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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttcaactttctttgcaaaattgtaatctagtatactgatgcaatacatggtttatgaacattttgacacgaagtgttgttgcagggtctcacaacacatttcactgaatattcttcttttttgtcatgggctattcgtttcagGACAATATTTCACATGACTCTGACTTGGGTAACACCTTAAGTATGGTGTCCTTGGTTGGTGTCTTG

Basic information

species Zea mays
transcript GRMZM2G098679_T03
intron # 11
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|37375628|gb|CF624264.1|CF624264
EST:     TGGGGATGACCCTAAGCCTTCTTGTGGTTGCTGTTGTATTTTACATCAAG                         GACAATATTTCACATGACTCTGACTTGGGTAACACCTTAAGTATGGTGTCC
genomic: TTGGGATGACCCTAAGCCTTCTTGTGGTTGCTGTTGTATTTTACATCAAGgtaagttcaa ... ttcgtttcagGACAATATTTCACATGACTCTGACTTGGGTAACACCTTAAGTATGGTGTCC
EST: gi|211280254|gb|FL478194.1|FL478194
EST:     TTGGGATGACCCTAAGCCTTCTTGTGGTTGCTGTTGTATTTTACATCAAG                         GACAATATTTCACATGACTCTGACTTGGGTAACACCTTAAGTATGGTGTCC
genomic: TTGGGATGACCCTAAGCCTTCTTGTGGTTGCTGTTGTATTTTACATCAAGgtaagttcaa ... ttcgtttcagGACAATATTTCACATGACTCTGACTTGGGTAACACCTTAAGTATGGTGTCC
EST: gi|148953878|gb|EC899256.2|EC899256
EST:     TTGGGATGACCCTAAGCCTTCTTGTGGTTGCTGTTGTATTTTACATCAAG                         GACAATATTTCACATGACTCTGACTTGGGTAACACCTTAAGTATGGTGTCC
genomic: TTGGGATGACCCTAAGCCTTCTTGTGGTTGCTGTTGTATTTTACATCAAGgtaagttcaa ... ttcgtttcagGACAATATTTCACATGACTCTGACTTGGGTAACACCTTAAGTATGGTGTCC
EST: gi|60401580|gb|DN234387.1|DN234387
EST:     TTGGGATGACCCTAAGCCTTCTTGTGGTTGCTGTTGTATTTTACATCAAG                         GACAATATTTCACATGACTCTGACTTGGGTAACACCTTAAGTATGGTGTCC
genomic: TTGGGATGACCCTAAGCCTTCTTGTGGTTGCTGTTGTATTTTACATCAAGgtaagttcaa ... ttcgtttcagGACAATATTTCACATGACTCTGACTTGGGTAACACCTTAAGTATGGTGTCC
EST: gi|211084269|gb|FL474824.1|FL474824
EST:     TGGGATGACCCTAAGCCTTCTTGTGGTTGCTGTTGTATTTTACATCAAAG                         GACAATATTTCACATGACTCTGACTTGGGTAACACCTTAAGTATGGTGTC
genomic: TGGGATGACCCTAAGCCTTCTTGTGGTTGCTGTTGTATTTTACATC-AAGgtaagttcaa ... ttcgtttcagGACAATATTTCACATGACTCTGACTTGGGTAACACCTTAAGTATGGTGTC

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), 37 (downstream exon)
Score: 17

ATTTCTTCTTTTGGGATGACCCTAAGCCTTCTTGTGGTTGCTGTTGTATTTTACATCAAGgtaagttcaa ... ttcgtttcagGACAATATTTCACATGACTCTGACTTGGGTAACACCTTAAGTATGGTGTCCTTGGTTGGTGTCTTG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 599

ATTTCTTCTTTTGGGATGACCCTAAGCCTTCTTGTGGTTGCTGTTGTATTTTACATCAAGgtaagttcaa ... ttcgtttcagGACAATATTTCACATGACTCTGACTTGGGTAACACCTTAAGTATGGTGTCCTTGGTTGGTGTCTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 612

ATTTCTTCTTTTGGGATGACCCTAAGCCTTCTTGTGGTTGCTGTTGTATTTTACATCAAGgtaagttcaa ... ttcgtttcagGACAATATTTCACATGACTCTGACTTGGGTAACACCTTAAGTATGGTGTCCTTGGTTGGTGTCTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 154

ATTTCTTCTTTTGGGATGACCCTAAGCCTTCTTGTGGTTGCTGTTGTATTTTACATCAAGgtaagttcaa ... ttcgtttcagGACAATATTTCACATGACTCTGACTTGGGTAACACCTTAAGTATGGTGTCCTTGGTTGGTGTCTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcacaacacatttcactgaatattcttcttttttgtcatgggctattcgtttcagGACAATATTTCACATGACTCTGACTTGGGTAACACCTTAAGTATGGTGTCCTTGGTTGGTGTCTTG
 gtctcac  putative branch site (score: 154)
                                             ttcgtttc  putative PPT
                  aatattcttctttttt  TA-rich tract