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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtcaaattttaaactaatacatgatgtgaagtgtaactcaaaacgagtaaggaagctgtgaaaacgggacgattgaacttatttcgaaccacaacttcagGACTTGGTATCGAGGAACGCTGGCCATTCGAAGGCAGAGCTGGCAGACTTGCTATACAGTATCCTCCGGTTCGAGCCATCAGAACGTCTGACAGCGCAAG

Basic information

species Zea mays
transcript GRMZM2G366935_T05
intron # 10
splice site 3'
intron type U2

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|32832652|gb|CD972330.1|CD972330
EST:     CTGTTTCAAGAGAAAGCATCAGAGCTGTGAAGAAACTGGATCGACTAAAG                         GACTTGGTATCGAGGAACGCTGGCCATTCGAAGGCAGAGCTGGCAGACTTG
genomic: CTGTTTCAAGAGAAAGCATCAGAGCTGTGAAGAAACTGGATCGACTAAAGgttttagttc ... acaacttcagGACTTGGTATCGAGGAACGCTGGCCATTCGAAGGCAGAGCTGGCAGACTTG
EST: gi|5607698|gb|AI901365.1|AI901365
EST:     CTGTTTCAAGAGAAAGCATCAGAGCTGTGAAGAAACTGGATCGACTAAAG                         GACTTGGTATCGAGGAACGCTGGCCATTCGAAGGCAGAGCTGGCAGACTTG
genomic: CTGTTTCAAGAGAAAGCATCAGAGCTGTGAAGAAACTGGATCGACTAAAGgttttagttc ... acaacttcagGACTTGGTATCGAGGAACGCTGGCCATTCGAAGGCAGAGCTGGCAGACTTG
EST: gi|60356689|gb|DN223662.1|DN223662
EST:     CTGTTTCAAGAGAAAGCATCAGAGCTGTGAAGAAACTGGATCGACTAAAG                         GACTTGGTATCGAGGAACGCTGGCCATTCGAAGGCAGAGCTGGCAGACTTG
genomic: CTGTTTCAAGAGAAAGCATCAGAGCTGTGAAGAAACTGGATCGACTAAAGgttttagttc ... acaacttcagGACTTGGTATCGAGGAACGCTGGCCATTCGAAGGCAGAGCTGGCAGACTTG
EST: gi|166490845|gb|EG161148.1|EG161148
EST:     AGAAAGCATCAGAGCTGTGAAGAAACTGGATCGACTAAAG                         GACTTGGTATCGAGGAACGCTGGCCATTCGAAGGCAGAGCTGGC
genomic: AGAAAGCATCAGAGCTGTGAAGAAACTGGATCGACTAAAGgttttagttc ... acaacttcagGACTTGGTATCGAGGAACGCTGGCCATTCGAAGGCAGAGCTGGC

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: 48 (upstream exon), 49 (downstream exon)
Score: 228

AAATATTTCAGGAGGGCAACACGTTTAAATTGGCCTGAAGGTGCTGTTTCAAGAGAAAGCATCAGAGCTGTGAAGAAACTGGATCGACTAAAGgttttagttc ... acaacttcagGACTTGGTATCGAGGAACGCTGGCCATTCGAAGGCAGAGCTGGCAGACTTGCTATACAGTATCCTCCGGTTCGAGCCATCAGAACGTCTGACAGCGCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 155

AAATATTTCAGGAGGGCAACACGTTTAAATTGGCCTGAAGGTGCTGTTTCAAGAGAAAGCATCAGAGCTGTGAAGAAACTGGATCGACTAAAGgttttagttc ... acaacttcagGACTTGGTATCGAGGAACGCTGGCCATTCGAAGGCAGAGCTGGCAGACTTGCTATACAGTATCCTCCGGTTCGAGCCATCAGAACGTCTGACAGCGCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 227

AAATATTTCAGGAGGGCAACACGTTTAAATTGGCCTGAAGGTGCTGTTTCAAGAGAAAGCATCAGAGCTGTGAAGAAACTGGATCGACTAAAGgttttagttc ... acaacttcagGACTTGGTATCGAGGAACGCTGGCCATTCGAAGGCAGAGCTGGCAGACTTGCTATACAGTATCCTCCGGTTCGAGCCATCAGAACGTCTGACAGCGCAAG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 102

AAATATTTCAGGAGGGCAACACGTTTAAATTGGCCTGAAGGTGCTGTTTCAAGAGAAAGCATCAGAGCTGTGAAGAAACTGGATCGACTAAAGgttttagttc ... acaacttcagGACTTGGTATCGAGGAACGCTGGCCATTCGAAGGCAGAGCTGGCAGACTTGCTATACAGTATCCTCCGGTTCGAGCCATCAGAACGTCTGACAGCGCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtaaggaagctgtgaaaacgggacgattgaacttatttcgaaccacaacttcagGACTTGGTATCGAGGAACGCTGGCCATTCGAAGGCAGAGCTGGCAGACTTGCTATACAGTATCCTCCGGTTCGAGCCATCAGAACGTCTGACAGCGCAAG
                              aacttattt  TA-rich tract