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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacttgatattctttacctttttgtctaaacctcagatcgaacatccatttgcacttgctaatgatatgtttacagGACAAATGGGGGAAAAATCTCTACTTAGCTTCCATTTGCTATGGAAGAACGGTGTCATGAGGTCTGCCCAGTTTGGCTGGGGCACACTGTAGAGTTTATT

Basic information

species Zea mays
transcript GRMZM2G116151_T03
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os05g11140.2 (Oryza sativa), 3'ss of exon 15
gtaacttgatattctttacctttttgtctaaacctcagatcgaacatccatttgcacttgctaatgatatgtttacagGACAAATGGGGGAAAAATCTCTACTTAGCTTCCATTTGCTATGGAAGAACGGTGTCATGAGGTCTGC--CCAGTTTGGCTGGGGCACACTGTAGAGTTTATT
|||| ||||| |||| |     ||   || |||  |    |     | ||  |  | |   |  | |||| | | ||||| ||||||  ||| ||||| ||| |||||||||||||||||||||||||||||||||||||||  |   | |||||||||     |  |||||||||||||
gtaatttgattttctgtctaaattctactgaacagccatact--tgtgcaactataatgatt--taatatatctgcagGAGAAATGGTCGAAGAATCTTTACCTAGCTTCCATTTGCTATGGAAGAACGGTGTCATGAGGTCCACATTCTGTTTGGCTGC--TTCTTTGTAGAGTTTATT

upper sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os05g11140.3 (Oryza sativa), 3'ss of exon 15
gtaacttgatattctttacctttttgtctaaacctcagatcgaacatccatttgcacttgctaatgatatgtttacagGACAAATGGGGGAAAAATCTCTACTTAGCTTCCATTTGCTATGGAAGAACGGTGTCATGAGGTCTGCCCAGTTTGGCTGGGGCACACTGTAGAGTTTATT
|||| ||||| |||| |     ||   || |||  |    |     | ||  |  | |   |  | |||| | | ||||| ||||||  ||| ||||| ||| ||||||||||||||||||||||||||||||||||||                                       
gtaatttgattttctgtctaaattctactgaacagccatact--tgtgcaactataatgatt--taatatatctgcagGAGAAATGGTCGAAGAATCTTTACCTAGCTTCCATTTGCTATGGAAGAACGGTGTCATGAG---------------------------------------
















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|5706211|gb|AI941987.1|AI941987
EST:     AAACACAGGAAACTCTAAGAACGTCTGCTTTCCCCAGCCAGCATGTGAAG                         GACAAATGGGGGAAAAATCTCTACTTAGCTTCCATTTGCTATGGAAGAACG
genomic: AAACACAGGAGACTCTAAGAACGTCTGCTTTCCCCAGCCAGCATGTGAAGgtaacttgat ... atgtttacagGACAAATGGGGGAAAAATCTCTACTTAGCTTCCATTTGCTATGGAAGAACG
EST: gi|31357223|gb|CD441580.1|CD441580
EST:     AAACACAGGAGACTCTAAGAACGTCTGCTTTCCCCAGCCAGCATGTGAAG                         GACAAATGGGGGAAAAATCTCTACTTAGCTTCCATTTGCTATGGAAGAACG
genomic: AAACACAGGAGACTCTAAGAACGTCTGCTTTCCCCAGCCAGCATGTGAAGgtaacttgat ... atgtttacagGACAAATGGGGGAAAAATCTCTACTTAGCTTCCATTTGCTATGGAAGAACG
EST: gi|89248581|gb|DY620367.1|DY620367
EST:     AAACACAGGAGACTCTAAGAACGTCTGCTTTCCCCAGCCAGCATGTGAAG                         GACAAATGGGGGAAAAATCTCTACTTAGCTTCCATTTGCTATGGAAGAACG
genomic: AAACACAGGAGACTCTAAGAACGTCTGCTTTCCCCAGCCAGCATGTGAAGgtaacttgat ... atgtttacagGACAAATGGGGGAAAAATCTCTACTTAGCTTCCATTTGCTATGGAAGAACG
EST: gi|211347555|gb|FL462315.1|FL462315
EST:     AAACACAGGAGACTCTAAGAACGTCTGCTTTCCCCAGCCAGCATGTGAAG                         GACAAATGGGGGAAAAATCTCTACTTAGCTTCCATTTGCTATGGAAGAACG
genomic: AAACACAGGAGACTCTAAGAACGTCTGCTTTCCCCAGCCAGCATGTGAAGgtaacttgat ... atgtttacagGACAAATGGGGGAAAAATCTCTACTTAGCTTCCATTTGCTATGGAAGAACG
EST: gi|30088200|gb|CB886405.1|CB886405
EST:     AAACACAGGAGACTCTAAGAACGTCTGCTTTCCCCAGCCAGCATGTGAAG                         GACAAATGGGGGAAAAATCTCTACTTAGCTTCCATTTGCTATGGAAGAACG
genomic: AAACACAGGAGACTCTAAGAACGTCTGCTTTCCCCAGCCAGCATGTGAAGgtaacttgat ... atgtttacagGACAAATGGGGGAAAAATCTCTACTTAGCTTCCATTTGCTATGGAAGAACG
EST: gi|101387537|gb|EB815783.1|EB815783
EST:     AAACACAGGAGACTCTAAGAACGTCTGCTTTCCCCAGCCAGCATGTGAAG                         GACAAATGGGGGAAAAATCTCTACTTAGCTTCCATTTGCTATGGAAGAACG
genomic: AAACACAGGAGACTCTAAGAACGTCTGCTTTCCCCAGCCAGCATGTGAAGgtaacttgat ... atgtttacagGACAAATGGGGGAAAAATCTCTACTTAGCTTCCATTTGCTATGGAAGAACG
EST: gi|32165081|gb|CD670399.1|CD670399
EST:     AAACACAGGAGACTCTAAGAACGTCTGCTTTCCCCAGCCAGCATGTGAAG                         GACAAATGGGGGAAAAATCTCTACTTAGCTTCCATTTGCTATGGAAGAACG
genomic: AAACACAGGAGACTCTAAGAACGTCTGCTTTCCCCAGCCAGCATGTGAAGgtaacttgat ... atgtttacagGACAAATGGGGGAAAAATCTCTACTTAGCTTCCATTTGCTATGGAAGAACG
EST: gi|30031897|gb|CB833748.1|CB833748
EST:     AAACACAGGAGACTCTAAGAACGTCTGCTTTCCCCAGCCAGCATGTGAAG                         GACAAATGGGGGAAAAATCTCTACTTAGCTTCCATTTGCTATGGAAGAACG
genomic: AAACACAGGAGACTCTAAGAACGTCTGCTTTCCCCAGCCAGCATGTGAAGgtaacttgat ... atgtttacagGACAAATGGGGGAAAAATCTCTACTTAGCTTCCATTTGCTATGGAAGAACG
EST: gi|71756720|gb|DR954657.1|DR954657
EST:     AAACACAGGAGACTCTAAGAACGTCTGCTTTCCCCAGCCAGCATGTGAAG                         GACAAATGGGGGAAAAATCTCTACTTAGCTTCCATTTGCTATGGAAGAACG
genomic: AAACACAGGAGACTCTAAGAACGTCTGCTTTCCCCAGCCAGCATGTGAAGgtaacttgat ... atgtttacagGACAAATGGGGGAAAAATCTCTACTTAGCTTCCATTTGCTATGGAAGAACG
EST: gi|67013328|gb|CO442077.1|CO442077
EST:     AAACACAGGAGACTCTAAGAACGTCTGCTTTCCCCAGCCAGCATGTGAAG                         GACAAATGGGGGAAAAATCTCTACTTAGCTTCCATTTGCTATGGAAGAACG
genomic: AAACACAGGAGACTCTAAGAACGTCTGCTTTCCCCAGCCAGCATGTGAAGgtaacttgat ... atgtttacagGACAAATGGGGGAAAAATCTCTACTTAGCTTCCATTTGCTATGGAAGAACG

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: 47 (upstream exon), 47 (downstream exon)
Score: 47

GGATCAGGCAGCGTTTATCTTGAGCATCCCCAAAAGGAAACCTGCTGATGAAACACAGGAGACTCTAAGAACGTCTGCTTTCCCCAGCCAGCATGTGAAGgtaacttgat ... atgtttacagGACAAATGGGGGAAAAATCTCTACTTAGCTTCCATTTGCTATGGAAGAACGGTGTCATGAGGTCTGCCCAGTTTGGCTGGGGCACACTGTAGAGTTTATT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 85

GGATCAGGCAGCGTTTATCTTGAGCATCCCCAAAAGGAAACCTGCTGATGAAACACAGGAGACTCTAAGAACGTCTGCTTTCCCCAGCCAGCATGTGAAGgtaacttgat ... atgtttacagGACAAATGGGGGAAAAATCTCTACTTAGCTTCCATTTGCTATGGAAGAACGGTGTCATGAGGTCTGCCCAGTTTGGCTGGGGCACACTGTAGAGTTTATT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 42

GGATCAGGCAGCGTTTATCTTGAGCATCCCCAAAAGGAAACCTGCTGATGAAACACAGGAGACTCTAAGAACGTCTGCTTTCCCCAGCCAGCATGTGAAGgtaacttgat ... atgtttacagGACAAATGGGGGAAAAATCTCTACTTAGCTTCCATTTGCTATGGAAGAACGGTGTCATGAGGTCTGCCCAGTTTGGCTGGGGCACACTGTAGAGTTTATT


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 17

GGATCAGGCAGCGTTTATCTTGAGCATCCCCAAAAGGAAACCTGCTGATGAAACACAGGAGACTCTAAGAACGTCTGCTTTCCCCAGCCAGCATGTGAAGgtaacttgat ... atgtttacagGACAAATGGGGGAAAAATCTCTACTTAGCTTCCATTTGCTATGGAAGAACGGTGTCATGAGGTCTGCCCAGTTTGGCTGGGGCACACTGTAGAGTTTATT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtctaaacctcagatcgaacatccatttgcacttgctaatgatatgtttacagGACAAATGGGGGAAAAATCTCTACTTAGCTTCCATTTGCTATGGAAGAACGGTGTCATGAGGTCTGCCCAGTTTGGCTGGGGCACACTGTAGAGTTTATT
                                   tgctaat  putative branch site (score: 17)
                                      taatgatatgttta  TA-rich tract