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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtttttgaccatatattttttattgtagttgttctgtttctttagattcatagaccccttggaggcaaccacatgattgtttcaaagagcgtaaggaagttgtattttggcattgatgaaatatcctgtctcagGTTGAGAAGTGGTTGGAGAAGCTGGAAGAAACTGAAATGAGAACCAAACTCTATATTAAGACCTCAATAGTTACAGTGTCAATGATG

Basic information

species Zea mays
transcript GRMZM2G020721_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G020721_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os03g19970.1 (Oryza sativa), 3'ss of exon 9
gtatgtttttgaccatatattttttattgtagttgttctgtttctttagattcatagaccccttggaggcaaccacatgattgtttcaaagagcgtaaggaagttgtattttggcattgatgaaatatcc-----tgtctcagGTTGAGAAGTGGTTGGAGAAGCTGGAAGAAACTGAAATGAGAACCAAACTCTATATTAAGACCTCAATAGTTACAGTGTCAATGATG
                                    |||| ||||||   ||   ||     |  ||| ||     |  |||||      |      ||  | | |||||||  |||  || ||  ||       |||  ||||||||||||||| |||||||||| |||||| |||||| || ||| ||||||||||||||| |||  |||||| || |  |  | | |
------------------------------------tctggttctttcagttttgagggtgtt--gagtcatttgtaaaattgt----gggcatacgagagaatagtatttta-catcaataaatcatttgtttgtgttgcagGTTGAGAAGTGGATGGAGAAGCTTGAAGAAGCTGAAACGAAAACTAAACTCTATATTAAGGCCTTGATAGTTTCAATTGCTTTAACG
















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|5895688|gb|AW036934.1|AW036934
EST:     ATCGCTACATTTGGATTGTGGGGATGATATATGCATATTACCATCCAACT                         GTTGAGAAGTGGTTGGAGAAGCTGGAAGAAACTGAAATGAGAACCAAACTC
genomic: ATCGCTACATTTGGATCGTGGGGATGATATATGCATATTACCATCCAACTgtatgttttt ... cctgtctcagGTTGAGAAGTGGTTGGAGAAGCTGGAAGAAACTGAAATGAGAACCAAACTC
EST: gi|5901242|gb|AW042342.1|AW042342
EST:     ATCGCTACATTTGGATTGTGGGGATGATATATGCATATTACCATCCAACT                         GTTGAGAAGTGGTTGGAGAAGCTGGAAGAAACTGAAATGAGAACCAAACTC
genomic: ATCGCTACATTTGGATCGTGGGGATGATATATGCATATTACCATCCAACTgtatgttttt ... cctgtctcagGTTGAGAAGTGGTTGGAGAAGCTGGAAGAAACTGAAATGAGAACCAAACTC
EST: gi|5847179|gb|AW000258.1|AW000258
EST:     ATGGCTACATTTGGATTGTGGGGATGATATATGCATATTACCATCCAACT                         GTTGAGAAGTGGTTGGAGAAGCTGGAAGAAACTGAAATGAGAACCAAACTC
genomic: ATCGCTACATTTGGATCGTGGGGATGATATATGCATATTACCATCCAACTgtatgttttt ... cctgtctcagGTTGAGAAGTGGTTGGAGAAGCTGGAAGAAACTGAAATGAGAACCAAACTC
EST: gi|5895689|gb|AW036935.1|AW036935
EST:     ATCGCTACATTTGGATCGTGGGGATGATATATGCATATTACCATCCAACT                         GTTGAGAAGTGGTTGGAGAAGCTGGAAGAAACTGAAATGAGAACCAAACTC
genomic: ATCGCTACATTTGGATCGTGGGGATGATATATGCATATTACCATCCAACTgtatgttttt ... cctgtctcagGTTGAGAAGTGGTTGGAGAAGCTGGAAGAAACTGAAATGAGAACCAAACTC
EST: gi|5343255|gb|AI795560.1|AI795560
EST:     ATCGCTACATTTGGATTGTGGGGATGATATATGCATATTACCATCCAACT                         GTTGAGAAGTGGTTGGAGAAGCTGGAAGAAACTGAAATGAGAACCAAACTC
genomic: ATCGCTACATTTGGATCGTGGGGATGATATATGCATATTACCATCCAACTgtatgttttt ... cctgtctcagGTTGAGAAGTGGTTGGAGAAGCTGGAAGAAACTGAAATGAGAACCAAACTC
EST: gi|32936459|gb|CF041278.1|CF041278
EST:     GCATATTACCATCCAACT                         GTCGAGAAGTGGTTGGAGAAGCTGGAAGAAACTGAAATGAGAACCAAACTC
genomic: GCATATTACCATCCAACTgtatgttttt ... cctgtctcagGTTGAGAAGTGGTTGGAGAAGCTGGAAGAAACTGAAATGAGAACCAAACTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcaaagagcgtaaggaagttgtattttggcattgatgaaatatcctgtctcagGTTGAGAAGTGGTTGGAGAAGCTGGAAGAAACTGAAATGAGAACCAAACTCTATATTAAGACCTCAATAGTTACAGTGTCAATGATG
                               cattgat  putative branch site (score: 4)
                                            tcctgtctc  putative PPT
                    ttgtatttt  TA-rich tract