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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taaatttctgctgtctctgtttcatgagcagcacatccttctacatctattgttttctgattaccatactctaagtttggccttgcaattttaatttcagTTAGAATGCTCAGGGAAGAGTTGCAGTTGCTTCAAGAGCCTGGCTCATATGTTGGTGAGGTGGTGAAGGTCATGGGGAAATCAAAGGTTCTGGTGAAG

Basic information

species Zea mays
transcript GRMZM2G137528_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G137528_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g11050.1 (Oryza sativa), 3'ss of exon 1
------taaatttctgctgtctctgtttcatgagcagcacatccttctacatctattgttttctgattaccatactctaagtttggccttgcaattttaattt-cagTTAGAATGCTCAGGGAAGAGTTGCAGTTGCTTCAAGAGCCTGGCTCATATGTTGGTGAGGTGGTGAAGGTCATGGGGAAATCAAAGGTTCTGGTGAAG
      |  |||| ||  || |||  || |||      | ||  |     |||| ||  ||  | | ||     |||||| | ||    |||||||| |  || ||||||||||||||||||||||| |||||||||||||||| |||||||| ||||||||||||||||||||||||||||| |||||||||||||| ||||||
ctatccttgatttgtggagt-tctacttgatgcatgtgaaatgtt-----atctttttcttctttactatttccctctaaatatg-ttgtgcaatttcatcttgcagTTAGAATGCTCAGGGAAGAGCTGCAGTTGCTTCAAGAACCTGGCTCGTATGTTGGTGAGGTGGTGAAGGTCATGGGTAAATCAAAGGTTCTAGTGAAG

upper sequence: GRMZM2G137528_T02 (Zea mays), 3'ss of exon 1
lower sequence: Vv04s0008g04690.t01 (Vitis vinifera), 3'ss of exon 1
taaatttctgctgtctctgtttcatgagcagcacatccttctacatctattgttttctgatta---ccatactctaagt--ttggccttg-caattttaatttcagTTAGAATGCTCAGGGAAGAGTTGCAGTTGCTTCAAGAGCCTGGCTCATATGTTGGTGAGGTGGTGAAGGTCATGGGGAAATCAAAGGTTCTGGTGAAG
    |  | | ||      |  ||| || |   | |  ||      |||||  || ||    |     | | | | | |  |   |||||    | |||  |||||| || |||||||| ||||| |||||| |||||||||||||||| |||||||||||||| || || || || ||||| ||||| |||||| |||| |||
--ggtcacagttgc----atagcattaggaattcttttttgctttcctattccttactagaaaaattgaaattttgattaatgaaccttggtggtgttacattcagTGAGGATGCTCAGAGAAGAATTGCAGCTGCTTCAAGAGCCTGGATCATATGTTGGTGAAGTAGTCAAAGTTATGGGAAAATCGAAGGTTTTGGTTAAG

upper sequence: GRMZM2G137528_T02 (Zea mays), 3'ss of exon 1
lower sequence: Vv09s0002g05800.t01 (Vitis vinifera), 3'ss of exon 1
---taaatttctgctgtctctgtttcatgagcagcacatccttctacatctattgttttctgattaccatactctaagtttggccttgcaattttaatttcagTTAGAATGCTCAGGGAAGAGTTGCAGTTGCTTCAAGAGCCTGGCTCATATGTTGGTGAGGTGGTGAAGGTCATGGGGAAATCAAAGGTTCTGGTGAAG
    | ||| ||| | |     ||     || |  | |  |||     |||     ||   |  |    ||   |         | |  | |||||||  |||| || ||||| || |||||||||||  | ||||| |||||||| |||||||||||||| || || || || |||||||| ||||||||  | || |||
gaccagattactgttctaagaattcagccagtaataaaatcttgagtttcttcaactt---gggtggtttatgatgttcacatgcatatatttttaatgacagTGAGGATGCTTAGAGAAGAGTTGCAACTTCTTCAGGAGCCTGGATCATATGTTGGTGAAGTTGTCAAAGTTATGGGGAAGTCAAAGGTCTTAGTTAAG

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|32828073|gb|CD967751.1|CD967751
EST:     CCACAACCTCAACCGTCTCGAGGCCCAGCGCAATGACCTCAACTCCCGAG                         TTAGAATGCTCAGGGAAGAGTTGCAGTTGCTTCAAGAGCCTGGCTCATATG
genomic: CCACAACCTCAACCGTCTCGAGGCCCAGCGCAATGACCTCAACTCCCGAGgtagcatttc ... ttaatttcagTTAGAATGCTCAGGGAAGAGTTGCAGTTGCTTCAAGAGCCTGGCTCATATG
EST: gi|211028259|gb|FL437884.1|FL437884
EST:     CCACAACCTCAACCGTCTCGAGGCCCAGCGCAATGACCTCAACTCCCGAG                         TTAGAATGCTCAGGGAAGAGTTGCAGTTGCTTCAAGAGCCTGGCTCATATG
genomic: CCACAACCTCAACCGTCTCGAGGCCCAGCGCAATGACCTCAACTCCCGAGgtagcatttc ... ttaatttcagTTAGAATGCTCAGGGAAGAGTTGCAGTTGCTTCAAGAGCCTGGCTCATATG
EST: gi|32805431|gb|CD957665.1|CD957665
EST:     CCACAACCTCAACCGTCTCGAGGCCCAGCGCAATGACCTCAACTCCCGAG                         TTAGAATGCTCAGGGAGGAGTTGCAGTTGCTTCAAGAGCCTGGCTCATATG
genomic: CCACAACCTCAACCGTCTCGAGGCCCAGCGCAATGACCTCAACTCCCGAGgtagcatttc ... ttaatttcagTTAGAATGCTCAGGGAAGAGTTGCAGTTGCTTCAAGAGCCTGGCTCATATG
EST: gi|9742895|gb|BE519043.1|BE519043
EST:     CTATATTCTCAACCGTCTCGAGGCCCAGCGCAATGACCTCAACTCCCGAG                         TTAGAATGCTCAGGGAAGAGTTGCAGTTGCTTCAAGAGCCTGGCTCATATG
genomic: CCACAACCTCAACCGTCTCGAGGCCCAGCGCAATGACCTCAACTCCCGAGgtagcatttc ... ttaatttcagTTAGAATGCTCAGGGAAGAGTTGCAGTTGCTTCAAGAGCCTGGCTCATATG
EST: gi|32827753|gb|CD967431.1|CD967431
EST:     CCACAACCTCAACCGTCTCGAGGCCCAGCGCAATGACCTCAACTCCCGAG                         TTAGAATGCTCAGGGAAGAGTTGCAGTTGCTCCAAGAGCCTGGCTCATATG
genomic: CCACAACCTCAACCGTCTCGAGGCCCAGCGCAATGACCTCAACTCCCGAGgtagcatttc ... ttaatttcagTTAGAATGCTCAGGGAAGAGTTGCAGTTGCTTCAAGAGCCTGGCTCATATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctattgttttctgattaccatactctaagtttggccttgcaattttaatttcagTTAGAATGCTCAGGGAAGAGTTGCAGTTGCTTCAAGAGCCTGGCTCATATGTTGGTGAGGTGGTGAAGGTCATGGGGAAATCAAAGGTTCTGGTGAAG
                                           ttttaat  putative branch site (score: 3)
                                     ttgcaattttaattt  TA-rich tract