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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcgatctgggccctaggatttctgaacattaatgatgtaggtcaaaaggagatttattatttttgctttctgcagGAAGATTTTTGTCGGAGGCGTTGCTTGGGAGACAACTGAAG

Basic information

species Zea mays
transcript GRMZM2G167356_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G167356_T04 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g12850.1 (Oryza sativa), 3'ss of exon 2
---------------------gtgagcgatctggg-------ccctaggatttctgaacattaatgatgtaggtcaaaaggagat----ttattatttttgctttctgcagGAAGATTTTTGTCGGAGGCGTTGCTTGGGAGACAACTGAAG
                     |  || ||| | ||            |  |||  | |  |    || |  | |  | ||  |||     | || | ||   ||| |||||||||||||| |||||||||||||||||||||||||| ||||
gtgggtggcttcgtggcttgggctagggattttgggggtttgtttcggatttttcggatttgggagagggggtttgagagctgatgtaactgttttgttctttttttgcagGAAGATTTTCGTCGGAGGCGTTGCTTGGGAGACAACCGAAG
















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|211045050|gb|FL383276.1|FL383276
EST:     GGCGATGCTGGCGGAGAGGATGTGAGGGGGGCGGGCGGCGACTCATCGGG                         GAAGATTTTTGTCGGAGGCGTTGCTTGGGAGACAACTGAAG
genomic: GGCGATGCTGGCGGAGAGGATGTGAGGGGGGCGGGCGGCGACTCATCGGGgtgagcgatc ... ctttctgcagGAAGATTTTTGTCGGAGGCGTTGCTTGGGAGACAACTGAAG
EST: gi|9255383|gb|BE345851.1|BE345851
EST:     ATGTGAGGGGGGCGGGCGGCGACTCATCGGG                         GAAGATTCTTGTCGGAGGCGTTGCTTGGGAGACAACTGAAG
genomic: ATGTGAGGGGGGCGGGCGGCGACTCATCGGGgtgagcgatc ... ctttctgcagGAAGATTTTTGTCGGAGGCGTTGCTTGGGAGACAACTGAAG
EST: gi|148946214|gb|EC891510.2|EC891510
EST:     GGCGATGCTGGCGGAGAGGATGTGAGGGGGGCGGGCGGCGACTCATCGGG                         GAAGATTTTTGTCGGAGGCGTTGCTTGGGAGACAACTGAAG
genomic: GGCGATGCTGGCGGAGAGGATGTGAGGGGGGCGGGCGGCGACTCATCGGGgtgagcgatc ... ctttctgcagGAAGATTTTTGTCGGAGGCGTTGCTTGGGAGACAACTGAAG
EST: gi|211107234|gb|FL370789.1|FL370789
EST:     GGCGATGCTGGCGGAGAGGATGTGAGGGGGGCGGGCGGCGACTCATCGGG                         GAAGATTTTTGTCGGAGGCGTTGCTTGGGAGACAACTGAAG
genomic: GGCGATGCTGGCGGAGAGGATGTGAGGGGGGCGGGCGGCGACTCATCGGGgtgagcgatc ... ctttctgcagGAAGATTTTTGTCGGAGGCGTTGCTTGGGAGACAACTGAAG
EST: gi|148932748|gb|EE285380.2|EE285380
EST:     GGCGATGCTGGCGGAGAGGATGTGAGGGGGGCGGGCGGCGACTCATCGGG                         GAAGATTTTTGTCGGAGGCGTTGCTTGGGAGACAACTGAAG
genomic: GGCGATGCTGGCGGAGAGGATGTGAGGGGGGCGGGCGGCGACTCATCGGGgtgagcgatc ... ctttctgcagGAAGATTTTTGTCGGAGGCGTTGCTTGGGAGACAACTGAAG
EST: gi|148939672|gb|EC884331.2|EC884331
EST:     GGCGATGCTGGCGGAGAGGATGTGAGGGGGGCGGGCGGCGACTCATCGGG                         GAAGATTTTTGTCGGAGGCGTTGCTTGGGAGACAACTGAAG
genomic: GGCGATGCTGGCGGAGAGGATGTGAGGGGGGCGGGCGGCGACTCATCGGGgtgagcgatc ... ctttctgcagGAAGATTTTTGTCGGAGGCGTTGCTTGGGAGACAACTGAAG
EST: gi|148935082|gb|EC879124.2|EC879124
EST:     GGCGATGCTGGCGGAGAGGATGTGAGGGGGGCGGGCGGCGACTCATCGGG                         GAAGATTTTTGTCGGAGGCGTTGCTTGGGAGACAACTGAAG
genomic: GGCGATGCTGGCGGAGAGGATGTGAGGGGGGCGGGCGGCGACTCATCGGGgtgagcgatc ... ctttctgcagGAAGATTTTTGTCGGAGGCGTTGCTTGGGAGACAACTGAAG
EST: gi|78116552|gb|DV534939.1|DV534939
EST:     GGCGATGCTGGCGGAGAGGATGTGAGGGGGGCGGGCGGCGACTCATCGGG                         GAAGATTTTTGTCGGAGGCGTTGCTTGGGAGACAACTGAAG
genomic: GGCGATGCTGGCGGAGAGGATGTGAGGGGGGCGGGCGGCGACTCATCGGGgtgagcgatc ... ctttctgcagGAAGATTTTTGTCGGAGGCGTTGCTTGGGAGACAACTGAAG
EST: gi|71439287|gb|DR820337.1|DR820337
EST:     GGCGATGCTGGCGGAGAGGATGTGAGGGGGGCGGGCGGCGACTCATCGGG                         GAAGATTTTTGTCGGAGGCGTTGCTTGGGAGACAACTGAAG
genomic: GGCGATGCTGGCGGAGAGGATGTGAGGGGGGCGGGCGGCGACTCATCGGGgtgagcgatc ... ctttctgcagGAAGATTTTTGTCGGAGGCGTTGCTTGGGAGACAACTGAAG
EST: gi|211449696|gb|FL381428.1|FL381428
EST:     GGCGATGCTGGCGGAGAGGATGTGAGGGGGGCGGGCGGCGACTCATCGGG                         GAAGATTTTTGTCGGAGGCGTTGCTTGGGAGACAACTGAAG
genomic: GGCGATGCTGGCGGAGAGGATGTGAGGGGGGCGGGCGGCGACTCATCGGGgtgagcgatc ... ctttctgcagGAAGATTTTTGTCGGAGGCGTTGCTTGGGAGACAACTGAAG
EST: gi|211319685|gb|FL416782.1|FL416782
EST:     GGCGATGCTGGCGGAGAGGATGTGAGGGGGGCGGGCGGCGACTCATCGGG                         GAAGATTTTTGTCGGAGGCGTTGCTTGGGAGACAACTGAAG
genomic: GGCGATGCTGGCGGAGAGGATGTGAGGGGGGCGGGCGGCGACTCATCGGGgtgagcgatc ... ctttctgcagGAAGATTTTTGTCGGAGGCGTTGCTTGGGAGACAACTGAAG
EST: gi|78108850|gb|DV527267.1|DV527267
EST:     GGCGATGCTGGCGGAGAGGATGTGAGGGGGGCGGGCGGCGACTCATCGGG                         GAAGATTTTTGTCGGAGGCGTTGCTTGGGAGACAACTGAAG
genomic: GGCGATGCTGGCGGAGAGGATGTGAGGGGGGCGGGCGGCGACTCATCGGGgtgagcgatc ... ctttctgcagGAAGATTTTTGTCGGAGGCGTTGCTTGGGAGACAACTGAAG
EST: gi|71427627|gb|DR808677.1|DR808677
EST:     GGCGATGCTGGCGGAGAGGATGTGAGGGGGGCGGGCGGCGACTCATCGGG                         GAAGATTTTTGTCGGAGGCGTTGCTTGGGAGACAACTGAAG
genomic: GGCGATGCTGGCGGAGAGGATGTGAGGGGGGCGGGCGGCGACTCATCGGGgtgagcgatc ... ctttctgcagGAAGATTTTTGTCGGAGGCGTTGCTTGGGAGACAACTGAAG
EST: gi|71432722|gb|DR813772.1|DR813772
EST:     GGCGATGCTGGCGGAGAGGATGTGAGGGGGGCGGGCGGCGACTCATCGGG                         GAAGATTTTTGTCGGAGGCGTTGCTTGGGAGACAACTGAAG
genomic: GGCGATGCTGGCGGAGAGGATGTGAGGGGGGCGGGCGGCGACTCATCGGGgtgagcgatc ... ctttctgcagGAAGATTTTTGTCGGAGGCGTTGCTTGGGAGACAACTGAAG
EST: gi|78076701|gb|DV505135.1|DV505135
EST:     GGCGATGCTGGCGGAGAGGATGTGAGGGGGGCGGGCGGCGACTCATCGGG                         GAAGATTTTTGTCGGAGGCGTTGCTTGGGAGACAACTGAAG
genomic: GGCGATGCTGGCGGAGAGGATGTGAGGGGGGCGGGCGGCGACTCATCGGGgtgagcgatc ... ctttctgcagGAAGATTTTTGTCGGAGGCGTTGCTTGGGAGACAACTGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgaacattaatgatgtaggtcaaaaggagatttattatttttgctttctgcagGAAGATTTTTGTCGGAGGCGTTGCTTGGGAGACAACTGAAG
      cattaat  putative branch site (score: 3)
                                    ttatttttgctttct  putative PPT
                       aaaaggagatttatta  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcgatctgggccctaggatttctgaacattaatgatgtaggtcaaaaggagatttattatttttgctttctgcagGAAGATTTTTGTCGGAGGCGTTGCTTGGGAGACAACTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG