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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaacccttgacacagagctgcaaagtccatcatttgcactgaagcattcctgacgttgcttgttttgcgctgtatagGTGAAGAGCGGCGCTGACGACCGGGCAGTCCTTGAATACACGCATGGTTTATATCAGGATTTGGGCATACAGGATCTGACGGTCCAAACTGATGAGTTTG

Basic information

species Zea mays
transcript GRMZM2G017365_T09
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017365_T03 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os02g58580.1 (Oryza sativa), 3'ss of exon 8
-----------------gtaaaacc---cttgacacagagctgca-aagtccatcatttgcactgaagcattcctgacgttgcttgttttgcgctgtatagGTGAAGAGCGGCGCTGACGACCGGGCAGTCCTTGAATACACGCATGGTTTATATCAGGATTTGGGCATACAGGATCTGACGGTCCAAACTGATGAGTTTG
                 ||||        ||| |    | ||  | ||| || |       | |||   | | |     ||| |||| ||| | ||||||||||||||  || | |||   || | | || || || ||   |||||| |||||||| ||||||||||||||||| |||||  ||||||| ||||| |  |
ggtattaccaaaacttggtaaggtttattttggctacaatctaaacaagcccctagcccctagtgactgagttcgcgttttggttgtgttgtg-tgtatagGTGAAGAATGGTGGTGATTGCCAGTCCGTGCTCGACTATGTGCATGGATTATATCAAGATTTGGGCATACAGGACCTGACCATCCAAACCGATGAATAAG
















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|166652595|gb|EG287254.1|EG287254
EST:     GATTCTGGGAGCTTGTTCCTGGTCAGGCAGTTGGATCTCTCTCCATTAGG                         GTGAAGAGCGGCGCTGACGACCGGGCAGTCC
genomic: GATTCTGGGAGCTTGTTCCTGGTCAGGCAGTTGGATCTCTCTCCATTAGGgtaaaaccct ... cgctgtatagGTGAAGAGCGGCGCTGACGACCGGGCAGTCC
EST: gi|76014355|gb|DT941525.1|DT941525
EST:     GATTCTGGGAGCTTGTTCCTGGTCAGGCAGTTGGATCTCTCTCCATTAGG                         GTGAAGAGCGGCGCTGACGACCGGGCAGTCCTTGAATACACGCATGGTTTA
genomic: GATTCTGGGAGCTTGTTCCTGGTCAGGCAGTTGGATCTCTCTCCATTAGGgtaaaaccct ... cgctgtatagGTGAAGAGCGGCGCTGACGACCGGGCAGTCCTTGAATACACGCATGGTTTA
EST: gi|211384669|gb|FL388814.1|FL388814
EST:     GATTCTGGGAGCTTGTTCCTGGTCAGGCAGTTGGATCTCTCTCCATTAGG                         GTGAAGAGCGGCGCTGACGACCGGGCAGTCCTTGAATACACGCATGGTTTA
genomic: GATTCTGGGAGCTTGTTCCTGGTCAGGCAGTTGGATCTCTCTCCATTAGGgtaaaaccct ... cgctgtatagGTGAAGAGCGGCGCTGACGACCGGGCAGTCCTTGAATACACGCATGGTTTA
EST: gi|211489499|gb|FL457182.1|FL457182
EST:     GATTCTGGGAGCTTGTTCCTGGTCAGGCAGTTGGATCTCTCTCCATTAGG                         GTGAAGAGCGGCGCTGACGACCGGGCAGTCCTTGAATACACGCATGGTTTA
genomic: GATTCTGGGAGCTTGTTCCTGGTCAGGCAGTTGGATCTCTCTCCATTAGGgtaaaaccct ... cgctgtatagGTGAAGAGCGGCGCTGACGACCGGGCAGTCCTTGAATACACGCATGGTTTA
EST: gi|71442151|gb|DR823201.1|DR823201
EST:     GATTCTGGGAGCTTGTTCCTGGTCAGGCAGTTGGATCTCTCTCCATTAGG                         GTGAAGAGCGGCGCTGACGACCGGGCAGTCCTTGAATACACGCATGGTTTA
genomic: GATTCTGGGAGCTTGTTCCTGGTCAGGCAGTTGGATCTCTCTCCATTAGGgtaaaaccct ... cgctgtatagGTGAAGAGCGGCGCTGACGACCGGGCAGTCCTTGAATACACGCATGGTTTA
EST: gi|211206137|gb|FL466217.1|FL466217
EST:     GATTCTGGGAGCTTGTTCCTGGTCAGGCAGTTGGATCTCTCTCCATTAGG                         GTGAAGAGCGGCGCTGACGACCGGGCAGTCCTTGAATACACGCATGGTTTA
genomic: GATTCTGGGAGCTTGTTCCTGGTCAGGCAGTTGGATCTCTCTCCATTAGGgtaaaaccct ... cgctgtatagGTGAAGAGCGGCGCTGACGACCGGGCAGTCCTTGAATACACGCATGGTTTA

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: 33 (upstream exon), 17 (downstream exon)
Score: 1

ATTGCTGCTTGTGAAGATGTCTCCGAAGTATGGCAAGGTCGATTCTGGGAGCTTGTTCCTGGTCAGGCAGTTGGATCTCTCTCCATTAGGgtaaaaccct ... cgctgtatagGTGAAGAGCGGCGCTGACGACCGGGCAGTCCTTGAATACACGCATGGTTTATATCAGGATTTGGGCATACAGGATCTGACGGTCCAAACTGATGAGTTTG


Block sizes: 41 (upstream exon), 33 (downstream exon)
Score: 3

ATTGCTGCTTGTGAAGATGTCTCCGAAGTATGGCAAGGTCGATTCTGGGAGCTTGTTCCTGGTCAGGCAGTTGGATCTCTCTCCATTAGGgtaaaaccct ... cgctgtatagGTGAAGAGCGGCGCTGACGACCGGGCAGTCCTTGAATACACGCATGGTTTATATCAGGATTTGGGCATACAGGATCTGACGGTCCAAACTGATGAGTTTG


Block sizes: 40 (upstream exon), 49 (downstream exon)
Score: 3

ATTGCTGCTTGTGAAGATGTCTCCGAAGTATGGCAAGGTCGATTCTGGGAGCTTGTTCCTGGTCAGGCAGTTGGATCTCTCTCCATTAGGgtaaaaccct ... cgctgtatagGTGAAGAGCGGCGCTGACGACCGGGCAGTCCTTGAATACACGCATGGTTTATATCAGGATTTGGGCATACAGGATCTGACGGTCCAAACTGATGAGTTTG


Block sizes: 24 (upstream exon), 26 (downstream exon)
Score: 2

ATTGCTGCTTGTGAAGATGTCTCCGAAGTATGGCAAGGTCGATTCTGGGAGCTTGTTCCTGGTCAGGCAGTTGGATCTCTCTCCATTAGGgtaaaaccct ... cgctgtatagGTGAAGAGCGGCGCTGACGACCGGGCAGTCCTTGAATACACGCATGGTTTATATCAGGATTTGGGCATACAGGATCTGACGGTCCAAACTGATGAGTTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagtccatcatttgcactgaagcattcctgacgttgcttgttttgcgctgtatagGTGAAGAGCGGCGCTGACGACCGGGCAGTCCTTGAATACACGCATGGTTTATATCAGGATTTGGGCATACAGGATCTGACGGTCCAAACTGATGAGTTTG
                         tcctgac  putative branch site (score: 2)
      atcattt  TA-rich tract