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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagctatcataaaatcttttgcactgtctcctggtcttttttcccgtaccgttatttggttattcacaccctccgatttttttttactcttgcagTCGGCCGGAAGGACCGTGGCAATGGTTGGTGATGGAATCAACGATTCTCCAGCGCTTGTATCAGCCGACGTTGGCCTGGCGATTGGCGCAGGCACTGACG

Basic information

species Oryza sativa
transcript LOC_Os04g46940.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g46940.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G144083_T01 (Zea mays), 3'ss of exon 5
-----------gtgagctatcataaaatcttttgcact-gtctcctgg-----tcttttttcccgtaccgttatttggttattcacaccctccgatttttttttactc------ttgcagTCGGCCGGAAGGACCGTGGCAATGGTTGGTGATGGAATCAACGATTCTCCAGCGCTTGTATCAGCCGACGTTGGCCTGGCGATTGGCGCAGGCACTGACG
            |  | | |        |||||| ||| || |||  |     |||    ||  || | |||| ||  |  | |  | | ||   |   |  | || |      | ||||  | | |||||||||||||| |||||||| || || |||||||| || || ||||| || || |||||||| || |||||||| ||||| || || ||||
gtgaggtatctatccggtgtttcgtttccttttgtactcgtttccaagagcgctctggactctggtccagttaattactagtacgtagcttctcctgagtcctgacacaaactgtcgcagCTGTCTGGAAGGACCGTGGCGATGGTTGGCGACGGGATCAACGACTCCCCCGCGCTCGTCTCGGCCGACGTGGGGCTGGCGATAGGCGCGGGGACGGACG

upper sequence: LOC_Os04g46940.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv02s0025g03630.t01 (Vitis vinifera), 3'ss of exon 11
gtgagctatcataaaatcttttgcactgtctcctggtcttttttcccgtaccgttatttggttattcaca---ccctccgatttttttttactcttgcagTCGGCCGGAAGGACCGTGGCAATGGTTGGTGATGGAATCAACGATTCTCCAGCGCTTGTATCAGCCGACGTTGGCCTGGCGATTGGCGCAGGCACTGACG
          |||||   ||    | |  ||||  | | |   |   | ||  ||   || |||||| ||   |  |   || || | ||  |    ||| || | ||    ||||||||||||||||| ||||| |||||||| || ||||| |||||  | || || |||||  |||||||||| |||||||| ||| 
--------gtataaa---ttgaaaattagctccaagacatgaataatg-actatt-cgtgattattcccaatgctgtagaatcttgtctttattccacagGCGTCGGGCTATACCGTGGCAATGGTTGGAGATGGCATCAACGACTCACCAGCTCTTGTCGCTGCAGATGTTGGAATGGCGATTGGTGCAGGCACAGACA

upper sequence: LOC_Os04g46940.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv02s0025g03630.t01 (Vitis vinifera), 3'ss of exon 5
gtgagctatcataaaatcttttgcactgtctcctggtcttttttcccgtaccgttatttggttattcacaccctccgatttttttttactcttgcagTCGGCCGGAAGGACCGTGGCAATGGTTGGTGATGGAATCAACGATTCTCCAGCGCTTGTATCAGCCGACGTTGGCCTGGCGATTGGCGCAGGCACTGACG
           ||  |   |    | |   |||  | | |   |   | | | || |     | || |         ||  | |  |  |    ||| |  | ||    ||||||||||||||||| ||||| ||||||||||||||||| |||||| | ||  | |||||  |||| ||||| |||||||| ||| 
----------gtatgaatgtgaaaaatagttccaagacatgcataatg-atcattctcaatctgttaaat-------atcatgtcctcattccacagGCTTCGGGCCATACCGTGGCAATGGTTGGAGATGGCATCAACGATTCTCCAGCCCTTGTAGCTGCAAATGTTGGAATGGCAATTGGTGCAGGCACAGACA

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|88231611|gb|CI231460.1|CI231460
EST:     CGAAACCAGAGCAGAAAGCTGAGAAGGTGAAAGAACTTCAG                         TCGGCCGGAAGGACCGTGGCAATGGTTGGTGATGGAATCAACGATTCTCCA
genomic: CGAAACCAGAGCAGAAAGCTGAGAAGGTGAAAGAACTTCAGgtgagctatc ... actcttgcagTCGGCCGGAAGGACCGTGGCAATGGTTGGTGATGGAATCAACGATTCTCCA
EST: gi|86496757|gb|CI139390.1|CI139390
EST:     GAGAAGGTGAAAGAACTTCAG                         TCGGCCGGAAGGACCGTGGCAATGGTTGGTGATGGAATCAACGATTCTCCA
genomic: GAGAAGGTGAAAGAACTTCAGgtgagctatc ... actcttgcagTCGGCCGGAAGGACCGTGGCAATGGTTGGTGATGGAATCAACGATTCTCCA
EST: gi|86517983|gb|CI158189.1|CI158189
EST:     TTGCAGAAGCGAAACCAGAGCAGAAAGCTGAGAAGGTGAAAGAACTTCAG                         TCGGCCGGAAGGACCGTGGCAATGGTTGGTGATGGAATCAACGATTCTCCA
genomic: TTGCAGAAGCGAAACCAGAGCAGAAAGCTGAGAAGGTGAAAGAACTTCAGgtgagctatc ... actcttgcagTCGGCCGGAAGGACCGTGGCAATGGTTGGTGATGGAATCAACGATTCTCCA
EST: gi|88198882|gb|CI197205.1|CI197205
EST:     TTGCAGAAGCGAAACCAGAGCAGAAAGCTGAGAAGGTGAAAGAACTTCAG                         TCGGCCGGAAGGACCGTGGCAATGGTTGGTGATGGAATCAACGATTCTCCA
genomic: TTGCAGAAGCGAAACCAGAGCAGAAAGCTGAGAAGGTGAAAGAACTTCAGgtgagctatc ... actcttgcagTCGGCCGGAAGGACCGTGGCAATGGTTGGTGATGGAATCAACGATTCTCCA
EST: gi|88234706|gb|CI234555.1|CI234555
EST:     TTGCAGAAGCGAAACCAGAGCAGAAAGCTGAGAAGGTGAAAGAACTTCAG                         TCGGCCGGAAGGACCGTGGCAATGGTTGGTGGTGGAATCAACGATTCTCCA
genomic: TTGCAGAAGCGAAACCAGAGCAGAAAGCTGAGAAGGTGAAAGAACTTCAGgtgagctatc ... actcttgcagTCGGCCGGAAGGACCGTGGCAATGGTTGGTGATGGAATCAACGATTCTCCA
EST: gi|86496753|gb|CI139386.1|CI139386
EST:     TTGCAGAAGCGAAACCAGAGCAGAAAGCTGAGAAGGTGAAAGAACTTCAG                         TCGGCCGGAAGGACCGTGGCAATGGTTGGTGATGGAATCAACGATTCTCCA
genomic: TTGCAGAAGCGAAACCAGAGCAGAAAGCTGAGAAGGTGAAAGAACTTCAGgtgagctatc ... actcttgcagTCGGCCGGAAGGACCGTGGCAATGGTTGGTGATGGAATCAACGATTCTCCA
EST: gi|87007410|gb|CI279081.1|CI279081
EST:     GAAAGCTGAGAAGGTGAAAGAACTTCAG                         TCGGCCGGAAGGACCGTGGCAATGGTTGGTGATGGAATCAACGATTCTCCA
genomic: GAAAGCTGAGAAGGTGAAAGAACTTCAGgtgagctatc ... actcttgcagTCGGCCGGAAGGACCGTGGCAATGGTTGGTGATGGAATCAACGATTCTCCA
EST: gi|86437288|gb|CI119010.1|CI119010
EST:     TTGCAGAAGCGAAACCAGAGCAGAAAGCTGAGAAGGTGAAAGAACTTCAG                         TCGGCCGGAAGGACCGTGGCAATGGTTGGTGATGGAATCAACGATTCTCCA
genomic: TTGCAGAAGCGAAACCAGAGCAGAAAGCTGAGAAGGTGAAAGAACTTCAGgtgagctatc ... actcttgcagTCGGCCGGAAGGACCGTGGCAATGGTTGGTGATGGAATCAACGATTCTCCA
EST: gi|29641070|gb|CB646077.1|CB646077
EST:     TTGCAGAAGCGAAACCAGAGCAGAAAGCTGAGAAGGTGAAAGAACTTCAG                         TCGGCCGGAAGGACCGTGGCAATGGTTGGTGATGGAATCAACGATTCTCCA
genomic: TTGCAGAAGCGAAACCAGAGCAGAAAGCTGAGAAGGTGAAAGAACTTCAGgtgagctatc ... actcttgcagTCGGCCGGAAGGACCGTGGCAATGGTTGGTGATGGAATCAACGATTCTCCA
EST: gi|25803017|gb|CA758978.1|CA758978
EST:     -TGCAGAAGCGAAACCAGAGCAGAAAGCTGAGAAGGTGAAAGAACTTCAG                         TCGGCCGGAAGGACCGTGGCAATGGTTGGTGATGGAATCAACGATTCTCCA
genomic: TTGCAGAAGCGAAACCAGAGCAGAAAGCTGAGAAGGTGAAAGAACTTCAGgtgagctatc ... actcttgcagTCGGCCGGAAGGACCGTGGCAATGGTTGGTGATGGAATCAACGATTCTCCA
EST: gi|27548492|gb|CA766376.2|CA766376
EST:     TTGCAGAAGCGAAACCAGAGCAGAAAGCTGAGAAGGTGAAAGAACCTCAG                         TCGGCCGGAAGGACCGTGGCAATGGTTGGTGATGGAATCAACGATTCTCCA
genomic: TTGCAGAAGCGAAACCAGAGCAGAAAGCTGAGAAGGTGAAAGAACTTCAGgtgagctatc ... actcttgcagTCGGCCGGAAGGACCGTGGCAATGGTTGGTGATGGAATCAACGATTCTCCA
EST: gi|88996396|gb|CI259900.1|CI259900
EST:     TTGCAGAAGTGAAACCAGAGCAGAAAGCTGAGAAGGTGAAAGAACTTCAG                         TCGGCCGGAAGGACCGTGGCAATGGTTGGTGATGGAATCAACGATTCTCCA
genomic: TTGCAGAAGCGAAACCAGAGCAGAAAGCTGAGAAGGTGAAAGAACTTCAGgtgagctatc ... actcttgcagTCGGCCGGAAGGACCGTGGCAATGGTTGGTGATGGAATCAACGATTCTCCA

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: 55 (upstream exon), 64 (downstream exon)
Score: 15

CTGGGGGACTGCCAATGCCATTAGCTAAGAGCTTGGCATTGAGAACACAGTTGCAGAAGCGAAACCAGAGCAGAAAGCTGAGAAGGTGAAAGAACTTCAGgtgagctatc ... actcttgcagTCGGCCGGAAGGACCGTGGCAATGGTTGGTGATGGAATCAACGATTCTCCAGCGCTTGTATCAGCCGACGTTGGCCTGGCGATTGGCGCAGGCACTGACG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcccgtaccgttatttggttattcacaccctccgatttttttttactcttgcagTCGGCCGGAAGGACCGTGGCAATGGTTGGTGATGGAATCAACGATTCTCCAGCGCTTGTATCAGCCGACGTTGGCCTGGCGATTGGCGCAGGCACTGACG
                            ccctccgatttttttt  CT-rich tract
                                   atttttttttactctt  TA-rich tract