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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatttttccagccatctttcacttttttttttggttcctaatctttcactgtgtaaatctacatatagtttccatcaccactaacccttgctggaggaactaatgaaacggctttctcctcctaccttgcctgccgcagGATCTTCGGGAACCAGCTCCTCTTCCTCCTGGGCCTCGGCTTCACCAACGCCTCCTACGCCGCGGCGTTCCAGCCGGCCATACCGGTGTTCACGTTCCTC

Basic information

species Zea mays
transcript GRMZM2G134930_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G134930_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os06g49500.2 (Oryza sativa), 3'ss of exon 1
gtgatttttccagccatctttcacttttttttttggttcctaatctttcactgtgtaaatctacatatagtttccatcaccactaacccttgctggaggaactaatgaaacggctttctcctcctaccttgcctgccgcagGATCTTCGGGAACCAGCTCCTCTTCCTCCTGGGCCTCGGCTTCACCAACGCCTCCTACGCCGCGGCGTTCCAGCCGGCCATACCGGTGTTCACGTTCCTC
                                                                     || | ||||    |   | |||  |           |         || ||   | | ||   || |  |||||||||||||||||||||||| ||||| ||||||||| ||||||||||||||||||||||||| || |||||||| ||||||||||||||||| ||||||
---------------------------------------------------------------------gtattcatcgattcctcctcttcttcttcttctccttctgctcatcttatcgatcgatctcttcttctccagGATCTTCGGGAACCAGCTCCTGTTCCTGCTGGGCCTCAGCTTCACCAACGCCTCCTACGCCGCAGCCTTCCAGCCAGCCATACCGGTGTTCACATTCCTC
















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|148963460|gb|EE014479.2|EE014479
EST:     CCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCCCTGG                         GATCTTTCGG-AACCAGCTCCCTCTT
genomic: C-GGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGGgtgatttttc ... cctgccgcagGATCTT-CGGGAACCAGCTCC-TCTT
EST: gi|71434594|gb|DR815644.1|DR815644
EST:     CGGTGACTCCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGG                         GATCTTCGGGAACCCGGCTCCTCTTCCTCCTGGGGCCTCGG
genomic: CGGTGACTCC-TCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGGgtgatttttc ... cctgccgcagGATCTTCGGGAACCAG-CTCCTCTTCCTCCTGGG-CCTCGG
EST: gi|18384215|gb|BM417414.1|BM417414
EST:     CCGGTGACGCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGG                         GATCTTCGGGAACCAGCTCCTCTTCCTCCTGGGCCTCGGC
genomic: CCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGGgtgatttttc ... cctgccgcagGATCTTCGGGAACCAGCTCCTCTTCCTCCTGGGCCTCGGC
EST: gi|94476183|gb|EB705141.1|EB705141
EST:     CCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGG                         GATCTTCGGGAACCAGCTCCTCTTCCTCCTGGGCCTCGGCTTCACCAACGC
genomic: CCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGGgtgatttttc ... cctgccgcagGATCTTCGGGAACCAGCTCCTCTTCCTCCTGGGCCTCGGCTTCACCAACGC
EST: gi|88758283|gb|DY542424.1|DY542424
EST:     CCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGG                         GATCTTCGGGAACCAGCTCCTCTTCCTCCTGGGCCTCGGCTTCACCAACGC
genomic: CCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGGgtgatttttc ... cctgccgcagGATCTTCGGGAACCAGCTCCTCTTCCTCCTGGGCCTCGGCTTCACCAACGC
EST: gi|148951696|gb|EC897448.2|EC897448
EST:     CCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGG                         GATCTTCGGGAACCAGCTCCTCTTCCTCCTGGGCCTCGGCTTCACCAACGC
genomic: CCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGGgtgatttttc ... cctgccgcagGATCTTCGGGAACCAGCTCCTCTTCCTCCTGGGCCTCGGCTTCACCAACGC
EST: gi|149058751|gb|EE156769.2|EE156769
EST:     CCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGG                         GATCTTCGGGAACCAGCTCCTCTTCCTCCTGGGCCTCGGCTTCACCAACGC
genomic: CCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGGgtgatttttc ... cctgccgcagGATCTTCGGGAACCAGCTCCTCTTCCTCCTGGGCCTCGGCTTCACCAACGC
EST: gi|78106564|gb|DV524982.1|DV524982
EST:     CCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGG                         GATCTTCGGGAACCAGCTCCTCTTCCTCCTGGGCCTCGGCTTCACCAACGC
genomic: CCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGGgtgatttttc ... cctgccgcagGATCTTCGGGAACCAGCTCCTCTTCCTCCTGGGCCTCGGCTTCACCAACGC
EST: gi|89762148|gb|DY689879.1|DY689879
EST:     CCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGG                         GATCTTCGGGAACCAGCTCCTCTTCCTCCTGGGCCTCGGCTTCACCAACGC
genomic: CCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGGgtgatttttc ... cctgccgcagGATCTTCGGGAACCAGCTCCTCTTCCTCCTGGGCCTCGGCTTCACCAACGC
EST: gi|148971932|gb|EE022716.2|EE022716
EST:     CCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGG                         GATCTTCGGGAACCAGCTCCTCTTCCTCCTGGGCCTCGGCTTCACCAACGC
genomic: CCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGGgtgatttttc ... cctgccgcagGATCTTCGGGAACCAGCTCCTCTTCCTCCTGGGCCTCGGCTTCACCAACGC
EST: gi|148966599|gb|EE017634.2|EE017634
EST:     CCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGG                         GATCTTCGGGAACCAGCTCCTCTTCCTCCTGGGCCTCGGCTTCACCAACGC
genomic: CCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGGgtgatttttc ... cctgccgcagGATCTTCGGGAACCAGCTCCTCTTCCTCCTGGGCCTCGGCTTCACCAACGC
EST: gi|78114582|gb|DV532970.1|DV532970
EST:     CCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGG                         GATCTTCGGGAACCAGCTCCTCTTCCTCCTGGGCCTCGGCTTCACCAACGC
genomic: CCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGGgtgatttttc ... cctgccgcagGATCTTCGGGAACCAGCTCCTCTTCCTCCTGGGCCTCGGCTTCACCAACGC
EST: gi|87153844|gb|DY398633.1|DY398633
EST:     CCGGTGACGCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGG                         GATCTTCGGGAACCAGCTCCTCTTCCTCCTGGGCCTCGGCTTCACCAACGC
genomic: CCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGGgtgatttttc ... cctgccgcagGATCTTCGGGAACCAGCTCCTCTTCCTCCTGGGCCTCGGCTTCACCAACGC
EST: gi|149101866|gb|EE287429.2|EE287429
EST:     CCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGG                         GATCTTCGGGAACCAGCTCCTCTTCCTCCTGGGCCTCGGCTTCACCAACGC
genomic: CCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGGgtgatttttc ... cctgccgcagGATCTTCGGGAACCAGCTCCTCTTCCTCCTGGGCCTCGGCTTCACCAACGC

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: 46 (upstream exon), 46 (downstream exon)
Score: 17

AAACGTGCGGCGCCCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGGgtgatttttc ... cctgccgcagGATCTTCGGGAACCAGCTCCTCTTCCTCCTGGGCCTCGGCTTCACCAACGCCTCCTACGCCGCGGCGTTCCAGCCGGCCATACCGGTGTTCACGTTCCTC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 227

AAACGTGCGGCGCCCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGGgtgatttttc ... cctgccgcagGATCTTCGGGAACCAGCTCCTCTTCCTCCTGGGCCTCGGCTTCACCAACGCCTCCTACGCCGCGGCGTTCCAGCCGGCCATACCGGTGTTCACGTTCCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 176

AAACGTGCGGCGCCCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGGgtgatttttc ... cctgccgcagGATCTTCGGGAACCAGCTCCTCTTCCTCCTGGGCCTCGGCTTCACCAACGCCTCCTACGCCGCGGCGTTCCAGCCGGCCATACCGGTGTTCACGTTCCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 36

AAACGTGCGGCGCCCGGTGACTCCTCGCCTCCTCGCGTCCTTCGCTCTCCTCGGATTCACTGGgtgatttttc ... cctgccgcagGATCTTCGGGAACCAGCTCCTCTTCCTCCTGGGCCTCGGCTTCACCAACGCCTCCTACGCCGCGGCGTTCCAGCCGGCCATACCGGTGTTCACGTTCCTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccttgctggaggaactaatgaaacggctttctcctcctaccttgcctgccgcagGATCTTCGGGAACCAGCTCCTCTTCCTCCTGGGCCTCGGCTTCACCAACGCCTCCTACGCCGCGGCGTTCCAGCCGGCCATACCGGTGTTCACGTTCCTC
             aactaat  putative branch site (score: 36)
                           ctttctcctcctacct  putative PPT
                taatgaaa  TA-rich tract