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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggctacttttagtgtatttacgcagtgtttaaacttgaacaatgttctgctctgctgttgatctacattatttcaaattgcttatttctgaatacattaaattcagCCTACCATTCATTACTGCTACTGCTGATGGGCCAAAACACATCGAGGCAACCCTCTCGAGAGCCAAATTCGAGGAACTATGTTCAGACCTTATAGACAG

Basic information

species Zea mays
transcript GRMZM2G001500_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G001500_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os12g14070.1 (Oryza sativa), 3'ss of exon 4
gtaggctacttttagtgtatttacgcagtgtttaaacttgaacaatgttctgctctgctgttgatctacattatttcaaattgcttatttctgaatacattaaatt-cagCCTACCATTCATTACTGCTACTGCTGATGGGCCAAAACACATCGAGGCAACCCTCTCGAGAGCCAAATTCGAGGAACTATGTTCAGACCTTATAGACAG
||  ||| ||||     | ||  | ||| || |            | |  |||||   || |||| |   || ||  ||||   |       ||||   || |||| |||| | || ||||| |||||||||||||||||||| |||||||||||| |||| ||||| ||||||||||| ||||| |||||||| ||||| || || ||
gtgagcttctttccaattgttctcacagagtat------------tctattgctcatttggtgatttttcttctt--aaataatt-------gaatgtcttgaattgcagCTTGCCTTTCATAACTGCTACTGCTGATGGGCCTAAACACATCGAGACAACTCTCTCCAGAGCCAAATTTGAGGAGCTATGTTCGGACCTCATTGATAG

upper sequence: GRMZM2G001500_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv17s0000g03310.t01 (Vitis vinifera), 3'ss of exon 4
gtaggctacttttagtgtatttacgcagtgtttaaacttgaacaatgttctgctctgctgttgatctacattatttcaaattgcttatttctgaatacattaaattcagCCTACCATTCATTACTGCTACTGCTGATGGGCCAAAACACATCGAGGCAACCCTCTCGAGAGCCAAATTCGAGGAACTATGTTCAGACCTTATAGACAG
      ||  || | ||| | |   | |  | |  |     | ||   |||  |||  |    || |  | |  |  ||||| ||  |||              | |||| | || ||||||||||| ||||| ||||| || |||||||||||| | |||||  | || |||||||| |||||| ||||||| ||| |  | || ||
-----gtatgttgattgtctgtctactgcctattgat---gataaaactct-ttctcatacctattttaactgatagaaatttctgtttt--------------tccagCTTGCCGTTCATTACTGCCACTGCAGATGGACCCAAACACATCGAGACTACCCTTACAAGGGCCAAATTTGAGGAATTATGTTCTGACTTACTTGATAG
















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|91875430|gb|EB405387.1|EB405387
EST:     GCAGAGAAAGCTAAGATGGAACTGTCAACGCTGACACAGGCAAATATTAG                         CCTACCATTCATTACTGCTACTGCTGATGGGCCAAAACACATCGAGGCAAC
genomic: GCAGAGAAAGCTAAGATGGAACTGTCAACGCTGACACAGGCAAATATTAGgtaggctact ... ttaaattcagCCTACCATTCATTACTGCTACTGCTGATGGGCCAAAACACATCGAGGCAAC
EST: gi|211323721|gb|FL059667.1|FL059667
EST:     GCAGAGAAAGCTAAGATGGAACTGTCAACGCTGACACAGGCAAATATTAG                         CCTACCATTCATTACTGCTACTGCTGATGGGCCAAAACACATCGAGGC
genomic: GCAGAGAAAGCTAAGATGGAACTGTCAACGCTGACACAGGCAAATATTAGgtaggctact ... ttaaattcagCCTACCATTCATTACTGCTACTGCTGATGGGCCAAAACACATCGAGGC
EST: gi|211323718|gb|FL059664.1|FL059664
EST:     GCAGAGAAAGCTAAGATGGAACTGTCAACGCTGACACAGGCAAATATTAG                         CCTACCATTCATTACTGCTACTGCTGATGGGCCAAAACACATCGAGGCAAC
genomic: GCAGAGAAAGCTAAGATGGAACTGTCAACGCTGACACAGGCAAATATTAGgtaggctact ... ttaaattcagCCTACCATTCATTACTGCTACTGCTGATGGGCCAAAACACATCGAGGCAAC
EST: gi|211323719|gb|FL059665.1|FL059665
EST:     GCAGAGAAAGCTAAGATGGAACTGTCAACGCTGACACAGGCAAATATTAG                         CCTACCATTCATTACTGCTACTGCTGATGGGCCAA
genomic: GCAGAGAAAGCTAAGATGGAACTGTCAACGCTGACACAGGCAAATATTAGgtaggctact ... ttaaattcagCCTACCATTCATTACTGCTACTGCTGATGGGCCAA
EST: gi|211323722|gb|FL059668.1|FL059668
EST:     GCAGAGAAAGCTAAGATGGAACTGTCAACGCTGACACAGGCAAATATTAG                         CCTACCATTCATTACTGCTACTGCTGATGGGCCAAAACACATCGAGGCAA
genomic: GCAGAGAAAGCTAAGATGGAACTGTCAACGCTGACACAGGCAAATATTAGgtaggctact ... ttaaattcagCCTACCATTCATTACTGCTACTGCTGATGGGCCAAAACACATCGAGGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgctgttgatctacattatttcaaattgcttatttctgaatacattaaattcagCCTACCATTCATTACTGCTACTGCTGATGGGCCAAAACACATCGAGGCAACCCTCTCGAGAGCCAAATTCGAGGAACTATGTTCAGACCTTATAGACAG
    tgttgat  putative branch site (score: 4)
                              ttatttctgaatacat  TA-rich tract