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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGGACTATGTGTACCCTTACTCACCATAAAAAGTCTGTCCGAGCTATGGCGCTTCATCCAAAGGAgtaattttttattcatgatttgattttcaatattgactacaatgttatggacccttatatagcaacccttttttcag

Basic information

species Zea mays
transcript GRMZM2G017089_T01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017089_T01 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os03g21990.1 (Oryza sativa), 5'ss of exon 14
GGAGGACTATGTGTACCCTTACTCACCATAAAAAGTCTGTCCGAGCTATGGCGCTTCATCCAAAGGAgtaattttttat----tcatgatttgattttcaatattgactacaatgttatggacccttatatagcaacccttttttcag
| |||||||||||||| ||||| || ||||| || || || || ||||||||||| |||||||| |||| | |||  ||    | |   ||| ||  |   || |  ||||  || |    |   |||||          || | |||
GAAGGACTATGTGTACTCTTACACATCATAAGAAATCAGTTCGGGCTATGGCGCTGCATCCAAAAGAgttagtttcaatgccattaaattttcatactatctagtatctaccctgctggaaataattataattttttttcttgtgcag
















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|78021762|gb|DV490149.1|DV490149
EST:     CTTACTCACCATAAAAAGTCTGTCCGAGCTATGGCGCTTCATCCAAAGGA                         GAAAGCATTTGCATCAGCATCAGCAGACAACGTAAAGAAGTTTAACCTTCC
genomic: CTTACTCACCATAAAAAGTCTGTCCGAGCTATGGCGCTTCATCCAAAGGAgtaatttttt ... cttttttcagGAAAGCATTTGCATCAGCATCAGCAGACAACGTAAAGAAGTTTAACCTTCC
EST: gi|148951459|gb|EC897184.2|EC897184
EST:     AAAGTCTGTTCGAGCTATGGCGCTTCATCCAAAGGA                         GAAAGCATTTGCATCAGCATCAGCAGACAACGTAAAGAAGTTTAACCTTCC
genomic: AAAGTCTGTCCGAGCTATGGCGCTTCATCCAAAGGAgtaatttttt ... cttttttcagGAAAGCATTTGCATCAGCATCAGCAGACAACGTAAAGAAGTTTAACCTTCC
EST: gi|37376961|gb|CF625047.1|CF625047
EST:     TCTGTCCGAGCTATGGCGCTTCATCCAAAGGA                         GAAAGCATTTGCATCAGCATCAGCAGACAACGTAAAGAAGTTTAACCTTCC
genomic: TCTGTCCGAGCTATGGCGCTTCATCCAAAGGAgtaatttttt ... cttttttcagGAAAGCATTTGCATCAGCATCAGCAGACAACGTAAAGAAGTTTAACCTTCC
EST: gi|116814103|gb|EC856623.1|EC856623
EST:     CTTACTCACCATAAAAAGTCTGTCCGAGCTATGGCGCTTCATCCAAAGGA                         GAAGGCATTTGCATCAGCATCAGCAGACAACGTAAAGAAGTTTAACCTTCC
genomic: CTTACTCACCATAAAAAGTCTGTCCGAGCTATGGCGCTTCATCCAAAGGAgtaatttttt ... cttttttcagGAAAGCATTTGCATCAGCATCAGCAGACAACGTAAAGAAGTTTAACCTTCC
EST: gi|71432304|gb|DR813354.1|DR813354
EST:     CTTACTCACCATAAAAAGTCTGTCCGAGCTATGGCGCTTCATCCAAAGGA                         GAAAGCATTTGCATCAGCATCAGCAGACAACGTAAAGAAGTTTAACCTTCC
genomic: CTTACTCACCATAAAAAGTCTGTCCGAGCTATGGCGCTTCATCCAAAGGAgtaatttttt ... cttttttcagGAAAGCATTTGCATCAGCATCAGCAGACAACGTAAAGAAGTTTAACCTTCC
EST: gi|31406178|gb|CD484910.1|CD484910
EST:     AAAAAGTCTGTCCGAGCTATGGCGCTTCATCCAAAGGA                         GAAAGCATTTGCATCAGCATCAGCAGACAACGTAAAGAAGTTTAACCTTCC
genomic: AAAAAGTCTGTCCGAGCTATGGCGCTTCATCCAAAGGAgtaatttttt ... cttttttcagGAAAGCATTTGCATCAGCATCAGCAGACAACGTAAAGAAGTTTAACCTTCC
EST: gi|32933315|gb|CF038127.1|CF038127
EST:     CTTACTCACCATAAAAAGTCTGTCCGAGCTATGGCGCTTCATCCAAAGGA                         GAAAGCATTTGCATCAGCATCAGCAGACAACGTAAAGAAGTTTAACCTTCC
genomic: CTTACTCACCATAAAAAGTCTGTCCGAGCTATGGCGCTTCATCCAAAGGAgtaatttttt ... cttttttcagGAAAGCATTTGCATCAGCATCAGCAGACAACGTAAAGAAGTTTAACCTTCC
EST: gi|60357310|gb|DN224283.1|DN224283
EST:     CTTACTCACCATAAAAAGTCTGTCCGAGCTATGGCGCTTCATCCAAAGGA                         GAAAGCATTTGCATCAGCATCAGCAGACAACGTAAAGAAGTTTAACCTTCC
genomic: CTTACTCACCATAAAAAGTCTGTCCGAGCTATGGCGCTTCATCCAAAGGAgtaatttttt ... cttttttcagGAAAGCATTTGCATCAGCATCAGCAGACAACGTAAAGAAGTTTAACCTTCC
EST: gi|93012802|gb|EB638322.1|EB638322
EST:     CTTACTCACCATAAAAAGTCTGTCCGAGCTATGGCGCTTCATCCAAAGGA                         GAAAGCATTTGCATCAGCATCAGCAGACAACGTAAAGAAGTTTAACCTTCC
genomic: CTTACTCACCATAAAAAGTCTGTCCGAGCTATGGCGCTTCATCCAAAGGAgtaatttttt ... cttttttcagGAAAGCATTTGCATCAGCATCAGCAGACAACGTAAAGAAGTTTAACCTTCC
EST: gi|110491423|gb|EE013510.1|EE013510
EST:     CTTACTCCCCATAAAAAGTCTGTCCGAGCTATGGCGCTTCATCCAAAGGA                         GAAAGCATTTGCATCAGCATCAGCAGACAACGTAAAGAAGTTTAACCTTCC
genomic: CTTACTCACCATAAAAAGTCTGTCCGAGCTATGGCGCTTCATCCAAAGGAgtaatttttt ... cttttttcagGAAAGCATTTGCATCAGCATCAGCAGACAACGTAAAGAAGTTTAACCTTCC
EST: gi|6538870|gb|AW225009.1|AW225009
EST:     TCATCCAAAGGA                         GAAAGC-TTTGCATCAGCATCAGCAGNCAACGTAAAGAAGTTTAACCTTCC
genomic: TCATCCAAAGGAgtaatttttt ... cttttttcagGAAAGCATTTGCATCAGCATCAGCAGACAACGTAAAGAAGTTTAACCTTCC
EST: gi|71757914|gb|DR955851.1|DR955851
EST:     CTTACTCACCATAAAAAGTCTGTCCGAGCTATGGCGCTTCATCCAAAGGA                         GAAAGCATTTGCATCAGCATCAGCAGACAACGTAAAGAAGTTTAACCTTCC
genomic: CTTACTCACCATAAAAAGTCTGTCCGAGCTATGGCGCTTCATCCAAAGGAgtaatttttt ... cttttttcagGAAAGCATTTGCATCAGCATCAGCAGACAACGTAAAGAAGTTTAACCTTCC
EST: gi|33093989|gb|CF053983.1|CF053983
EST:     AGCTATGGCGCTTCATCCAAAGGA                         GAAAGCATTTGCATCAGCATCAGCAGACAACGTAAAGAAGTTTAACCTTCC
genomic: AGCTATGGCGCTTCATCCAAAGGAgtaatttttt ... cttttttcagGAAAGCATTTGCATCAGCATCAGCAGACAACGTAAAGAAGTTTAACCTTCC
EST: gi|211016045|gb|FL237689.1|FL237689
EST:     CTTACTCACCATAAAAAGTCTGTCCGAGCTATGGCGCTTCATCCAAAGGA                         GAAAGCATTTGCATCAGCATCAGCAGACAACGTAAAGAAGTTTAACCTTCC
genomic: CTTACTCACCATAAAAAGTCTGTCCGAGCTATGGCGCTTCATCCAAAGGAgtaatttttt ... cttttttcagGAAAGCATTTGCATCAGCATCAGCAGACAACGTAAAGAAGTTTAACCTTCC
EST: gi|148950912|gb|EC896542.2|EC896542
EST:     CTTACTCACCATAAAAAGTCTGTCCGAGCTATGGCGCTTCATCCAAAGGA                         GAAAGCATTTGCATCAGCATCAGCAGACAACGTAAAGAAGTTTAACCTTCC
genomic: CTTACTCACCATAAAAAGTCTGTCCGAGCTATGGCGCTTCATCCAAAGGAgtaatttttt ... cttttttcagGAAAGCATTTGCATCAGCATCAGCAGACAACGTAAAGAAGTTTAACCTTCC
EST: gi|37382890|gb|CF628417.1|CF628417
EST:     AAAAAGTCTGTCCGAGCTATGGCGCTTCATCCAAAGGA                         GAAAGCA-TTGCTATCAGCATCAGCAGACAACGTAAAGAAGTTTAACCTTC
genomic: AAAAAGTCTGTCCGAGCTATGGCGCTTCATCCAAAGGAgtaatttttt ... cttttttcagGAAAGCATTTGC-ATCAGCATCAGCAGACAACGTAAAGAAGTTTAACCTTC
EST: gi|148943610|gb|EC888673.2|EC888673
EST:     CTTACTCACCATAAAAAGTCTGTCCGAGCTATGGCGCTTCATCCAAAGGA                         GAAAGCATTTGCATCAGCATCAGCAGACAACGTAAAGAAGTTTAACCTTCC
genomic: CTTACTCACCATAAAAAGTCTGTCCGAGCTATGGCGCTTCATCCAAAGGAgtaatttttt ... cttttttcagGAAAGCATTTGCATCAGCATCAGCAGACAACGTAAAGAAGTTTAACCTTCC
EST: gi|71432303|gb|DR813353.1|DR813353
EST:     CTTACTCACCATAAAAAGTCTGTCCGAGCTATGGCGCTTCATCCAAAGGA                         GAAAGCATTTGCATCAGCATCAGCAGACAACGTAAAGAAGTTTAACCTTCC
genomic: CTTACTCACCATAAAAAGTCTGTCCGAGCTATGGCGCTTCATCCAAAGGAgtaatttttt ... cttttttcagGAAAGCATTTGCATCAGCATCAGCAGACAACGTAAAGAAGTTTAACCTTCC
EST: gi|33091634|gb|CF051628.1|CF051628
EST:     CTTACTCACCATAAAAAGTCTGTCCGAGCTATGGCGCTTCATCCAAAGGA                         GAAAGCATTTGCATCAGCATCAGCAGACAACGTAAAGAAGTTTAACCTTCC
genomic: CTTACTCACCATAAAAAGTCTGTCCGAGCTATGGCGCTTCATCCAAAGGAgtaatttttt ... cttttttcagGAAAGCATTTGCATCAGCATCAGCAGACAACGTAAAGAAGTTTAACCTTCC
EST: gi|31909551|gb|CD650975.1|CD650975
EST:     CATAAAAAGTCTGTCCGAGCTATGGCGCTTCATCCAAAGGA                         GAAAGCATTTGCATCAGCATCAGCAGACAACGTAAAGAAGTTTAACCTTCC
genomic: CATAAAAAGTCTGTCCGAGCTATGGCGCTTCATCCAAAGGAgtaatttttt ... cttttttcagGAAAGCATTTGCATCAGCATCAGCAGACAACGTAAAGAAGTTTAACCTTCC

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), 49 (downstream exon)
Score: 205

GGAGGACTATGTGTACCCTTACTCACCATAAAAAGTCTGTCCGAGCTATGGCGCTTCATCCAAAGGAgtaatttttt ... cttttttcagGAAAGCATTTGCATCAGCATCAGCAGACAACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 117

GGAGGACTATGTGTACCCTTACTCACCATAAAAAGTCTGTCCGAGCTATGGCGCTTCATCCAAAGGAgtaatttttt ... cttttttcagGAAAGCATTTGCATCAGCATCAGCAGACAACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 97

GGAGGACTATGTGTACCCTTACTCACCATAAAAAGTCTGTCCGAGCTATGGCGCTTCATCCAAAGGAgtaatttttt ... cttttttcagGAAAGCATTTGCATCAGCATCAGCAGACAACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 79

GGAGGACTATGTGTACCCTTACTCACCATAAAAAGTCTGTCCGAGCTATGGCGCTTCATCCAAAGGAgtaatttttt ... cttttttcagGAAAGCATTTGCATCAGCATCAGCAGACAACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCT