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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatttttacaatgattggtctggctggatttgatcactcttttctcacacctttccgctcctattgtcattctaaatctgctctaataatctttttgtagGTGGATACCAACCTGGAATCACCAAATGATATTGTACCAGAAGGGGTGCCATTTACAGGACCAAAATACAGAATTGCTCCATACTCTTCCATTCTGCTCA

Basic information

species Oryza sativa
transcript LOC_Os09g29404.1
intron # 22
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g29404.3 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G076508_T01 (Zea mays), 3'ss of exon 8
-------aatttttacaatgattggtctggctggatttgatcactcttttctcacacctttccgctcctattgtcattctaaatctgctctaataatctttttgtagGTGGATACCAACCTGGAATCACCAAATGATATTGTACCAGAAGGGGTGCCATTTACAGGACCAAAATACAGAATTGCTCCATACTCTTCCATTCTGCTCA
       | | | | |  |  ||||||||||| | ||   |    ||| | ||    ||| ||    || | || |   || |  ||||   ||      |    |||||||||||||||||||||||||||| |||||||| ||||||||||||||||| |||||  ||   ||||| |||||||| |||||||   ||       
caattttactgtattcgttacttggtctggctagcttctgtgctgcttctatcttgacttccc----ctttagttaccttacagttgct---atgtcgcctccacagGTGGATACCAACCTGGAATCACCAAAGGATATTGTCCCAGAAGGGGTGCCATTCACAGGTTCAGGGTACAGGATTGCTCCTTACTCTTTTTTTGAAGATT

upper sequence: LOC_Os09g29404.3 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G150796_T02 (Zea mays), 3'ss of exon 22
-aatttt--tacaatgattggtctggctggatttgatcactcttttctcacacctttccgctcctattgtcattctaaatctgctctaataatctttttgtagGTGGATACCAACCTGGAATCACCAAATGATATTGTACCAGAAGGGGTGCCATTTACAGGACCAAAATACAGAATTGCTCCATACTCTTCCATTCTGCTCA
 ||||||  |  | |  ||  |   |   |  | | |       | ||   | |||  |   |||   || |   || |  | ||   |||     |    |||||||||||||||||||||||||||| |||||||| ||||||||||||||||| |||||  ||   ||||| |||||||| |||||||||||  |||| |
caattttgttgtattcgttacttgtgtctggctagcttttgtgctgcttctatcttaacttcccttcagttaccttacaatttct---atatcgcctccacagGTGGATACCAACCTGGAATCACCAAAGGATATTGTCCCAGAAGGGGTGCCATTCACAGGTTCAGGGTACAGGATTGCTCCCTACTCTTCCATCTTGCTTA
















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|218485255|gb|FG969936.1|FG969936
EST:     TGGACGCTGTAATTCCCCCACCACCACACCATAAATGTTGGAACCGTGTG                         GTGGATACCAACCTGGAATCACCAAATGATATTGTACCAGAAGGGGTGCCA
genomic: TGGACGCTGTAATTCCCCCACCACCACACCATAAATGTTGGAACCGTGTGgtatggatac ... ctttttgtagGTGGATACCAACCTGGAATCACCAAATGATATTGTACCAGAAGGGGTGCCA
EST: gi|11442710|gb|BF430613.1|BF430613
EST:     TGGACGCTGTAATTCCCCCACCACCACACCATAAATGTTGGAACCGTGTG                         GTGGATACCAACCTGGAATCACCAAATGATATTGTACCAGAAGGGGTGCCA
genomic: TGGACGCTGTAATTCCCCCACCACCACACCATAAATGTTGGAACCGTGTGgtatggatac ... ctttttgtagGTGGATACCAACCTGGAATCACCAAATGATATTGTACCAGAAGGGGTGCCA
EST: gi|29640551|gb|CB645560.1|CB645560
EST:     TGGACGCTGTAATTCCCCCACCACCACACCATAAATGTTGGAACCGTGTG                         GTGGATACCAACCTGGAATCACCAAATGATATTGTACCAGAAGGGGTGCCA
genomic: TGGACGCTGTAATTCCCCCACCACCACACCATAAATGTTGGAACCGTGTGgtatggatac ... ctttttgtagGTGGATACCAACCTGGAATCACCAAATGATATTGTACCAGAAGGGGTGCCA
EST: gi|218486693|gb|FG956345.1|FG956345
EST:     TGGACGCTGTAATTCCCCCACCACCACACCATAAATGTTGGAACCGTGTG                         GTGGATACCAACCTGGAATCACCAAATGATATTGTACCAGAAGGGGTGCCA
genomic: TGGACGCTGTAATTCCCCCACCACCACACCATAAATGTTGGAACCGTGTGgtatggatac ... ctttttgtagGTGGATACCAACCTGGAATCACCAAATGATATTGTACCAGAAGGGGTGCCA
EST: gi|58678014|gb|CK066701.1|CK066701
EST:     TGGACGCTGTAATTCCCCCACCACCACACCATAAATGTTGGAACCGTGTG                         GTGGATACCAACCTGGAATCACCAAATGATATTGTACCAGAAGGGGTGCCA
genomic: TGGACGCTGTAATTCCCCCACCACCACACCATAAATGTTGGAACCGTGTGgtatggatac ... ctttttgtagGTGGATACCAACCTGGAATCACCAAATGATATTGTACCAGAAGGGGTGCCA
EST: gi|86428642|gb|CI075323.1|CI075323
EST:     TGGACGCTGTAATTCCCCCACCATCACACCATAAATGTTGGAACCGTGTG                         GTGGATACCAACCTGGAATCACCTAATGATATTGTACCAGAAGGGGTGCAA
genomic: TGGACGCTGTAATTCCCCCACCACCACACCATAAATGTTGGAACCGTGTGgtatggatac ... ctttttgtagGTGGATACCAACCTGGAATCACCAAATGATATTGTACCAGAAGGGGTGCCA
EST: gi|58594962|gb|CF993270.1|CF993270
EST:     TGGACGCTGTAATTCCCCCACCAGCACACCATAAATGTTGGAACCGTGTG                         GTGGATACCAACCTGGAATCACCAAATGATATTGTACCAGAAGGGGTGCCA
genomic: TGGACGCTGTAATTCCCCCACCACCACACCATAAATGTTGGAACCGTGTGgtatggatac ... ctttttgtagGTGGATACCAACCTGGAATCACCAAATGATATTGTACCAGAAGGGGTGCCA

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: 23 (upstream exon), 53 (downstream exon)
Score: 1

CAACTCTGGTGGAGATATCTATTTGGCATTCAATGCACATGACTATTTTGTGGACGCTGTAATTCCCCCACCACCACACCATAAATGTTGGAACCGTGTGgtatggatac ... ctttttgtagGTGGATACCAACCTGGAATCACCAAATGATATTGTACCAGAAGGGGTGCCATTTACAGGACCAAAATACAGAATTGCTCCATACTCTTCCATTCTGCTCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacacctttccgctcctattgtcattctaaatctgctctaataatctttttgtagGTGGATACCAACCTGGAATCACCAAATGATATTGTACCAGAAGGGGTGCCATTTACAGGACCAAAATACAGAATTGCTCCATACTCTTCCATTCTGCTCA
                                            tctttttgt  CT-rich tract
                                      taataatctttttgta  TA-rich tract