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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgaaaccttctttccaacattcttgtggttgaactttgctatgcaagtgttatttgttactgatttgttcgatcattcaattgcctatgatgtttttagatctgacgacacatcattttttgtttaactgcaacagTGCCGCTGTGTTTCATAATGCAAGCACAAGGTTTTGTGATGGGACGCGTTTTGGGCTAGGTGCTGAG

Basic information

species Zea mays
transcript GRMZM2G028535_T01
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G028535_T02 (Zea mays), 3'ss of exon 17
lower sequence: LOC_Os01g62900.1 (Oryza sativa), 3'ss of exon 17
gtactgaaaccttctttccaacattcttgtggttgaactttgctatgcaagtgttatttgttactgatttgttcgatcattcaattgcctatgatgtttttagatctgacgacacatcattttttgtttaactgcaacagTGCCGCTGTGTTTCATAATGCAAGCACAAGGTTTTGTGATGGGACGCGTTTTGGGCTAGGTGCTGAG
                                           | |  || |  | |   || |  |  | ||   |    |  ||   ||  |  |   |  ||     ||    | ||| ||   | || ||||||||||| || || || ||||||||||||||| |||| ||||||||| | || ||||| ||||||||||||
------------------------------------------gtgtttaactaatttcctttgcacaactattatgtttgccgctt--ttagtacataccttaattaatgga---gttattcttctataaattgcaacagTGCTGCGGTATTCCATAATGCAAGCACACGGTTCTGTGATGGGGCTCGCTTTGGTCTAGGTGCTGAG

upper sequence: GRMZM2G028535_T02 (Zea mays), 3'ss of exon 17
lower sequence: Vv13s0019g02360.t01 (Vitis vinifera), 3'ss of exon 17
gtactgaaaccttctttccaacattcttgtggttgaactttgctatgcaagtgttatttgttactgatttgttcgatcattcaattgcctatgatgtttttagatctgacgacacatcattt--tttgtttaactgcaacagTGCCGCTGTGTTTCATAATGCAAGCACAAGGTTTTGTGATGGGACGCGTTTTGGGCTAGGTGCTGAG
                                       || ||     | |||||  | ||    || |   | ||  |    |     |     | |||| || ||    ||  | || |  ||||| ||  |    |||||| ||||| ||||| ||||| |||||||| |||||||||||| | |||||||| || || || |||
---------------------------------------ttacttccagaatgttagct-ttttaaatatacgcaatgctgttgtctttcacatcttgtttacat-tggtagcaagtaatgtggtttgtgtatat-tggcagTGCTGCTGTCTTTCACAATGCTAGCACAAGATTTTGTGATGGGGCTCGTTTTGGACTTGGGGCCGAG

upper sequence: GRMZM2G028535_T02 (Zea mays), 3'ss of exon 17
lower sequence: PP1S22_40V6.2 (Physcomitrella patens), 3'ss of exon 17
gtactgaaaccttctttccaacattcttgtggttgaactttgctatgcaagtgttatttgttactgat-ttgttcgatcattcaattgcctatgatgtttttagatctgacgacacatcattttttgtttaactgcaacagTGCCGCTGTGTTTCATAATGCAAGCACAAGGTTTTGTGATGGGACGCGTTTTGGGCTAGGTGCTGAG
                                   | |||   |  ||   | |  |||| |  | ||  ||||||   |||  |||     ||   || ||  | |  |  | | |  | |  ||| || | |    |||||||||||| ||||||||||| || ||  | |||| ||||||  | ||||||||||| |||||||||
----------------------------------taccttcattgcgctc-tctcttttgcttgtaatactgttcg--tattgtattcaggctgtcattgttgtaac--attaaataatactgcttgcttcatt--tgcagTGCCGCTGTATTTCATAATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTTTGGGCTTGGTGCTGAG

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|60344250|gb|DN211223.1|DN211223
EST:     ATCACAACTGATAGAAGTGCTGCAGAGGCCTTTCTGCAGCAAGTTGATAG                         TGCCGCTGTGTTTCATAATGCAAGCACAAGGTTTTGTGATGGGACGCGTTT
genomic: ATCACAACTGATAGAAGTGCTGCAGAGGCCTTTCTGCAGCAAGTTGATAGgtactgaaac ... actgcaacagTGCCGCTGTGTTTCATAATGCAAGCACAAGGTTTTGTGATGGGACGCGTTT
EST: gi|67017479|gb|CO446228.1|CO446228
EST:     ATCACAACTGATAGAAGTGCTGCGGAGGCCTTTCTGCAGCAAGTTGATAG                         TGCCGCTGTGTTTCATAATGCAAGCACAAGGTTTTGTGATGGGACGCGTTT
genomic: ATCACAACTGATAGAAGTGCTGCAGAGGCCTTTCTGCAGCAAGTTGATAGgtactgaaac ... actgcaacagTGCCGCTGTGTTTCATAATGCAAGCACAAGGTTTTGTGATGGGACGCGTTT
EST: gi|6564250|gb|AW231872.1|AW231872
EST:     ATCGCAACTGATAGAAGTGCTGCGGAGGCCTTTCTGCAGCAAGTTGATAG                         TGCCGCTGTGTTTCATAATGCAAGCACAAGGTTTTGTGATGGGACGCGTTT
genomic: ATCACAACTGATAGAAGTGCTGCAGAGGCCTTTCTGCAGCAAGTTGATAGgtactgaaac ... actgcaacagTGCCGCTGTGTTTCATAATGCAAGCACAAGGTTTTGTGATGGGACGCGTTT
EST: gi|6022040|gb|AW066983.1|AW066983
EST:     TCTGCAGCAAGTTGATAG                         TGCCGCTGTGTTTCATAATGCAAGCNCAAGGTTTTGTGATGGGACGCGTTT
genomic: TCTGCAGCAAGTTGATAGgtactgaaac ... actgcaacagTGCCGCTGTGTTTCATAATGCAAGCACAAGGTTTTGTGATGGGACGCGTTT
EST: gi|211181079|gb|FL441227.1|FL441227
EST:     ATCACAACTGATAGAAGTGCTGCAGAGGCCTTTCTGCAGCAAGTTGATAG                         TGCCGCTGTGTTTCATAATGCAAGCACAAGGTTTTGTGATGGGACGCGTTT
genomic: ATCACAACTGATAGAAGTGCTGCAGAGGCCTTTCTGCAGCAAGTTGATAGgtactgaaac ... actgcaacagTGCCGCTGTGTTTCATAATGCAAGCACAAGGTTTTGTGATGGGACGCGTTT
EST: gi|60355192|gb|DN222165.1|DN222165
EST:     ATCACAACTGATAGAAGTGCTGCAGAGGCCTTTCTGCAGCAAGTTGATAG                         TGCCGCTGTGTTTCATAATGCAAGCACAAGGTTTTGTGATGGGACGCGTTT
genomic: ATCACAACTGATAGAAGTGCTGCAGAGGCCTTTCTGCAGCAAGTTGATAGgtactgaaac ... actgcaacagTGCCGCTGTGTTTCATAATGCAAGCACAAGGTTTTGTGATGGGACGCGTTT
EST: gi|101391685|gb|EB817779.1|EB817779
EST:     ATCACAACTGATAGAAGTGCTGCAGAGGCCTTTCTGCAGCAAGTTGATAG                         TGCCGCTGTGTTTCATAATGCAAGCACAAGGTTTTGTGATGGGACGCGTTT
genomic: ATCACAACTGATAGAAGTGCTGCAGAGGCCTTTCTGCAGCAAGTTGATAGgtactgaaac ... actgcaacagTGCCGCTGTGTTTCATAATGCAAGCACAAGGTTTTGTGATGGGACGCGTTT
EST: gi|6564119|gb|AW231741.1|AW231741
EST:     AACTGATAGAAGTGCTGCGGAGGCCTTTTTGCAGCAAGTTGATAG                         TGCCGCTGTGTTTCATAATGCAAGCCCAAGGTTTTGTGATGGGACGCGTTT
genomic: AACTGATAGAAGTGCTGCAGAGGCCTTTCTGCAGCAAGTTGATAGgtactgaaac ... actgcaacagTGCCGCTGTGTTTCATAATGCAAGCACAAGGTTTTGTGATGGGACGCGTTT
EST: gi|149066719|gb|EE286860.2|EE286860
EST:     ATCACAACTGATAGAAGTGCTGCAGAGGCCTTTCTGCAGCAAGTTGATAG                         TGCCGCTGTGTTTCATAATGCAAGCACAAGGTTTTGTGATGGGACGCGTTT
genomic: ATCACAACTGATAGAAGTGCTGCAGAGGCCTTTCTGCAGCAAGTTGATAGgtactgaaac ... actgcaacagTGCCGCTGTGTTTCATAATGCAAGCACAAGGTTTTGTGATGGGACGCGTTT
EST: gi|211181077|gb|FL441225.1|FL441225
EST:     ATCACAACTGATAGAAGTGCTGCAGAGGCCTTTCTGCAGCAAGTTGATAG                         TGCCGCTGTGTTTCATAATGCAAGCACAAGGTTTTGTGATGGGACGCGTTT
genomic: ATCACAACTGATAGAAGTGCTGCAGAGGCCTTTCTGCAGCAAGTTGATAGgtactgaaac ... actgcaacagTGCCGCTGTGTTTCATAATGCAAGCACAAGGTTTTGTGATGGGACGCGTTT
EST: gi|61118748|gb|DN559709.1|DN559709
EST:     ATCACAACTGATAAAAGTGCTGCAAAGGCCTTTCTGCAGCAAGTTGATAG                         TGCCGCTGTGTTTCATAATGCAAGCACAAGGTTTTGTGATGGGACGCGTTT
genomic: ATCACAACTGATAGAAGTGCTGCAGAGGCCTTTCTGCAGCAAGTTGATAGgtactgaaac ... actgcaacagTGCCGCTGTGTTTCATAATGCAAGCACAAGGTTTTGTGATGGGACGCGTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcctatgatgtttttagatctgacgacacatcattttttgtttaactgcaacagTGCCGCTGTGTTTCATAATGCAAGCACAAGGTTTTGTGATGGGACGCGTTTTGGGCTAGGTGCTGAG
                                        gtttaac  putative branch site (score: 3)
                              atcattttttgtttaa  TA-rich tract