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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttgcatacatactgctagcttccatgcatgcatgtgccttactattctcacgcactgtgtggccgcctggacatgcatggttggatactctggatcagATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACCGCAAGTACCCCAACGGAGCGCGGCCGAACAGGGCGGCGACGTCCGGCTA

Basic information

species Zea mays
transcript GRMZM2G179885_T04
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G179885_T04 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os07g37920.1 (Oryza sativa), 3'ss of exon 1
--ctttgcatacatactgctagcttccatgcatgcatgtgccttactattctcacgcact-gtgtg-gccgcctggacatgcatggttggatactctggatcagATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACCGCAAGTACCCCAACGGAGCGCGGCCGAACAGGGCGGCGACGTCCGGCTA
    ||| ||   || |||| | | | ||  ||  ||    |   ||  | ||    ||| || || ||    |   | ||||||  | | |    || |||||| |||||||  ||||| |||||||||||||| ||||||||||||||||||||||||||||| ||||| |||||||||||| ||||||||||||| || ||
tagcttggatgtgtagtgctcgat-cgatcgatcgatcgatcgatctggtgtcgtttacttgtttgtgcgatttatgcgtgcatgcatcggt---ttgtatcagAGAAGGCGAACTTCGGGGAGCAGGAGTGGTATTTCTTCAGCCCGAGGGACCGCAAGTACCCGAACGGGGCGCGGCCGAACCGGGCGGCGACGTCGGGGTA

upper sequence: GRMZM2G179885_T04 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA13G35560.1 (Glycine max), 3'ss of exon 1
-----------------------------------ctttgcatacatactgctagcttccatgcatgcatgtgccttactattct----cacgcactgtgtggccgcctggacatgcatggttggatac-tctggat--cagATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACCGCAAGTACCCCAACGGAGCGCGGCCGAACAGGGCGGCGACGTCCGGCTA
                                    |     |  |   |   | ||   |||  |   | |  |||  |||| |     |   ||| | ||      |    ||   |  ||   |   | ||| |  ||| ||||||  | || || |||||||||||||| ||||| |  ||||||||| | ||||| || ||||| ||| |||| |||||||||||||| || || ||
gtatgttcttcaatttcatccaacgaatcaaaagattcaaactttacgttcaaaactcaaatgggtttgttttactttttattttgtattatttactttttgtatttattatgatttttctttatttttgtgtggttggcagCTAAGGCCGCGTTTGGGGAGCAGGAGTGGTATTTCTTTACTCCGAGGGACAGGAAGTATCCGAACGGCGCGAGGCCAAACAGGGCGGCGACATCTGGGTA

upper sequence: GRMZM2G179885_T04 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA12G34990.1 (Glycine max), 3'ss of exon 1
--------------------------------ctttgcatacatactgctagcttcca---tgcatgcatgtgccttactattctcacgcactgtgtggccgcctggacatgcatggttggatactctggatcagATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACCGCAAGTACCCCAACGGAGCGCGGCCGAACAGGGCGGCGACGTCCGGCTA
                                |     || || ||| |  | |   |      |||  | ||| ||  | || | |   | | |      |  |   | |  ||  || | |  |    | ||| ||||||  | || || |||||||||||||| ||||| |  ||||||||| | ||||| || ||||| ||| |||| ||||||||||| || || || ||
gtatgttcttcaattaatttcatccaacgaatcaaaagattcaaacttcacgttcaaaactcaaatgggtctgctttgttttttttatttattattattatgatttttc-tttatattttgtttgtggttaacagCTAAGGCCGCGTTTGGGGAGCAGGAGTGGTATTTCTTTACACCGAGGGACAGGAAGTATCCGAACGGCGCGAGGCCAAACAGGGCGGCCACATCAGGGTA

upper sequence: GRMZM2G179885_T04 (Zea mays), 3'ss of exon 2
lower sequence: Vv19s0014g03300.t01 (Vitis vinifera), 3'ss of exon 1
---ctttgcatacatactgctagcttccatgcatgcatgtgccttactat-tctcacgcactgtgtg------gccgcctggacatgcatggttggatactctggat---cagATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACCGCAAGTACCCCAACGGAGCGCGGCCGAACAGGGCGGCGACGTCCGGCTA
     || ||| || ||  |        |||  |     |   | | ||| | | | | | ||| ||      |       || |  |||| |   ||    |  ||   ||| |||||| |  || || || ||||| ||||||||||||||||| || ||||| |||||||| ||||| || ||||| ||  | |||||||| || || ||
gtaacttacat-caaaccccagctaattatgattaagattatgtgattatgtatgatgaattgtatgtaaaaggttagaaagaaagccatgctgatatttgatcaattctcagCTAAGGCCAGTTTTGGAGAACAGGAATGGTACTTCTTCAGCCCTAGAGACCGGAAGTACCCAAACGGGGCTCGGCCTAATCGAGCGGCGACTTCTGGTTA

upper sequence: GRMZM2G179885_T04 (Zea mays), 3'ss of exon 2
lower sequence: Vv00s0375g00040.t01 (Vitis vinifera), 3'ss of exon 1
ctttgcatacatactgctagcttccatgcatgcatgt-gccttactattctcacgcactgtgtggccgcctggacatgcatggttggatactctggatcagATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACCGCAAGTACCCCAACGGAGCGCGGCCGAACAGGGCGGCGACGTCCGGCTA
                 ||  |   |  ||    | | |  || |  || |    |  ||| |     | ||   |||||||| |   |       || || |||||| || || || ||||| ||||||||||||||||| || |||||||| || ||||||||||| || ||||| ||  |||| ||||| || || ||
----------------gtaattcatactcaattgttttgtttttcgttttttgttcgttgttttagtacttgttgatgcatgggtttttgaaaattat-agGTAAGGCTACGTTTGGGGAGCAAGAGTGGTACTTCTTCAGTCCTAGGGACCGGAAATACCCCAACGGCGCACGGCCTAATCGGGCTGCGACTTCTGGGTA

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|148991087|gb|EE032535.2|EE032535
EST:     GGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTA-C-----C-T--G                         ATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACC
genomic: GGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTACCTGGTACGTAAGgtagcgcgcg ... tctggatcagATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACC
EST: gi|149076918|gb|EE165574.2|EE165574
EST:     GGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTA-C-----C-T--G                         ATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACC
genomic: GGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTACCTGGTACGTAAGgtagcgcgcg ... tctggatcagATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACC
EST: gi|148958368|gb|EC904597.2|EC904597
EST:     GGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTA-C-----C-T--G                         ATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACC
genomic: GGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTACCTGGTACGTAAGgtagcgcgcg ... tctggatcagATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACC
EST: gi|71441634|gb|DR822684.1|DR822684
EST:     GGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTACCTGGTACGTAAG                         ATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACC
genomic: GGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTACCTGGTACGTAAGgtagcgcgcg ... tctggatcagATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACC
EST: gi|148991089|gb|EE032537.2|EE032537
EST:     GGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTA-C-----C-T--G                         ATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACC
genomic: GGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTACCTGGTACGTAAGgtagcgcgcg ... tctggatcagATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACC
EST: gi|149099136|gb|EE185159.2|EE185159
EST:     GGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTA-C-----C-T--G                         ATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACC
genomic: GGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTACCTGGTACGTAAGgtagcgcgcg ... tctggatcagATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACC
EST: gi|148941728|gb|EC886680.2|EC886680
EST:     GGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTA-C-----C-T--G                         ATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACC
genomic: GGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTACCTGGTACGTAAGgtagcgcgcg ... tctggatcagATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACC
EST: gi|148931258|gb|EC874064.2|EC874064
EST:     GGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTA-C-----C-T--G                         ATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACC
genomic: GGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTACCTGGTACGTAAGgtagcgcgcg ... tctggatcagATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACC
EST: gi|71435611|gb|DR816661.1|DR816661
EST:     GGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTA-C-----C-T--G                         ATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACC
genomic: GGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTACCTGGTACGTAAGgtagcgcgcg ... tctggatcagATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACC
EST: gi|148969855|gb|EE020751.2|EE020751
EST:     GGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTA-C-----C-T--G                         ATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACC
genomic: GGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTACCTGGTACGTAAGgtagcgcgcg ... tctggatcagATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attctcacgcactgtgtggccgcctggacatgcatggttggatactctggatcagATAAGGCGACATTCGGCGAGCAGGAGTGGTACTTCTTCAGCCCGAGGGACCGCAAGTACCCCAACGGAGCGCGGCCGAACAGGGCGGCGACGTCCGGCTA
 ttctcac  putative branch site (score: 2)