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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggctactggattgtgttacttatttatttgatccttttgtccttttacctgttcaagtgtcctatcttaacttctatttttactggtttcatttgttagGCATAGTTTAAAGGAAGTTTTGGACACACCAGGTGTGATGGCACTGATAAAAGATACAAAAGCAGCACAGGAG

Basic information

species Zea mays
transcript GRMZM2G044011_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044011_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os04g56480.3 (Oryza sativa), 3'ss of exon 10
-tggctactggattgtgttacttatttatttgatc-cttttgtccttttacctgttcaagtgtcctatcttaacttctatttttactggtttcatttgtt--agGCATAGTTTAAAGGAAGTTTTGGACACACCAGGTGTGATGGCACTGATAAAAGATACAAAAGCAGCACAGGAG
     ||||  | |    ||  |||| ||||| |  | | | | |    | ||||   | ||     |||    || |  ||| | |||||   ||||||  ||||||||  | |||||||||||||| |  ||| |||||||| |||| |||||||||||||| || || ||||||
aaatttactctaattatatatctattcatttggttgcctatattcccccagctgtctcaatg----gtctctgttttttgtttgattggttatgtttgttaaagGCATAGCCTGAAGGAAGTTTTGGATAGCCCAAGTGTGATGACACTAATAAAAGATACAAAGGCGGCGCAGGAG

upper sequence: GRMZM2G044011_T01 (Zea mays), 3'ss of exon 11
lower sequence: Vv04s0023g00140.t01 (Vitis vinifera), 3'ss of exon 11
tggctactggattgtgttacttatttat-ttgatccttttgtccttttacctgttcaagtgtcctatcttaacttctatttttactggtttcatttgt-tagGCATAGTTTAAAGGAAGTTTTGGACACACCAGGTGTGATGGCACTGATAAAAGATACAAAAGCAGCACAGGAG
  | || || | | | || |||   | | ||      ||| |  ||     |||| |       |  ||||   |   ||  |      ||  | |||  |||||||||||||| || ||||||||  |||||  |||||||    ||||||| ||||||||||||||||| |||
--gatattgtacttttttgctttcatgtgttagatggtttattattaaggttgttaactgcagatgccttattattacttgatgtcaaatttttgtgtacagGCATAGTTTAAAAGAGGTTTTGGATGCACCAAATGTGATGAACATGATAAAGGATACAAAAGCAGCACAAGAG
















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|211495349|gb|FL234479.1|FL234479
EST:     ATTGAGAACAAGCAACGCCTTGTTCTGGCACATGCAACATCAGGTTACAA                         GCATAGTTTAAAGGAAGTTTTGGATACACCAGGTGTGATGGCACTGATAAA
genomic: ATTGAGAACAAGCAACGCCTTGTTCTGGCGCATGCAACATCAGGTTACAAgtgagttctt ... catttgttagGCATAGTTTAAAGGAAGTTTTGGACACACCAGGTGTGATGGCACTGATAAA
EST: gi|91048656|gb|EB159074.1|EB159074
EST:     ATTGAGAACAAGCAACGCCTTGTTCTGGCGCATGCAACATCAGGTTACAA                         GCATAGTTTAAAGGAAGTTTTGGACACACCAGGTGTGATGGCACTGATAAA
genomic: ATTGAGAACAAGCAACGCCTTGTTCTGGCGCATGCAACATCAGGTTACAAgtgagttctt ... catttgttagGCATAGTTTAAAGGAAGTTTTGGACACACCAGGTGTGATGGCACTGATAAA
EST: gi|67018605|gb|CO447354.1|CO447354
EST:     ATTGAGAACAAGCAACGCCTTGTTCTGGCGCATGCAACATCAGGTTACAA                         GCATAGTTTAAAGGAAGTTTTGGATACACCAGGTGTGATGGCACTAATAAA
genomic: ATTGAGAACAAGCAACGCCTTGTTCTGGCGCATGCAACATCAGGTTACAAgtgagttctt ... catttgttagGCATAGTTTAAAGGAAGTTTTGGACACACCAGGTGTGATGGCACTGATAAA
EST: gi|67024357|gb|CO453106.1|CO453106
EST:     ATTGAGAACAAGCAACGCCTTGTTCTGGCGCATGCAACATCAGGTTACAA                         GCATAGTTTAAAGGAAGTTTTGGATACACCAGGTGTGATGGCACTAATAAA
genomic: ATTGAGAACAAGCAACGCCTTGTTCTGGCGCATGCAACATCAGGTTACAAgtgagttctt ... catttgttagGCATAGTTTAAAGGAAGTTTTGGACACACCAGGTGTGATGGCACTGATAAA
EST: gi|40303701|gb|CK348088.1|CK348088
EST:     ATTGAGAACAAGCAACGCCTTGTTCTGGCGCATGCAACATCAGGTTACAA                         GCATAGTTTAAAGGAAGTTTTGGACACACCAGGTGTGATGGCACTGATAAA
genomic: ATTGAGAACAAGCAACGCCTTGTTCTGGCGCATGCAACATCAGGTTACAAgtgagttctt ... catttgttagGCATAGTTTAAAGGAAGTTTTGGACACACCAGGTGTGATGGCACTGATAAA
EST: gi|71763506|gb|DR961443.1|DR961443
EST:     ATTGAGAACAAGCAACGCCTTGTTCTGGCGCATGCAACATCAGGTTACAA                         GCATAGTTTAAAGGAAGTTTTGGACACACCAGGTGTGATGGCACTGATAAA
genomic: ATTGAGAACAAGCAACGCCTTGTTCTGGCGCATGCAACATCAGGTTACAAgtgagttctt ... catttgttagGCATAGTTTAAAGGAAGTTTTGGACACACCAGGTGTGATGGCACTGATAAA
EST: gi|74236267|gb|DT644181.1|DT644181
EST:     ATTGAGAACAAGCAACGCCTTGTTCTGGCGCATGCAACATCAGGTTACAA                         GCATAGTTTAAAGGAAGTTTTGGGCACACCAGGTGTGATGGCACTGATAAA
genomic: ATTGAGAACAAGCAACGCCTTGTTCTGGCGCATGCAACATCAGGTTACAAgtgagttctt ... catttgttagGCATAGTTTAAAGGAAGTTTTGGACACACCAGGTGTGATGGCACTGATAAA
EST: gi|71442136|gb|DR823186.1|DR823186
EST:     ATTGAGAACAAGCAACGCCTTGTTCTGGCGCATGCAACATCAGGTTACAA                         GCATAGTTTAAAGGAAGTTTTGGACACACCAGGTGTGATGGCACTGATAAA
genomic: ATTGAGAACAAGCAACGCCTTGTTCTGGCGCATGCAACATCAGGTTACAAgtgagttctt ... catttgttagGCATAGTTTAAAGGAAGTTTTGGACACACCAGGTGTGATGGCACTGATAAA
EST: gi|50333168|gb|CO528294.1|CO528294
EST:     ATTGAGAACAAGCAACGCCTTGTTCTGGCGCATGCAACATCAGGTTACAA                         GCATAGTTTAAAGGAAGTTTTGGACACACCAGGTGTGATGGCACTGATAAA
genomic: ATTGAGAACAAGCAACGCCTTGTTCTGGCGCATGCAACATCAGGTTACAAgtgagttctt ... catttgttagGCATAGTTTAAAGGAAGTTTTGGACACACCAGGTGTGATGGCACTGATAAA
EST: gi|67021632|gb|CO450381.1|CO450381
EST:     ATTGAGAACAAGCAACGCCTTGTTCTGGCGCATGCAACATCAGGTTACAA                         GCATAGTTTAAAGGAAGTTTTGGATACACCAGGTGTGATGGCACTAATAAA
genomic: ATTGAGAACAAGCAACGCCTTGTTCTGGCGCATGCAACATCAGGTTACAAgtgagttctt ... catttgttagGCATAGTTTAAAGGAAGTTTTGGACACACCAGGTGTGATGGCACTGATAAA
EST: gi|71302744|gb|DR787484.1|DR787484
EST:     ATTGAGAACAAGCAACGCCTTGTTCTGGCGCATGCAACATCAGGTTACAA                         GCATAGTTTAAAGGAAGTTTTGGACACACCAGGTGTGATGGCACTGATAAA
genomic: ATTGAGAACAAGCAACGCCTTGTTCTGGCGCATGCAACATCAGGTTACAAgtgagttctt ... catttgttagGCATAGTTTAAAGGAAGTTTTGGACACACCAGGTGTGATGGCACTGATAAA
EST: gi|76016282|gb|DT943452.1|DT943452
EST:     ATTGAGAACAAGCAACGCCTTGTTCTGGCGCATGCAACATCAGGTTACAA                         GCATAGTTTAAAGGAAGTTTTGGACACACCAGGTGTGATGGCACTGATAAA
genomic: ATTGAGAACAAGCAACGCCTTGTTCTGGCGCATGCAACATCAGGTTACAAgtgagttctt ... catttgttagGCATAGTTTAAAGGAAGTTTTGGACACACCAGGTGTGATGGCACTGATAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttacctgttcaagtgtcctatcttaacttctatttttactggtttcatttgttagGCATAGTTTAAAGGAAGTTTTGGACACACCAGGTGTGATGGCACTGATAAAAGATACAAAAGCAGCACAGGAG
                    tcttaac  putative branch site (score: 2)
                                          tttcattt  putative PPT
                      ttaacttctattttta  TA-rich tract