGTGGCCCTCCAGAGCGAGG
EST: gi|33690134|gb|CF318373.1|CF318373
EST:     GGCAAAATTAAGATCGGAATCAACG                         GTTTCGGAAGGATCGGGAGGCTCGTGGCCAGGGTGGCCCTCC
genomic: GGCAAGATTAAGATCGGAATCAACGgtgagtttgc ... ttttgttcagGTTTCGGAAGGATCGGGAGGCTCGTGGCCAGGGTGGCCCTCC
EST: gi|29612746|gb|CB617759.1|CB617759
EST:     GGCAAGATTAAGATCGGAATCAACG                         GTTTCGGAAGGATCGGGAGGCTCGTGGCCAGGGTGGCCCTCCAGAGCGAGG
genomic: GGCAAGATTAAGATCGGAATCAACGgtgagtttgc ... ttttgttcagGTTTCGGAAGGATCGGGAGGCTCGTGGCCAGGGTGGCCCTCCAGAGCGAGG

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: 61 (upstream exon), 75 (downstream exon)
Score: 1011

GCAAGATTAAGATCGGAATCAACGgtgagtttgc ... ttttgttcagGTTTCGGAAGGATCGGGAGGCTCGTGGCCAGGGTGGCCCTCCAGAGCGAGGATGTCGAGCTCGTCGCCGTCAACGACCCCTTCATCACCACCGACTACAT




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