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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTTTTCGTAAGGAACCATTTTTCTACGGGCATGACAACCATGATCAACTTGTTAAGATAGCCAAGgttatcaattcagcctgcttgttgtttgcaatgaactgcttagctagctatgttgcttacttttgcaatgtcatgtagcttgcaagtgctgattattgttacatcctttatcag

Basic information

species Zea mays
transcript GRMZM2G143602_T03
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G143602_T03 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os07g02350.1 (Oryza sativa), 5'ss of exon 6
ATTTTTCGTAAGGAACCATTTTTCTACGGGCATGACAACCATGATCAACTTGTTAAGATAGCCAAGgttatcaattcagcctgcttgttgtttgcaatgaactgcttagctagctatgttgcttacttttgcaatgtcatgtagcttgcaagtgctgattattgttacatcctttatcag
|| || || ||||| ||||||||||| || ||||||||||||||||||||||||||||| || ||||| ||    ||||| || || |  |     ||||  || | |   |   |||      | ||      |  | | |   |   |  ||   | ||| |||  |||         
ATCTTCCGCAAGGAGCCATTTTTCTATGGTCATGACAACCATGATCAACTTGTTAAGATCGCAAAGgtgattt-ctcagcttgtttatgttaaaagatga--tgttcatacaagaatgaaatgcatttcatgtttagcttatcattcatac-tgtacactatggtt-tatc---------

upper sequence: GRMZM2G143602_T03 (Zea mays), 5'ss of exon 6
lower sequence: PP1S165_119V6.1 (Physcomitrella patens), 5'ss of exon 7
ATTTTTCGTAAGGAACCATTTTTCTACGGGCATGACAACCATGATCAACTTGTTAAGATAGCCAAGgt----tatcaattcagcctgcttgttgtttgcaatgaactgcttagctagctatgttgcttacttttgcaatgtcatgtagcttgca-----agtgctgattattgttacatcctttatcag-------------------
|| ||||| ||||| ||||| || || |||||||||||  ||||||||||||| ||||| || |||||    |  || ||||  |      |||  | |||  |  |   || |    | | ||  ||   | |  || ||||| |  ||  |      |  ||  | |  ||||     | |||||                     
ATATTTCGGAAGGAGCCATTCTTTTATGGGCATGACAATTATGATCAACTTGTGAAGATTGCTAAGgtgcagtggcagttcatacatagatttgccttcaagcagttatatatcactttttatttattttgtataaaaagtcatattactgtctttcgcaacgccaagttgtgttttgagccttatctttgtgggtgtctgataccag
















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|211466861|gb|FL187159.1|FL187159
EST:     CATTTTTCTACGGGCATGACAACCATGATCAACTTGTTAAGATAGCCAAG                         GTACTTGGGACAGATGGGCTGAATGTTTATTTGAACAAGTACAGAATTGAG
genomic: CATTTTTCTACGGGCATGACAACCATGATCAACTTGTTAAGATAGCCAAGgttatcaatt ... cctttatcagGTACTTGGGACAGATGGGCTGAATGTTTATTTGAACAAGTACAGAATTGAG
EST: gi|19822196|gb|BQ048220.1|BQ048220
EST:     CATTTTTCTACGGGCATGACAACCATGATCAACTTGTTAAGATAGCCAAG                         GTACTTGGGACAGATGGGCTGAATGCTTATTTGAACAAGTACAGAATTGAG
genomic: CATTTTTCTACGGGCATGACAACCATGATCAACTTGTTAAGATAGCCAAGgttatcaatt ... cctttatcagGTACTTGGGACAGATGGGCTGAATGTTTATTTGAACAAGTACAGAATTGAG
EST: gi|21389960|gb|BQ528009.1|BQ528009
EST:     CATTTTTCTACGGGCATGACAACCATGATCAACTTGTTAAGATAGCCAAG                         GTACTTGGGACAGATGGGCTGAATGCTTATTTGAACAAGTACAGAATTGAG
genomic: CATTTTTCTACGGGCATGACAACCATGATCAACTTGTTAAGATAGCCAAGgttatcaatt ... cctttatcagGTACTTGGGACAGATGGGCTGAATGTTTATTTGAACAAGTACAGAATTGAG
EST: gi|20507674|gb|BQ279724.1|BQ279724
EST:     CATTTTTCTACGGGCATGGCAACCATGATCAGCTTGTTAAGATAGCCAAG                         GTGCTTGGGACAGATGGGCTGAATGCTTATTTGAACAAGTACAGAATTGAG
genomic: CATTTTTCTACGGGCATGACAACCATGATCAACTTGTTAAGATAGCCAAGgttatcaatt ... cctttatcagGTACTTGGGACAGATGGGCTGAATGTTTATTTGAACAAGTACAGAATTGAG
EST: gi|6993987|gb|AW453201.1|AW453201
EST:     ATTTTTCTACGGGCATGACAACCATGATCAACTTGCTAAGATAGCCAAG                         GTACTTGGGACAGATGGGCTGAATGCTTATTTGAACAAGTACAGAATTGAG
genomic: ATTTTTCTACGGGCATGACAACCATGATCAACTTGTTAAGATAGCCAAGgttatcaatt ... cctttatcagGTACTTGGGACAGATGGGCTGAATGTTTATTTGAACAAGTACAGAATTGAG
EST: gi|60348663|gb|DN215636.1|DN215636
EST:     CATTTTTCTACGGGCATGACAACCATGATCAACTTGTTAAGATAGCCAAG                         GTACTTGGGACAGATGGGCTGAATGTTTATTTGAACAAGTACAGAATTGAG
genomic: CATTTTTCTACGGGCATGACAACCATGATCAACTTGTTAAGATAGCCAAGgttatcaatt ... cctttatcagGTACTTGGGACAGATGGGCTGAATGTTTATTTGAACAAGTACAGAATTGAG
EST: gi|71770653|gb|DR968590.1|DR968590
EST:     CATTTTTCTACGGGCATGACAACTATGATCAACTTGTTAAGATAGCCAAG                         GTACTTGGGACAGATGGGCTGAATG
genomic: CATTTTTCTACGGGCATGACAACCATGATCAACTTGTTAAGATAGCCAAGgttatcaatt ... cctttatcagGTACTTGGGACAGATGGGCTGAATG

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 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 538

ATTTTTCGTAAGGAACCATTTTTCTACGGGCATGACAACCATGATCAACTTGTTAAGATAGCCAAGgttatcaatt ... cctttatcagGTACTTGGGACAGATGGGCTGAATGTTTATTTGAACAAGTACAGAATTGAGCTTGACCCTCAGCTTGAAGCCCTCGTTGGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 281

ATTTTTCGTAAGGAACCATTTTTCTACGGGCATGACAACCATGATCAACTTGTTAAGATAGCCAAGgttatcaatt ... cctttatcagGTACTTGGGACAGATGGGCTGAATGTTTATTTGAACAAGTACAGAATTGAGCTTGACCCTCAGCTTGAAGCCCTCGTTGGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 324

ATTTTTCGTAAGGAACCATTTTTCTACGGGCATGACAACCATGATCAACTTGTTAAGATAGCCAAGgttatcaatt ... cctttatcagGTACTTGGGACAGATGGGCTGAATGTTTATTTGAACAAGTACAGAATTGAGCTTGACCCTCAGCTTGAAGCCCTCGTTGGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 332

ATTTTTCGTAAGGAACCATTTTTCTACGGGCATGACAACCATGATCAACTTGTTAAGATAGCCAAGgttatcaatt ... cctttatcagGTACTTGGGACAGATGGGCTGAATGTTTATTTGAACAAGTACAGAATTGAGCTTGACCCTCAGCTTGAAGCCCTCGTTGGAAG