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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTATGAGCGCCACAGTGGTACTGGCCGTGGTTATGAGATGAAGCGTGATGGTGCAGGGCGTGGGAACTGGGGAACTGCTACTGATGAGGCTCTTGCACAgtaggggaattttatctgtttatgatgcctcttgtcttggatagtgaaggcacagataactcatagtgttattcttggtatgtag

Basic information

species Oryza sativa
transcript LOC_Os01g52390.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g52390.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G055276_T02 (Zea mays), 5'ss of exon 2
ATTATGAGCGCCACAGTGGTACTGGCCGTGGTTATGAGATGAAGCGTGATGGTGCAGGGCGTGGGAACTGGGGAACTGCTACTGATGAGGCTCTTGCACAgtaggggaattt-tat-ctgttt-----atgatgcctct-tgtcttggatagtgaaggcacagataactcatagtgttattcttggtatgtag
| |||||||||||||| || ||||||| ||| |||||||||||||||||||| |||||||||||||||||||| ||||| ||||||||   | |||| ||||| ||  | |  |||  |||||     ||  |   ||| || ||  |    || | |     ||    | || ||     ||  ||   |||
ACTATGAGCGCCACAGCGGGACTGGCCATGGCTATGAGATGAAGCGTGATGGCGCAGGGCGTGGGAACTGGGGCACTGCCACTGATGAACTTATTGCCCAgtaaggagactagtatattgtttttagcatagtatttctgtgactatgcctctggaaggtttaattgtac-taatgaagccctctgtgactag

upper sequence: LOC_Os01g52390.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G116282_T02 (Zea mays), 5'ss of exon 2
ATTATGAGCGCCACAGTGGTACTGGCCGTGGTTATGAGATGAAGCGTGATGGTGCAGGGCGTGGGAACTGGGGAACTGCTACTGATGAGGCTCTTGCACAgtaggggaattt---tatctgtt--------tatgatgcctct-tgtcttggatagtgaaggcacagataactcatagtgttattcttggtatgtag
| |||||||||||||| || ||||||| ||| |||||||||||||||||||| |||||||||||||||||||| ||||| |||||||||  | |||| ||||| ||  | |    ||| | ||         ||  |   ||| || ||  |    || | |     ||    | || ||  |  ||  ||   |||
ACTATGAGCGCCACAGCGGGACTGGCCATGGCTATGAGATGAAGCGTGATGGCGCAGGGCGTGGGAACTGGGGCACTGCCACTGATGAGCTTATTGCCCAgtaaggagactagtatatttattgtttttagcatagtatttctgtgactatgcctctggaaggtttaattgtac-taatgaaaccctctgtgactag

upper sequence: LOC_Os01g52390.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G055276_T03 (Zea mays), 5'ss of exon 2
ATTATGAGCGCCACAGTGGTACTGGCCGTGGTTATGAGATGAAGCGTGATGGTGCAGGGCGTGGGAACTGGGGAACTGCTACTGATGAGGCTCTTGCACAgtaggggaattt-tat-ctgttt-----atgatgcctct-tgtct-tggatagtgaaggcacagata-actcatagtgttatt-----cttggtatgtag
| |||||||||||||| || ||||||| ||| |||||||||||||||||||| |||||||||||||||||||| ||||| ||||||||   | |||| ||||| ||  | |  |||  |||||     ||  |   ||| || || ||  |   |||||   |  |  ||| ||   |   |      || || ||| ||
ACTATGAGCGCCACAGCGGGACTGGCCATGGCTATGAGATGAAGCGTGATGGCGCAGGGCGTGGGAACTGGGGCACTGCCACTGATGAACTTATTGCCCAgtaaggagactagtatattgtttttagcatagtatttctgtgactatgcctctggaaggtttaattgtactaatgaagccctctgtgactagggatgcag

upper sequence: LOC_Os01g52390.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G116282_T04 (Zea mays), 5'ss of exon 2
-------------------------------------------------------ATTATGAGCGCCACAGTGGTACTGGCCGTGGTTATGAGATGAAGCGTGATGGTGCAGGGCGTGGGAACTGGGGAACTGCTACTGATGAGGCTCTTGCACAgtaggggaattttatctgtttatgatgcctcttgtcttggatagtgaaggcacagataactcatagtgttattcttggtatgtag
                                                       | |||||||||||||| || ||||||| ||| |||||||||||||||||||| |||||||||||||||||||| ||||| |||||||||  | |||| ||||| ||  | |   | | |||||  ||  | | |  | | ||                                           
GGTGGTTACAGGAATGTTGAGTTTGGTGATGACTCTGAGAGGCCACCACGGAGAAACTATGAGCGCCACAGCGGGACTGGCCATGGCTATGAGATGAAGCgtgatggcgcagggcgtgggaactggggcactgccactgatgagcttattgcccagtaaggagacta-gtatatttat--tgtttttagcatagtatttctgt-------------------------------------

upper sequence: LOC_Os01g52390.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv00s0620g00020.t01 (Vitis vinifera), 5'ss of exon 3
ATTATGAGCGCCACAGTGGTACTGGCCGTGGTTATGAGATGAAGCGTGATGGTGCAGGGCGTGGGAACTGGGGAACTGCTACTGATGAGGCTCTTGCACAgtaggggaattttatctgtttatgatgcctcttgtcttggatagtgaaggcacag--ataactcatagtgttattcttggtatgtag-------------------------------------------
                                 ||||||| ||||||||||| || || || ||||||||||||||| || ||||||||  |  | |   |       |||||  |   |     |     | || || |  | | |   |      ||    | |  ||| |   | | | | ||                                            
-------------------------------AAATGAGATTAAGCGTGATGGAGCTGGTCGAGGGAACTGGGGAACTCCTGCTGATGAGATTGCTCCgt-gagtacctattttgccaactgcaacttaaagtagttttagcaattaagaactttatcatgttccttcatgtgaggttagctctatatttatgtattaacttgaatttatttgctcctttcctaaattaag

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|218486753|gb|FG965219.1|FG965219
EST:     GGTGCAGGGCGTGGGAACTGGGGAACTGCTACTGATGAGGCTCTTGCACA                         GGAGACTGAGGAAGCCTTGAAGGTTGAGGAGAGTGCTCCTATTGCTGAGAA
genomic: GGTGCAGGGCGTGGGAACTGGGGAACTGCTACTGATGAGGCTCTTGCACAgtaggggaat ... tggtatgtagGGAGACTGAGGAAGCCTTGAAGGTTGAGGAGAGTGCTCCTATTGCTGAGAA
EST: gi|157652089|gb|EX451723.1|EX451723
EST:     GGTGCAGGNCGTGGGAACTGGGGAACTGCTACTGATGAGGCTCTTGCACA                         GGAGACTGAGGAAGCCTTGNAAGGTTGAGGAGAGTGCTCCTATTGCTGAGA
genomic: GGTGCAGGGCGTGGGAACTGGGGAACTGCTACTGATGAGGCTCTTGCACAgtaggggaat ... tggtatgtagGGAGACTGAGGAAGCCTTG-AAGGTTGAGGAGAGTGCTCCTATTGCTGAGA
EST: gi|427517|gb|D23584.1|D23584
EST:     GGGGAACTGCTACTGATGAGGCTCTTGCACA                         GGAGACTGAGGAAGCCTTGAAGGTTGAGGAGAGTGCTCCTATTGCTGAGAA
genomic: GGGGAACTGCTACTGATGAGGCTCTTGCACAgtaggggaat ... tggtatgtagGGAGACTGAGGAAGCCTTGAAGGTTGAGGAGAGTGCTCCTATTGCTGAGAA
EST: gi|427486|gb|D23553.1|D23553
EST:     GGGGAACTGCTACTGATGAGGCTCTTGCACA                         GGAGACTGAGGAAGCCTTGAAGGTTGAGGAGAGTNCTCCTATTGCTGAGAA
genomic: GGGGAACTGCTACTGATGAGGCTCTTGCACAgtaggggaat ... tggtatgtagGGAGACTGAGGAAGCCTTGAAGGTTGAGGAGAGTGCTCCTATTGCTGAGAA
EST: gi|55409956|gb|CV722332.1|CV722332
EST:     GGTGCAGGGCGTGGGAACTGGGGAACTGCTACTGATGAGGCTCTTGCACA                         GGAGACTGAGGAAGCCTTGAAGGTTGAGGAGAGTGCTCCTATTGCTGAGAA
genomic: GGTGCAGGGCGTGGGAACTGGGGAACTGCTACTGATGAGGCTCTTGCACAgtaggggaat ... tggtatgtagGGAGACTGAGGAAGCCTTGAAGGTTGAGGAGAGTGCTCCTATTGCTGAGAA
EST: gi|29686653|gb|CB682928.1|CB682928
EST:     GGTGCAGGGCGTGGGAACTGGGGAACTGCTACTGATGAGGCTCTTGCACA                         GGAGACTGAGGAAGCCTTGAAGGTTGAGGAGAGTGCTCCTATTGCTGAGAA
genomic: GGTGCAGGGCGTGGGAACTGGGGAACTGCTACTGATGAGGCTCTTGCACAgtaggggaat ... tggtatgtagGGAGACTGAGGAAGCCTTGAAGGTTGAGGAGAGTGCTCCTATTGCTGAGAA
EST: gi|218490755|gb|FG964437.1|FG964437
EST:     GGTGCAGGGCGTGGGAACTGGGGAACTGCTACTGATGAGGCTCTTGCACA                         GGAGACTGAGGAAGCCTTGAAGGTTGAGGAGAGTGCTCCTATTGCTGAGAA
genomic: GGTGCAGGGCGTGGGAACTGGGGAACTGCTACTGATGAGGCTCTTGCACAgtaggggaat ... tggtatgtagGGAGACTGAGGAAGCCTTGAAGGTTGAGGAGAGTGCTCCTATTGCTGAGAA
EST: gi|29614482|gb|CB619495.1|CB619495
EST:     ACTGGGGAACTGCTACTGATGAGGCTCTTGCACA                         GGAGACTGAGGAAGCCTTGAAGGTTGAGGAGAGTGCTCCTATTGCTGAGAA
genomic: ACTGGGGAACTGCTACTGATGAGGCTCTTGCACAgtaggggaat ... tggtatgtagGGAGACTGAGGAAGCCTTGAAGGTTGAGGAGAGTGCTCCTATTGCTGAGAA
EST: gi|300216202|gb|HO087987.1|HO087987
EST:     GGTGCAGGGCGTGGGAACTGGGGAACTGCTACTGATGAGGCTCTTGCACA                         GGAGACTGAGGAAGCCTTGAAGGTTGAGGAGAGTGCTCCTATTGCTGAGAA
genomic: GGTGCAGGGCGTGGGAACTGGGGAACTGCTACTGATGAGGCTCTTGCACAgtaggggaat ... tggtatgtagGGAGACTGAGGAAGCCTTGAAGGTTGAGGAGAGTGCTCCTATTGCTGAGAA

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: 57 (upstream exon), 72 (downstream exon)
Score: 90

ATTATGAGCGCCACAGTGGTACTGGCCGTGGTTATGAGATGAAGCGTGATGGTGCAGGGCGTGGGAACTGGGGAACTGCTACTGATGAGGCTCTTGCACAgtaggggaat ... tggtatgtagGGAGACTGAGGAAGCCTTGAAGGTTGAGGAGAGTGCTCCTATTGCTGAGAAACAGGGTGAGCAGGATGATGCTCCAACTGGAGAGAAGGATAACAAGGAG




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