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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagctagtttcggatgggtgtgttgatcaaaacagatatatcactgcatatacaggtaatgggaattaattatataaatctgaattgtttgtttcatcagGTAAGAAAGGAGAGGCTTGGGGATAGAATCACTGCACTTCACCAGATAGTGTCCCCATTTGGCAAG

Basic information

species Zea mays
transcript GRMZM2G083749_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G083749_T05 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g13000.1 (Oryza sativa), 3'ss of exon 3
-aagctagt-ttcggatgggtgtgttgatcaaaaca-gatatatcac-tgcata--tacaggtaatgggaattaattatataaatctgaattgtttgtttcatcagGTAAGAAAGGAGAGGCTTGGGGATAGAATCACTGCACTTCACCAGATAGTGTCCCCATTTGGCAAG
  | | | |      ||||   ||  ||||  | |  | || ||  | |||||    | |  ||||  | ||   || ||||   |  ||   ||| |||||   ||| || ||||||||||||||||| ||||| || || |||||||||||||| |||||||||||||||
agaacaaatacatcaatggaattgaagatcgtagcttgctacattgcatgcattacaatacataatttgtatctcttctata---ccaaacattttatttca---gGTCAGGAAGGAGAGGCTTGGGGACAGAATAACAGCTCTTCACCAGATAGTTTCCCCATTTGGCAAG

upper sequence: GRMZM2G083749_T05 (Zea mays), 3'ss of exon 3
lower sequence: Vv09s0002g04120.t01 (Vitis vinifera), 3'ss of exon 3
--aagctagtttcggatgggtgtgttgatcaaaacagatatatcactgcatatacaggtaatgggaattaattatataaatctgaattgtttgtttc---atcagGTAAGAAAGGAGAGGCTTGGGGATAGAATCACTGCACTTCACCAGATAGTGTCCCCATTTGGCAAG
  |   ||       | | | |   |  || | | | | | |  |||    ||     |||      ||  || |||| || | ||||  ||   ||   | ||||| |||||||||| ||| || |||||||| || || ||||||||| |||| ||||||||||| |||
aaacagtaaagaaaaaagagagaaattctctaga-aaacagaaaactagtaatt----taacattctttctttttatatatattaattaatttactctgaaccagGTGAGAAAGGAGAAGCTGGGTGATAGAATAACAGCCCTTCACCAGTTAGTTTCCCCATTTGGAAAG
















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|91874519|gb|EB404476.1|EB404476
EST:     CAAAGAAGGCTAGGGTTCAGACCTCTTCTTCAGCACAGTCTACCCTAAAG                         GTAAGAAAGGAGAGGCTTGGGGATAGAATCACTGCACTTCACCAGATAGTG
genomic: CAAAGAAGGCTAGGGTTCAGACCTCTTCTTCAGCACAGTCTACCCTAAAGgtttctccat ... gtttcatcagGTAAGAAAGGAGAGGCTTGGGGATAGAATCACTGCACTTCACCAGATAGTG
EST: gi|50339291|gb|CO534417.1|CO534417
EST:     CAAAGAAGGCTAGGGTTCAGACCTCTTCTTCAGCACAGTCTACCCTAAAG                         GTAAGAAAGGAGAGGCTTG
genomic: CAAAGAAGGCTAGGGTTCAGACCTCTTCTTCAGCACAGTCTACCCTAAAGgtttctccat ... gtttcatcagGTAAGAAAGGAGAGGCTTG
EST: gi|94472188|gb|EB701146.1|EB701146
EST:     CAAAGAAGGCTAGGGTTCAGACCTCTTCTTCAGCACAGTCTACCCTAAAG                         GGTA-GAAAGGAGAGGCT
genomic: CAAAGAAGGCTAGGGTTCAGACCTCTTCTTCAGCACAGTCTACCCTAAAGgtttctccat ... gtttcatcagG-TAAGAAAGGAGAGGCT
EST: gi|148981124|gb|EE027442.2|EE027442
EST:     CAAAGAAGGCTAGGGTTCAGACCTCTTCTTCAGCACAGTCTACCCTAAAG                         GTAAGAAAGGAGAGGCTTGGGGATAGAATCACTGCACTTCACCAGATAGTG
genomic: CAAAGAAGGCTAGGGTTCAGACCTCTTCTTCAGCACAGTCTACCCTAAAGgtttctccat ... gtttcatcagGTAAGAAAGGAGAGGCTTGGGGATAGAATCACTGCACTTCACCAGATAGTG
EST: gi|149095094|gb|EE180702.2|EE180702
EST:     CAAAGAAGGCTAGGGTTCAGACCTCTTCTTCAGCACAGTCTACCCTAAAG                         GTAAGAGAGGAGAGGCTTGGGGATAGAATCACTGCACTTCACCAGATAGTG
genomic: CAAAGAAGGCTAGGGTTCAGACCTCTTCTTCAGCACAGTCTACCCTAAAGgtttctccat ... gtttcatcagGTAAGAAAGGAGAGGCTTGGGGATAGAATCACTGCACTTCACCAGATAGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatatacaggtaatgggaattaattatataaatctgaattgtttgtttcatcagGTAAGAAAGGAGAGGCTTGGGGATAGAATCACTGCACTTCACCAGATAGTGTCCCCATTTGGCAAG
                  aattaat  putative branch site (score: 3)
                                          tttgtttc  putative PPT
                  aattaattatataaat  TA-rich tract