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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcctcttcacctgcagcagatcttcatttctattttattattcaaagaattgaggtaatcacgatgattttcctgtttccagGGATGTGACGCAAAGGCAGAGGGAGCTGATAGATGAGTTCGATAAAGAGGAGTGCGCAGACCGGGAAAGACCTGCGGTTGCCTCCGGATGAAGTTTTTGG

Basic information

species Zea mays
transcript GRMZM2G118316_T01
intron # 17
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|148947432|gb|EC892855.2|EC892855
EST:     TCGCCAGTGTTTGGGAATCAGTATGTACACTTCAATATCAGGGTTCCGAC                         GGATGTGACGCAAAGGCAGAGGGAGCTGATAGATGAGTTCGATAAAGAGGA
genomic: TCGCCAGTGTTTGGGAATCAGTATGTACACTTCAATATCAGGGTTCCGACgtatgcctct ... ctgtttccagGGATGTGACGCAAAGGCAGAGGGAGCTGATAGATGAGTTCGATAAAGAGGA
EST: gi|5607883|gb|AI901550.1|AI901550
EST:     TCGCCAGTGTTTGGGAATCAGTATGTACACTTCAATATCAGGGTTCCGAC                         GGAGGTGACGCAAAGGCAGAGGGAGCTGATAGATGAGTTCGATAAAGAGGA
genomic: TCGCCAGTGTTTGGGAATCAGTATGTACACTTCAATATCAGGGTTCCGACgtatgcctct ... ctgtttccagGGATGTGACGCAAAGGCAGAGGGAGCTGATAGATGAGTTCGATAAAGAGGA
EST: gi|149101261|gb|EE187373.2|EE187373
EST:     TCGCCAGTGTTTGGGAATCAGTATGTACACTTCAATATCAGGGTTCCGAC                         GGATGTGACGCAAAGGCAGAGGGAGCTGATAGATGAGTTCGATAAAGAGGA
genomic: TCGCCAGTGTTTGGGAATCAGTATGTACACTTCAATATCAGGGTTCCGACgtatgcctct ... ctgtttccagGGATGTGACGCAAAGGCAGAGGGAGCTGATAGATGAGTTCGATAAAGAGGA
EST: gi|60397506|gb|DN230322.1|DN230322
EST:     TCGCCAGTGTTTGGGAATCAGTATGTACACTTCAATATCAGGGTTCCGAC                         GGATGTGACGCAAAGGCAGAGGGAGCTGATAGATGAGTTCGATAAAGAGGA
genomic: TCGCCAGTGTTTGGGAATCAGTATGTACACTTCAATATCAGGGTTCCGACgtatgcctct ... ctgtttccagGGATGTGACGCAAAGGCAGAGGGAGCTGATAGATGAGTTCGATAAAGAGGA
EST: gi|93017255|gb|EB642775.1|EB642775
EST:     TCGCCAGTGTTTGGGAATCAGTATGTACACTTCAATATCAGGGTTCCGAC                         GGATGTGACGCAAAGGCAGAGGGAGCTGATAGATGAGTTCGATAAAGAGGA
genomic: TCGCCAGTGTTTGGGAATCAGTATGTACACTTCAATATCAGGGTTCCGACgtatgcctct ... ctgtttccagGGATGTGACGCAAAGGCAGAGGGAGCTGATAGATGAGTTCGATAAAGAGGA
EST: gi|71757144|gb|DR955081.1|DR955081
EST:     TCGCCAGTGTTTGGGAATCAGTATGTACACTTCAATATCAGGGTTCCGAC                         GGATGTGACGCAAAGGCAGAGGGAGCTGATAGATGAGTTCGATAAAGAGGA
genomic: TCGCCAGTGTTTGGGAATCAGTATGTACACTTCAATATCAGGGTTCCGACgtatgcctct ... ctgtttccagGGATGTGACGCAAAGGCAGAGGGAGCTGATAGATGAGTTCGATAAAGAGGA
EST: gi|211267316|gb|FL091730.1|FL091730
EST:     TCGCCAGTGTTTGGGAATCAGTATGTACACTTCAATATCAGGGTTCCGAC                         GGATGTGACGCANAGGCAGAGGGAGCTGATAGATGAGTTCGATAAAGAGGA
genomic: TCGCCAGTGTTTGGGAATCAGTATGTACACTTCAATATCAGGGTTCCGACgtatgcctct ... ctgtttccagGGATGTGACGCAAAGGCAGAGGGAGCTGATAGATGAGTTCGATAAAGAGGA
EST: gi|76922540|gb|DV169051.1|DV169051
EST:     TCGCCAGTGTTTGGGAATCAGTATGTACACTTCAATATCAGGGTTCCGAC                         GGATGTGACGCAAAGGCAGAGGGAGCTGATAGATGAGTTCGATAAAGAGGA
genomic: TCGCCAGTGTTTGGGAATCAGTATGTACACTTCAATATCAGGGTTCCGACgtatgcctct ... ctgtttccagGGATGTGACGCAAAGGCAGAGGGAGCTGATAGATGAGTTCGATAAAGAGGA
EST: gi|7135181|gb|AW497971.1|AW497971
EST:     TCGCCAGTGTTTGGGAATCAGTATGTACACTTCAATATCAGGGTTCCGAC                         GGAGGTGACGCAAAGGCAGAGGGAGCTGATAGATGAGTTCGATAAAGAGGA
genomic: TCGCCAGTGTTTGGGAATCAGTATGTACACTTCAATATCAGGGTTCCGACgtatgcctct ... ctgtttccagGGATGTGACGCAAAGGCAGAGGGAGCTGATAGATGAGTTCGATAAAGAGGA
EST: gi|17929416|gb|BM266376.1|BM266376
EST:     TCGCCAGTGTTTGGGAATCAGTATGTACACTTCAATATCAGGGTTCCGAC                         GGATGTGACGCAAAGGCAGAGGGAGCTGATAGATGAGTTCGATAAAGAGGA
genomic: TCGCCAGTGTTTGGGAATCAGTATGTACACTTCAATATCAGGGTTCCGACgtatgcctct ... ctgtttccagGGATGTGACGCAAAGGCAGAGGGAGCTGATAGATGAGTTCGATAAAGAGGA
EST: gi|86469547|gb|DY235917.1|DY235917
EST:     TCGCCAGTGTTTGGGAATCAGTATGTACACTTCAATATCAGGGTTCCGAC                         GGATGTGACGCAAAGGCAGAGGGAGCTGATAGATGAGTTCGATAAAGAGGA
genomic: TCGCCAGTGTTTGGGAATCAGTATGTACACTTCAATATCAGGGTTCCGACgtatgcctct ... ctgtttccagGGATGTGACGCAAAGGCAGAGGGAGCTGATAGATGAGTTCGATAAAGAGGA
EST: gi|60398827|gb|DN231643.1|DN231643
EST:     TCGCCAGTGTTTGGGAATCAGTATGTACACTTCAATATCAGGGTTCCGAC                         GGATGTGACGCAAAGGCAGAGGGAGCTGATAGATGAGTTCGATAAAGAGGA
genomic: TCGCCAGTGTTTGGGAATCAGTATGTACACTTCAATATCAGGGTTCCGACgtatgcctct ... ctgtttccagGGATGTGACGCAAAGGCAGAGGGAGCTGATAGATGAGTTCGATAAAGAGGA
EST: gi|71769071|gb|DR967008.1|DR967008
EST:     TCGCCAGTGTTTGGGAATCAGTATGTACACTTCAATATCAGGGTTCCGAC                         GGATGTGACGCAAAGGCAGAGGGAGCTGATAGATGAGTTCGATAAAGAGGA
genomic: TCGCCAGTGTTTGGGAATCAGTATGTACACTTCAATATCAGGGTTCCGACgtatgcctct ... ctgtttccagGGATGTGACGCAAAGGCAGAGGGAGCTGATAGATGAGTTCGATAAAGAGGA
EST: gi|71427930|gb|DR808980.1|DR808980
EST:     TCGCCAGTGTTTGGGAATCAGTATGTACACTTCAATATCAGGGTTCCGAC                         GGATGTGACGCAAAGGCAGAGGGAGCTGATAGATGAGTTCGATAAAGAGGA
genomic: TCGCCAGTGTTTGGGAATCAGTATGTACACTTCAATATCAGGGTTCCGACgtatgcctct ... ctgtttccagGGATGTGACGCAAAGGCAGAGGGAGCTGATAGATGAGTTCGATAAAGAGGA
EST: gi|211435107|gb|FL442358.1|FL442358
EST:     TCGCCAGTGTTTGGGAATCAGTATGTACACTTCAATATCAGGGTTCCGAC                         GGATGTGACGCAAAGGCAGAGGGAGCTGATAGATGAGTTCGATAAAGAGGA
genomic: TCGCCAGTGTTTGGGAATCAGTATGTACACTTCAATATCAGGGTTCCGACgtatgcctct ... ctgtttccagGGATGTGACGCAAAGGCAGAGGGAGCTGATAGATGAGTTCGATAAAGAGGA
EST: gi|6022509|gb|AW067542.1|AW067542
EST:     TCGCCAGTGTTTGGGAATCAGTATGTACACTTCAATATCAGGGTTCCGAC                         GGAGGTGACGCAAAGGCAGAGGGAGCTGATAGATGAGTTCGATAAAGAGGA
genomic: TCGCCAGTGTTTGGGAATCAGTATGTACACTTCAATATCAGGGTTCCGACgtatgcctct ... ctgtttccagGGATGTGACGCAAAGGCAGAGGGAGCTGATAGATGAGTTCGATAAAGAGGA
EST: gi|37397730|gb|CF636173.1|CF636173
EST:     TCGCCAGTGTTTGGGAATCAGTATGTACACTTCAATATCAGGGTTCCGAC                         GGAGGTGACGCAAAGGCAGAGGGAGCTGATAGATGAGTTCGATAAAGAGGA
genomic: TCGCCAGTGTTTGGGAATCAGTATGTACACTTCAATATCAGGGTTCCGACgtatgcctct ... ctgtttccagGGATGTGACGCAAAGGCAGAGGGAGCTGATAGATGAGTTCGATAAAGAGGA
EST: gi|148940825|gb|EC885654.2|EC885654
EST:     TCGCCAGTGTTTGGGAATCAGTATGTACACTTCAATATCAGGGTTCCGAC                         GGATGTGACGCAAAGGCAGAGGGAGCTGATAGATGAGTTCGATAAAGAGGA
genomic: TCGCCAGTGTTTGGGAATCAGTATGTACACTTCAATATCAGGGTTCCGACgtatgcctct ... ctgtttccagGGATGTGACGCAAAGGCAGAGGGAGCTGATAGATGAGTTCGATAAAGAGGA
EST: gi|67040336|gb|CO466591.1|CO466591
EST:     TCGCCAGTGTTTGGGAATCAGTATGTACACTTCAATATCAGGGTTCCGAC                         GGAGGTGACGCAAAGGCAGAGGGAGCTGATAGATGAGTTCGATAAAGAGGA
genomic: TCGCCAGTGTTTGGGAATCAGTATGTACACTTCAATATCAGGGTTCCGACgtatgcctct ... ctgtttccagGGATGTGACGCAAAGGCAGAGGGAGCTGATAGATGAGTTCGATAAAGAGGA
EST: gi|40337178|gb|CK371248.1|CK371248
EST:     TCGCCAGTGTTTGGGAATCAGTATGTACACTTCAATATCAGGGTTCCGAC                         GGAGGTGACGCAAAGGCAGAGGGAGCTGATAGATGAGTTCGATAAAGAGGA
genomic: TCGCCAGTGTTTGGGAATCAGTATGTACACTTCAATATCAGGGTTCCGACgtatgcctct ... ctgtttccagGGATGTGACGCAAAGGCAGAGGGAGCTGATAGATGAGTTCGATAAAGAGGA

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: 141

GAATAAAAGCGAGGAACTCGCCAGTGTTTGGGAATCAGTATGTACACTTCAATATCAGGGTTCCGACgtatgcctct ... ctgtttccagGGATGTGACGCAAAGGCAGAGGGAGCTGATAGATGAGTTCGATAAAGAGGAGTGCGCAGACCGGGAAAGACCTGCGGTTGCCTCCGGATGAAGTTTTTGG


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

GAATAAAAGCGAGGAACTCGCCAGTGTTTGGGAATCAGTATGTACACTTCAATATCAGGGTTCCGACgtatgcctct ... ctgtttccagGGATGTGACGCAAAGGCAGAGGGAGCTGATAGATGAGTTCGATAAAGAGGAGTGCGCAGACCGGGAAAGACCTGCGGTTGCCTCCGGATGAAGTTTTTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 182

GAATAAAAGCGAGGAACTCGCCAGTGTTTGGGAATCAGTATGTACACTTCAATATCAGGGTTCCGACgtatgcctct ... ctgtttccagGGATGTGACGCAAAGGCAGAGGGAGCTGATAGATGAGTTCGATAAAGAGGAGTGCGCAGACCGGGAAAGACCTGCGGTTGCCTCCGGATGAAGTTTTTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 68

GAATAAAAGCGAGGAACTCGCCAGTGTTTGGGAATCAGTATGTACACTTCAATATCAGGGTTCCGACgtatgcctct ... ctgtttccagGGATGTGACGCAAAGGCAGAGGGAGCTGATAGATGAGTTCGATAAAGAGGAGTGCGCAGACCGGGAAAGACCTGCGGTTGCCTCCGGATGAAGTTTTTGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctattttattattcaaagaattgaggtaatcacgatgattttcctgtttccagGGATGTGACGCAAAGGCAGAGGGAGCTGATAGATGAGTTCGATAAAGAGGAGTGCGCAGACCGGGAAAGACCTGCGGTTGCCTCCGGATGAAGTTTTTGG
                                        ttttcctgtttcc  CT-rich tract
     ttttattattcaaaga  TA-rich tract