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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTCTGGAAGGTTAGAGTAGAATTGCCTGATGCATATCCTTACAAATCTCCGTCGATTGGTTTCGTTAACAAGATTTATCATCCTAATGTGGATGAAATgtgaggatttgatgtccatacccttttctggaatgattgaagcttgtgtaatcaattgttgctgacctgcttttgttggacttgaaaatgtag

Basic information

species Oryza sativa
transcript LOC_Os10g31000.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g31000.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G150867_T02 (Zea mays), 5'ss of exon 3
GTGTCTGGAAGGTTAGAGTAGAATTGCCTGATGCATATCCTTACAAATCTCCGTCGATTGGTTTCGTTAACAAGATTTATCATCCTAATGTGGATGAAATgtgagga--tttgatgtccataccctttt-ctggaatgattgaagcttgtgtaatcaattgttgctgacctgcttttgttggacttgaaaatgtag
|| | |||| ||||||||||||| |||| ||||| |||||||||||||| || |||||||||||| | || ||||| ||||| || ||||| ||||||||||||| |  |||||  || ||  ||| || |       |||  | |     |||  |  |    |  | |  ||  ||   || |  ||  || ||
GTATATGGAGGGTTAGAGTAGAACTGCCAGATGCGTATCCTTACAAATCCCCATCGATTGGTTTCATCAATAAGATATATCACCCAAATGTCGATGAAATgtgagtacttttgaactcaatgacctgttaccttgtcaatttcaaccacattaaaaatctagctcctaaccactcctggatgaatgcaacctgcag

upper sequence: LOC_Os10g31000.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AC149818.2_FGT006 (Zea mays), 5'ss of exon 3
GTGTCTGGAAGGTTAGAGTAGAATTGCCTGATGCATATCCTTACAAATCTCCGTCGATTGGTTTCGTTAACAAGATTTATCATCCTAATGTGGATGAAATgtgagga--tttgatgtccat--acccttttctggaatgattgaagcttgtgtaatcaattgttgctgacctgcttttgttggacttgaaaatgtag
|||| |||||| |||||||||||||||| || ||||||||||||||||| || ||||| |||||| | || ||||| ||||| || ||||| || |||||||||| |  |||||  || ||  ||  ||  || |    ||| || |  |   ||  |  |       | |  ||| ||   || |  ||| || ||
GTGTATGGAAGATTAGAGTAGAATTGCCAGACGCATATCCTTACAAATCCCCATCGATCGGTTTCATCAATAAGATATATCACCCAAATGTCGACGAAATgtgagtagttttgaactcaatgaactgttaccttgtcaaattcaaccacg-acaacaatctagcttctaaccacttctggctgaatgcaaactgcag

upper sequence: LOC_Os10g31000.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA08G01940.3 (Glycine max), 5'ss of exon 3
GTGTCTGGAAGGTTAGAGTAGAATTGCCTGATGCATATCCTTACAAATCTCCGTCGATTGGTTTCGTTAACAAGATTTATCATCCTAATGTGGATGAAATgtgag--gatttgatgtccatacccttttctggaatgattgaagcttgtgtaatcaattgttgctgacctgcttttgttggacttga--aaatgtag--------------------------------------------------------
|||| ||||| || || || ||  | |||||||| |||||||| || ||||| || ||||| || || ||||| ||||  ||||||||||||||||| |||| ||  | ||  |||     |    ||  | |||| ||||    |    || | ||      |  |  ||||      | | |  |     ||| |                                                        
GTGTGTGGAAAGTAAGGGTGGATCTACCTGATGCCTATCCTTATAAGTCTCCATCTATTGGCTTTGTCAACAAAATTTTCCATCCTAATGTGGATGAGATgtaagttgtttcaatgcagccatagcttcattgaataattgtttatatcatatttaagcagcacaaatatgctccatgggaagtctattggctgttgcacacacacatagcaaaactcactagctcataaatatggttttctcttatgtttag

upper sequence: LOC_Os10g31000.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA18G46940.1 (Glycine max), 5'ss of exon 3
GTGTCTGGAAGGTTAGAGTAGAATTGCCTGATGCATATCCTTACAAATCTCCGTCGATTGGTTTCGTTAACAAGATTTATCATCCTAATGTGGATGAAATgtgaggatttgatgtccataccct------tttctggaatgattgaa--gcttgtgtaatcaattgttgctgacctgctttt------gttggacttgaaaatgtag------------------
 ||| ||||| || ||||| || ||||| ||||| ||||||||||||||||| || ||||| ||  | |||||||| ||||| || ||||| ||||| |||| || |  |  |    || | ||      | |||| | ||| |      | |||||| |  ||    |   |  ||  | |      ||  ||  |||  || | |                  
-TGTGTGGAAAGTAAGAGTTGAGTTGCCGGATGCTTATCCTTACAAATCTCCTTCCATTGGCTTTATCAACAAGATCTATCACCCAAATGTTGATGAGATGtaagcacatagtagtaatgctctgaaaattgtctgtattgagtagtttacatgtgtattagatataagaataattgtgtgtcggtgcgtctgatctgatcatcttggataacattaatttcagg

upper sequence: LOC_Os10g31000.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA09G39370.1 (Glycine max), 5'ss of exon 2
GTGTCTGGAAGGTTAGAGTAGAATTGCCTGATGCATATCCTTACAAATCTCCGTCGATTGGTTTCGTTAACAAGATTTATCATCCTAATGTGGATGAAATgtgaggatttgatgtccataccct------tttctggaatgattgaa-gcttgtgtaatcaattgttgctgacctgcttttgttggacttgaaaatgtag
|||| ||||| || ||||| || ||||| ||||| ||||||||||||||||| || ||||| ||  | |||||||| ||||| || ||||| ||||| |||| || |  |  |    || | ||      | |||| | ||| |    || ||| || |   |  | |   |  || |    |     | || ||| || 
GTGTGTGGAAAGTAAGAGTTGAGTTGCCGGATGCTTATCCTTACAAATCTCCTTCCATTGGATTTATCAACAAGATCTATCACCCGAATGTTGATGAGATgtaagcacatagtagtaatgctctgaaaattgtctgtattgagtagttgcgtgtctattagctgatagaatatatgataagatatatttagataatatat

upper sequence: LOC_Os10g31000.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AT5G41340.1 (Arabidopsis thaliana), 5'ss of exon 3
GTGTCTGGAAGGTTAGAGTAGAATTGCCTGATGCATATCCTTACAAATCTCCGTCGATTGGTTTCGTTAACAAGATTTATCATCCTAATGTGGATGAAATgtgaggatttgatgtccatacccttttctggaatgattgaagcttgtgtaatcaattgttgctgacctgcttttgttggacttgaaaatgtag
|||| |||||| | ||||| ||  | || ||||| |||||||| |||||||| ||  |||||||| |||  || ||||||||||||||||| |||||| ||| ||  |||    |  || |  |   || || || ||        | || |  | | ||  | | ||   || ||     |||   ||| ||
GTGTGTGGAAGATAAGAGTTGAGCTTCCAGATGCTTATCCTTATAAATCTCCATCTGTTGGTTTCATTACTAAAATTTATCATCCTAATGTTGATGAACTgtaagtctttt---taaattcaatccactaga-tgttttggatcaatttatttcaatctttttcatct---ttggtctcctttgtttatgcag

upper sequence: LOC_Os10g31000.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AT1G63800.1 (Arabidopsis thaliana), 5'ss of exon 3
GTGTCTGGAAGGTTAGAGTAGAATTGCCTGATGCATATCCTTACAAATCTCCGTCGATTGGTTTCGTTAACAAGATTTATCATCCTAATGTGGATGAAATgtgag---gatttgatgtccatacccttttctggaatgattgaag--cttgtgtaa---tcaattgttgctgacctgct----tttgttggacttgaaaatgtag
|||| |||||| | ||||| ||| | |||||||| |||||||| |||||||| ||  |||||||| ||| ||| || || || |||||||| |||||||||||||    ||   ||    | | | |||   ||| |||||      ||| |  ||   |  | || |||| |  || |     |  ||| |  ||   ||| ||
GTGTGTGGAAGATAAGAGTTGAACTTCCTGATGCTTATCCTTATAAATCTCCATCTGTTGGTTTCATTACCAAAATATACCACCCTAATGTCGATGAAATgtgagttcaatcgaatcagtagatcttttggaggagtgattatgttccttctccaaatcttgagtggtgcttatttgttatccctctttgtatgtggttatgcag

upper sequence: LOC_Os10g31000.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv15s0046g02280.t01 (Vitis vinifera), 5'ss of exon 3
GTGTCTGGAAGGTTAGAGTAGAATTGCCTGATGCATATCCTTACAAATCTCCGTCGATTGGTTTCGTTAACAAGATTTATCATCCTAATGTGGATGAAATgtgaggatttgatgtccatacccttttctggaatgattgaagcttgtgtaatcaattgttgctgacctgcttt-tgttggactt-gaaaatgtag--------------------------
|||| |||| | ||||||| ||  | || ||||| ||||||||||||||||| || ||||| || ||||| ||||| || || || ||||| |||||||||||||  ||| |   | |      ||  || |||   | | | ||| ||  |  ||||    | |  | |||  ||| ||| || | |||| |                            
GTGTTTGGAGGATTAGAGTTGAGCTTCCAGATGCTTATCCTTACAAATCTCCCTCAATTGGCTTTGTTAATAAGATCTACCACCCAAATGTTGATGAAATgtgagagtttaaatgctaag----ttgatgtaatttattatg-ttgggttgttcattgc-attcatatacttaatgtgggattttggaaatctgaccatgacggcatgtgttaaatttcag

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|163920118|gb|EG709876.1|EG709876
EST:     CCGTCGATTGGTTTCGTTAACAAGATTTATCATCCTAATGTGGATGAAAT                         GTCTGGTTCTGTGTGTTTGGATGTCATTAACCAGACGTGGAGCCCAATGTT
genomic: CCGTCGATTGGTTTCGTTAACAAGATTTATCATCCTAATGTGGATGAAATgtgaggattt ... gaaaatgtagGTCTGGTTCTGTGTGTTTGGATGTCATTAACCAGACGTGGAGCCCAATGTT
EST: gi|33654410|gb|CF277024.1|CF277024
EST:     TGTGGATGAAAT                         GTCTGGTTCTGTGTGTTTGGATGTCATTAACCAGACGTGGAGCCCAATGTT
genomic: TGTGGATGAAATgtgaggattt ... gaaaatgtagGTCTGGTTCTGTGTGTTTGGATGTCATTAACCAGACGTGGAGCCCAATGTT
EST: gi|58659537|gb|CK048217.1|CK048217
EST:     CCGTCGATTGGTTTCGTTAACAAGATTTATCATCCTAATGTGGATGAAAT                         GTCTGGTTCTGTGTGTTTGGATGTCATTAACCAGACGTGGAGCCCAATGTT
genomic: CCGTCGATTGGTTTCGTTAACAAGATTTATCATCCTAATGTGGATGAAATgtgaggattt ... gaaaatgtagGTCTGGTTCTGTGTGTTTGGATGTCATTAACCAGACGTGGAGCCCAATGTT
EST: gi|163926790|gb|EG715078.1|EG715078
EST:     CCGTCGATTGGTTTCGTTAACAAGATTTATCATCCTAATGTGGATGAAAT                         GTCTGGTTCTGTGTGTTTGGATGTCATTAACCAGACGTGGAGCCCAATGTT
genomic: CCGTCGATTGGTTTCGTTAACAAGATTTATCATCCTAATGTGGATGAAATgtgaggattt ... gaaaatgtagGTCTGGTTCTGTGTGTTTGGATGTCATTAACCAGACGTGGAGCCCAATGTT
EST: gi|38478467|gb|CF962600.1|CF962600
EST:     CCGTCGATTGGTTTCGTTAACAAGATTTATCATCCTAATGTGGATGAAAT                         GTCTGGTTCTGTGTGTTTGGATGTCATTAACCAGACGTGGAGCCCAATGTT
genomic: CCGTCGATTGGTTTCGTTAACAAGATTTATCATCCTAATGTGGATGAAATgtgaggattt ... gaaaatgtagGTCTGGTTCTGTGTGTTTGGATGTCATTAACCAGACGTGGAGCCCAATGTT
EST: gi|27410240|gb|CA923310.1|CA923310
EST:     CCGTCGATTGGTTTCGTTAACAAGATTTATCATCCTAATGTGGATGAAAT                         GTCTGGTTCTGTGTGTTTGGATGTCATTAACCAGACGTGGAGCCCAATGTT
genomic: CCGTCGATTGGTTTCGTTAACAAGATTTATCATCCTAATGTGGATGAAATgtgaggattt ... gaaaatgtagGTCTGGTTCTGTGTGTTTGGATGTCATTAACCAGACGTGGAGCCCAATGTT
EST: gi|163927163|gb|EG715184.1|EG715184
EST:     CCGTCGATTGGTTTCGTTAACAAGATTTATCATCCTAATGTGGATGAAAT                         GTCTGGTTCTGTGTGTTTGGATGTCATTAACCAGACGTGGAGCCCAATGTT
genomic: CCGTCGATTGGTTTCGTTAACAAGATTTATCATCCTAATGTGGATGAAATgtgaggattt ... gaaaatgtagGTCTGGTTCTGTGTGTTTGGATGTCATTAACCAGACGTGGAGCCCAATGTT
EST: gi|86896481|gb|CI328868.1|CI328868
EST:     CCGTCGATTGGTTTCGTTAACAAGATTTATCATCCTAATGTGGATGAAAT                         GTCTGGTTCTGTGTGTTTGGATGTCATTAACCAGACGTGGAGCCCAATGTT
genomic: CCGTCGATTGGTTTCGTTAACAAGATTTATCATCCTAATGTGGATGAAATgtgaggattt ... gaaaatgtagGTCTGGTTCTGTGTGTTTGGATGTCATTAACCAGACGTGGAGCCCAATGTT
EST: gi|58681245|gb|CK069932.1|CK069932
EST:     CCGTCGATTGGTTTCGTTAACAAGATTTATCATCCTAATGTGGATGAAAT                         GTCTGGTTCTGTGTGTTTGGATGTCATTAACCAGACGTGGAGCCCAATGTT
genomic: CCGTCGATTGGTTTCGTTAACAAGATTTATCATCCTAATGTGGATGAAATgtgaggattt ... gaaaatgtagGTCTGGTTCTGTGTGTTTGGATGTCATTAACCAGACGTGGAGCCCAATGTT
EST: gi|86854335|gb|CI254280.1|CI254280
EST:     ATCATCCTAATGTGGATGAAAT                         GTCTGGTTCTGTGTGTTTGGATGTCATTAACCAGACGTGGAGCCCAATGTT
genomic: ATCATCCTAATGTGGATGAAATgtgaggattt ... gaaaatgtagGTCTGGTTCTGTGTGTTTGGATGTCATTAACCAGACGTGGAGCCCAATGTT
EST: gi|218478509|gb|FG954791.1|FG954791
EST:     CCGTCGATTGGTTTCGTTAACAAGATTTATCATCCTAATGTGGATGAAAT                         GTCTGGTTCTGTGTGTTTGGATGTCATTAACCAGACGTGGAGCCCAATGTT
genomic: CCGTCGATTGGTTTCGTTAACAAGATTTATCATCCTAATGTGGATGAAATgtgaggattt ... gaaaatgtagGTCTGGTTCTGTGTGTTTGGATGTCATTAACCAGACGTGGAGCCCAATGTT

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), 53 (downstream exon)
Score: 73

GTGTCTGGAAGGTTAGAGTAGAATTGCCTGATGCATATCCTTACAAATCTCCGTCGATTGGTTTCGTTAACAAGATTTATCATCCTAATGTGGATGAAATgtgaggattt ... gaaaatgtagGTCTGGTTCTGTGTGTTTGGATGTCATTAACCAGACGTGGAGCCCAATGTTTG




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