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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTATCGAGCACCAGAGCTCATATTTGGTGCAACGGAATATACTACTGCTATTGATTTGTGGTCAACAGGCTGTGTCATGGCAGAGCTGCTTCTAGGACAGgtctggcatgttcagtttccctccctctggttcttacctttttgcttcttctgatatcattcatccatgtag

Basic information

species Zea mays
transcript GRMZM2G138676_T02
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G138676_T02 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os03g62500.1 (Oryza sativa), 5'ss of exon 8
TTATCGAGCACCAGAGCTCATATTTGGTGCAACGGAATATACTACTGCTATTGATTTGTGGTCAACAGGCTGTGTCATGGCAGAGCTGCTTCTAGGACAGgtctggcatgttcagtttccctccctctggttcttacctttttgcttcttctgatatcattcatccatgtag
|||  | |||||||||||||||||||||||||| |||||||||||||| |||||||||||||| ||||||||||||||||||||||| || || |||||||| |      ||||      |    | | | | ||      || ||| |||| ||| |||||||||||| ||
TTACAGGGCACCAGAGCTCATATTTGGTGCAACTGAATATACTACTGCCATTGATTTGTGGTCTACAGGCTGTGTCATGGCAGAGCTTCTGCTTGGACAGgttt----cattcatgcatacaatattttgcttttgttcaatttcttattctaataacattcatccatgcag

upper sequence: GRMZM2G138676_T02 (Zea mays), 5'ss of exon 8
lower sequence: Vv12s0035g01060.t01 (Vitis vinifera), 5'ss of exon 7
TTATCGAGCACCAGAGCTCATATTTGGTGCAACGGAATATACTACTGCTATTGATTTGTGGTCAACAGGCTGTGTCATGGCAGAGCTGCTTCTAGGACAGgtctggcatgttcagtttccc-tccctctggtt---cttacctttttgcttcttctga----tatcattcatccatgtag--------------------
||| || || ||||| |||||||||||||| || |||||||| |||||||| ||| | ||||| || |||||||| ||||| ||  ||||||| ||||||||    ||   | | ||||   |     ||  |   |||  |||||      |||  |    | | ||| |  | | ||                     
TTACCGTGCCCCAGAACTCATATTTGGTGCCACTGAATATACGACTGCTATAGATATTTGGTCTACTGGCTGTGTGATGGCTGAATTGCTTCTGGGACAGgtagtacactgttaatttcagatgtagttgacttgccttcgcttttcatcatttccaagtcctgttatttaggcttttatctaaccatcttctggtacag
















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|31355062|gb|CD439419.1|CD439419
EST:     TTGATTTGTGGTCAACAGGCTGTGTCATGGCAGAGCTGCTTCTAGGACAG                         CCTCTGTTTCCTGGAGAAAGTGGAGTCGACCAACTAGTTGAGATCATCAAG
genomic: TTGATTTGTGGTCAACAGGCTGTGTCATGGCAGAGCTGCTTCTAGGACAGgtctggcatg ... atccatgtagGCTCTGTTTCCTGGAGAAAGTGGAGTCGACCAACTAGTTGAGATCATCAAG
EST: gi|32931035|gb|CF035847.1|CF035847
EST:     TTGATTTGTGGTCAACNGACTGTGTCATGGCAGAGCTGCTTCTAGGACAG                         CCTCTGTTTCCTGGAGAAAGTGGAGTCGACCAACTAGTTGAGATCATCAAG
genomic: TTGATTTGTGGTCAACAGGCTGTGTCATGGCAGAGCTGCTTCTAGGACAGgtctggcatg ... atccatgtagGCTCTGTTTCCTGGAGAAAGTGGAGTCGACCAACTAGTTGAGATCATCAAG
EST: gi|71322556|gb|DR797955.1|DR797955
EST:     TTGATTTGTGGTCAACAGGCTGTGTCATGGCAGAGCTGCTTCTAGGACAG                         GCTCTGTTTCCTGGAGAAAGTGGAGTCGACCAACTAGTTGAGATCATCAAG
genomic: TTGATTTGTGGTCAACAGGCTGTGTCATGGCAGAGCTGCTTCTAGGACAGgtctggcatg ... atccatgtagGCTCTGTTTCCTGGAGAAAGTGGAGTCGACCAACTAGTTGAGATCATCAAG
EST: gi|71312506|gb|DR792786.1|DR792786
EST:     TTGATTTGTGGTCAACAGGCTGTGTCATGGCAGAGCTGCTTCTAGGACAG                         GCTCTGTTTCCTGGAGAAAGTGGAGTCGACCAACTAGTTGAGATCATCAAG
genomic: TTGATTTGTGGTCAACAGGCTGTGTCATGGCAGAGCTGCTTCTAGGACAGgtctggcatg ... atccatgtagGCTCTGTTTCCTGGAGAAAGTGGAGTCGACCAACTAGTTGAGATCATCAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTATCGAGCACCAGAGCTCATATTTGGTGCAACGGAATATACTACTGCTATTGATTTGTGGTCAACAGGCTGTGTCATGGCAGAGCTGCTTCTAGGACAGgtctggcatgttcagtttccctccctctggttcttacctttttgcttcttctgatatcattcatccatgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT