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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtctggacatttttggaacataagcacaggtggcttttctggcttggcgaaagatgattaacattcttcccttttacacggtttcattcagGTCTTGAGCATGAGTAGGGTAGGAGCTCCAGGAGCAGTTCTTCCCCTTCTCACAGAATCTAAGACTGAG

Basic information

species Zea mays
transcript GRMZM2G116785_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G116785_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os06g09370.2 (Oryza sativa), 3'ss of exon 8
gtatgtctg------gacatttttggaacataagcacaggtggcttttctggcttggcgaaagatgattaacattcttcccttttacacggtttcattcagGTCTTGAGCATGAGTAGGGTAGGAGCTCCAGGAGCAGTTCTTCCCCTTCTCACAGAATCTAAGACTGAG
|||  ||||      |   | |||||    |  |   ||||||      | |||        ||||  | ||| |||||          |  ||| |  |||| ||||||||||| ||| |||||||||| |||||||||||||||||||| |  |||||| | || |||
gtacatctgcagtcaggtttatttggtgtgtgggatgaggtgggggcgttagctccttttctgatggctgacagtcttctt--------gaattc-tgtagGTATTGAGCATGAGCAGGCTAGGAGCTCCTGGAGCAGTTCTTCCCCTTCTTAGGGAATCTCAAACCGAG
















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|84980927|gb|DW531276.1|DW531276
EST:     TGCTGGATGAAATTATTGATTATGTGAAGTTTCTTCAGCTTCAGGTCAAG                         GTCTTGAGCATGAGTAGGGTAGGAGCTCCAGGAGCAGTTCTTCCCCTTCTC
genomic: TGCTGGATGAAATTATTGATTATGTGAAGTTTCTTCAGCTTCAGGTCAAGgtatgtctgg ... tttcattcagGTCTTGAGCATGAGTAGGGTAGGAGCTCCAGGAGCAGTTCTTCCCCTTCTC
EST: gi|78026119|gb|DV494506.1|DV494506
EST:     TGCTGGATGAAATTATTGATTATGTGAAGTTTCTTCAGCTTCAGGTCAAG                         GTCTTGAGCATGAGTAGGGTAGGAGCTCCAGGAGCAGTTCTTCCCCTTCTC
genomic: TGCTGGATGAAATTATTGATTATGTGAAGTTTCTTCAGCTTCAGGTCAAGgtatgtctgg ... tttcattcagGTCTTGAGCATGAGTAGGGTAGGAGCTCCAGGAGCAGTTCTTCCCCTTCTC
EST: gi|71299175|gb|DR785590.1|DR785590
EST:     TGCTGGATGAAATTATTGATTATGTGAAGTTTCTTCAGCTTCAGGTCAAG                         GTCTTGAGCATGAGTAGGGTAGGAGCTCCAGGAGCAGTTCTTCCCCTTCTC
genomic: TGCTGGATGAAATTATTGATTATGTGAAGTTTCTTCAGCTTCAGGTCAAGgtatgtctgg ... tttcattcagGTCTTGAGCATGAGTAGGGTAGGAGCTCCAGGAGCAGTTCTTCCCCTTCTC
EST: gi|4887525|gb|AI677624.1|AI677624
EST:     TGCTGGATGAAATTATTGATTATGTGAAGTTTCTTCAGCTTCAGGTCAAG                         GTCTTGAGCATGAGTAGGGTAGGAGCTCCAGGAGCAGTTCTTCCCCTTCTC
genomic: TGCTGGATGAAATTATTGATTATGTGAAGTTTCTTCAGCTTCAGGTCAAGgtatgtctgg ... tttcattcagGTCTTGAGCATGAGTAGGGTAGGAGCTCCAGGAGCAGTTCTTCCCCTTCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctggcttggcgaaagatgattaacattcttcccttttacacggtttcattcagGTCTTGAGCATGAGTAGGGTAGGAGCTCCAGGAGCAGTTCTTCCCCTTCTCACAGAATCTAAGACTGAG
                   gattaac  putative branch site (score: 2)
                                             tttcattc  putative PPT
                    attaacatt  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
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtctggacatttttggaacataagcacaggtggcttttctggcttggcgaaagatgattaacattcttcccttttacacggtttcattcagGTCTTGAGCATGAGTAGGGTAGGAGCTCCAGGAGCAGTTCTTCCCCTTCTCACAGAATCTAAGACTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG