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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggtacatgacaccaagggattcaaacacttgtttttttttcttcccctggatactaaacggggtgatgttttcagGTCATTGATCTGGCAAGATTGAATCATGAGAACATAGCAAAGTTCTTAGGGTACTGCAGGGAGAGTGATCCATTCTCTCGGATGCTAGTCTTCGAGTACG

Basic information

species Zea mays
transcript GRMZM2G119759_T03
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G119759_T03 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os04g58700.1 (Oryza sativa), 3'ss of exon 9
gtatggtacatgacaccaagggattcaaacacttgtttttttttcttcccctggatactaaacggggtgatgttttcagGTCATTGATCTGGCAAGATTGAATCATGAGAACATAGCAAAGTTCTTAGGGTACTGCAGGGAGAGTGATCCATTCTCTCGGATGCTAGTCTTCGAGTACG
||| | | ||| |||| | | | | ||| ||| ||| || || | ||| |||| ||||| |||||||| ||||||||||||||||||||||| || | || || ||||| || ||||| |||||||| |||||||||| || || ||||
-----gtaaagcttagcaaa--attctgctgtgagaacagtatgttgtcccacaatattaatgggtgtaaa--ttttagGTTATTGACCTGGCAAGGTTGAATCATGAGAACATAGCAAAATTTCTGGGCTATTGCAGAGAAAGTGACCCATTCTCCAGGATGCTAGTGTTTGAATACG

upper sequence: GRMZM2G119759_T03 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os04g58700.2 (Oryza sativa), 3'ss of exon 9
gtatggtacatgacaccaagggattcaaacacttgtttttttttcttcccctggatactaaacggggtgatgttttcagGTCATTGATCTGGCAAGATTGAATCATGAGAACATAGCAAAGTTCTTAGGGTACTGCAGGGAGAGTGATCCATTCTCTCGGATGCTAGTCTTCGAGTACG---------------------------------
||| | | ||| |||| | | | | ||| ||| ||| || || | ||| |||| ||||| |||||||| ||||||||||||||||||||||| || | || || ||||| || ||||| |||||||| |||||||||| || || ||||
-----gtaaagcttagcaaa--attctgctgtgagaacagtatgttgtcccacaatattaatgggtgtaaa--ttttaggttattgacctggcaaggttgaatcatgagaacatagcaaaatttctgggctattgcagAGAAAGTGACCCATTCTCCAGGATGCTAGTGTTTGAATACGCATCAAACGGGACCCTGTTTGAGCACCTACACT
















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|149107663|gb|EE189542.2|EE189542
EST:     CCTTCGAAGGTCATTGGACTAGCCACCATGAACTCTTTTACCAAAACAAG                         GTCATTGATCTGGCAAGATTGAATCATGAGAACATAGCAAAGTTCTTAGGG
genomic: CCTTCGAAGGTCATTGGACTAGCCACCATGAACTCTTTTACCAAAACAAGgtatggtaca ... atgttttcagGTCATTGATCTGGCAAGATTGAATCATGAGAACATAGCAAAGTTCTTAGGG
EST: gi|91050218|gb|EB160636.1|EB160636
EST:     TTGGACTAGCCACCATGAACTCTTTTACCAAAACAAG                         GTCATTGATCTGGCAAGATTGAATCATGAGAACATAGCAAAGTTCTTAGGG
genomic: TTGGACTAGCCACCATGAACTCTTTTACCAAAACAAGgtatggtaca ... atgttttcagGTCATTGATCTGGCAAGATTGAATCATGAGAACATAGCAAAGTTCTTAGGG
EST: gi|71313398|gb|DR793250.1|DR793250
EST:     CCTTCGAAGGTCATTGGACTAGCCACCATGAACTCTTTTACCAAAACAAG                         GTCATTGATCTGGCAAGATTGAATCATGAGAACATAGCAAAGTTCTTAGGG
genomic: CCTTCGAAGGTCATTGGACTAGCCACCATGAACTCTTTTACCAAAACAAGgtatggtaca ... atgttttcagGTCATTGATCTGGCAAGATTGAATCATGAGAACATAGCAAAGTTCTTAGGG
EST: gi|149051626|gb|EE155736.2|EE155736
EST:     CCTTCGAAGGTCATTGGACTAGCCACCATGAACTCTTTTACCAAAACAAG                         GTCATTGATCTGGCAAGATTGAATCATGAGAACATAGCAAAGTTCTTAGGG
genomic: CCTTCGAAGGTCATTGGACTAGCCACCATGAACTCTTTTACCAAAACAAGgtatggtaca ... atgttttcagGTCATTGATCTGGCAAGATTGAATCATGAGAACATAGCAAAGTTCTTAGGG
EST: gi|78089519|gb|DV517893.1|DV517893
EST:     CCTTCGAAGGTCATTGGACTAGCCACCATGAACTCTTTTACCAAAACAAG                         GTCATTGATCTGGCAAGATTGAATCATGAGAACATAGCAAAGTTCTTAGGG
genomic: CCTTCGAAGGTCATTGGACTAGCCACCATGAACTCTTTTACCAAAACAAGgtatggtaca ... atgttttcagGTCATTGATCTGGCAAGATTGAATCATGAGAACATAGCAAAGTTCTTAGGG
EST: gi|148950050|gb|EC895582.2|EC895582
EST:     CCTTCGAAGGTCATTGGACTAGCCACCATGAACTCTTTTACCAAAACAAG                         GTCATTGATCTGGCAAGATTGAATCATGAGAACATAGCAAAGTTCTTAGGG
genomic: CCTTCGAAGGTCATTGGACTAGCCACCATGAACTCTTTTACCAAAACAAGgtatggtaca ... atgttttcagGTCATTGATCTGGCAAGATTGAATCATGAGAACATAGCAAAGTTCTTAGGG
EST: gi|50334832|gb|CO529958.1|CO529958
EST:     CACCATGAACTCTTTTACCAAAACAAG                         GTCATTGATCTGGCAAGATTGAATCATGAGAACATAGCAAAGTTCTTAGGG
genomic: CACCATGAACTCTTTTACCAAAACAAGgtatggtaca ... atgttttcagGTCATTGATCTGGCAAGATTGAATCATGAGAACATAGCAAAGTTCTTAGGG
EST: gi|71761155|gb|DR959092.1|DR959092
EST:     CTTTCGAAGGTCATTGGACTAGCCACCATGAACTCTTTTACCAAAACAAG                         GTCATTGATCTGGCAAGATTGAATCATGAGAACATAGCAAAGTTCTTAGGG
genomic: CCTTCGAAGGTCATTGGACTAGCCACCATGAACTCTTTTACCAAAACAAGgtatggtaca ... atgttttcagGTCATTGATCTGGCAAGATTGAATCATGAGAACATAGCAAAGTTCTTAGGG
EST: gi|71330749|gb|DR802161.1|DR802161
EST:     CCTTCGAAGGTCATTGGACTAGCCACCATGAACTCTTTTACCAAAACAAG                         GTCATTGATCTGGCAAGATTGAATCATGAGAACATAGCAAAGTTCTTAGGG
genomic: CCTTCGAAGGTCATTGGACTAGCCACCATGAACTCTTTTACCAAAACAAGgtatggtaca ... atgttttcagGTCATTGATCTGGCAAGATTGAATCATGAGAACATAGCAAAGTTCTTAGGG
EST: gi|149106783|gb|EE188679.2|EE188679
EST:     CCTTCGAAGGTCATTGGACTAGCCACCATGAACTCTTTTACCAAAACAAG                         GTCATTGATCTGGCAAGATTGAATCATGAGAACATAGCAAAGTTCTTAGGG
genomic: CCTTCGAAGGTCATTGGACTAGCCACCATGAACTCTTTTACCAAAACAAGgtatggtaca ... atgttttcagGTCATTGATCTGGCAAGATTGAATCATGAGAACATAGCAAAGTTCTTAGGG
EST: gi|101388114|gb|EB816071.1|EB816071
EST:     CCTTCGAAGGTCATTGGACTAGCCACCATGAACTCTTTTACCAAAACAAG                         GTCATTGATCTGGCAAGATTGAATCATGAGAACATAGCAAAGTTCTTAGGG
genomic: CCTTCGAAGGTCATTGGACTAGCCACCATGAACTCTTTTACCAAAACAAGgtatggtaca ... atgttttcagGTCATTGATCTGGCAAGATTGAATCATGAGAACATAGCAAAGTTCTTAGGG
EST: gi|149013195|gb|EE042830.2|EE042830
EST:     TTCGAAGGTCATTGGGACTAGCCACCATGAACTCTTTTTACCAAAACAAG                         GTCATTGATCTGGCAAGATTGAATCATGAGAACATAGCAAAGTTCTTAGGG
genomic: TTCGAAGGTCATT-GGACTAGCCACCATGAACTC-TTTTACCAAAACAAGgtatggtaca ... atgttttcagGTCATTGATCTGGCAAGATTGAATCATGAGAACATAGCAAAGTTCTTAGGG
EST: gi|149097302|gb|EE183131.2|EE183131
EST:     CCTTCGAAGGTCATTGGACTAGCCACCATGAACTCTTTTACCAAAACAAG                         GTCATTGATCTGGCAAGATTGAATCATGAGAACATAGCAAAGTTCTTAGGG
genomic: CCTTCGAAGGTCATTGGACTAGCCACCATGAACTCTTTTACCAAAACAAGgtatggtaca ... atgttttcagGTCATTGATCTGGCAAGATTGAATCATGAGAACATAGCAAAGTTCTTAGGG
EST: gi|78122547|gb|DV540931.1|DV540931
EST:     CCTTCGAAGGTCATTGGACTAGCCACCATGAACTCTTTTACCAAAACAAG                         GTCATTGATCTGGCAAGATTGAATCATGAGAACATAGCAAAGTTCTTAGGG
genomic: CCTTCGAAGGTCATTGGACTAGCCACCATGAACTCTTTTACCAAAACAAGgtatggtaca ... atgttttcagGTCATTGATCTGGCAAGATTGAATCATGAGAACATAGCAAAGTTCTTAGGG
EST: gi|148943639|gb|EC888703.2|EC888703
EST:     CCTTCGAAGGTCATTGGACTAGCCACCATGAACTCTTTTACCAAAACAAG                         GTCATTGATCTGGCAAGATTGAATCATGAGAACATAGCAAAGTTCTTAGGG
genomic: CCTTCGAAGGTCATTGGACTAGCCACCATGAACTCTTTTACCAAAACAAGgtatggtaca ... atgttttcagGTCATTGATCTGGCAAGATTGAATCATGAGAACATAGCAAAGTTCTTAGGG
EST: gi|78084470|gb|DV512863.1|DV512863
EST:     GGTCATTGGACTAGCCACCATGAACTC-TTTACCAAAACAAG                         GTCATTGATCTGGCAAGATTGAATCATGAGAACATAGCAAAGTTCTTAGGG
genomic: GGTCATTGGACTAGCCACCATGAACTCTTTTACCAAAACAAGgtatggtaca ... atgttttcagGTCATTGATCTGGCAAGATTGAATCATGAGAACATAGCAAAGTTCTTAGGG
EST: gi|149004762|gb|EE039259.2|EE039259
EST:     GGTCATTGGACTAGACACCATGAACTCTTTTACCAAAACAAG                         GTCATTGATCTGGCAAGATTGAATCATGAGAACATAGCAAAGTTCTTAGGG
genomic: GGTCATTGGACTAGCCACCATGAACTCTTTTACCAAAACAAGgtatggtaca ... atgttttcagGTCATTGATCTGGCAAGATTGAATCATGAGAACATAGCAAAGTTCTTAGGG
EST: gi|149095721|gb|EE181354.2|EE181354
EST:     CCTTCGAAGGTCATTGGACTAGCCACCATGAACTCTTTTACCAAAACAAG                         GTCATTGATCTGGCAAGATTGAATCATGAGAACATAGCAAAGTTCTTAGGG
genomic: CCTTCGAAGGTCATTGGACTAGCCACCATGAACTCTTTTACCAAAACAAGgtatggtaca ... atgttttcagGTCATTGATCTGGCAAGATTGAATCATGAGAACATAGCAAAGTTCTTAGGG
EST: gi|76910133|gb|DV163719.1|DV163719
EST:     ATTGGACTAGCCACCATGAACTCTTTTACCAAAACAAG                         GTCATTGATCTGGCAAGATTGAATCATGAGAACATAGCAAAGTTCTTAGGG
genomic: ATTGGACTAGCCACCATGAACTCTTTTACCAAAACAAGgtatggtaca ... atgttttcagGTCATTGATCTGGCAAGATTGAATCATGAGAACATAGCAAAGTTCTTAGGG
EST: gi|148975399|gb|EE025699.2|EE025699
EST:     CCTTCGAAGGTCATTGGACTAGCCACCATGAACTCTTTTACCAAAACAAG                         GTCATTGATCTGGCAAGATTGAATCATGAGAACATAGCAAAGTTCTTAGGG
genomic: CCTTCGAAGGTCATTGGACTAGCCACCATGAACTCTTTTACCAAAACAAGgtatggtaca ... atgttttcagGTCATTGATCTGGCAAGATTGAATCATGAGAACATAGCAAAGTTCTTAGGG
EST: gi|149031687|gb|EE154870.2|EE154870
EST:     CCTTCGAAGGTCATTGGACTAGCCACCATGAACTCTTTTACCAAAACAAG                         GTCATTGATCTGGCAAGATTGAATCATGAGAACATAGCAAAGTTCTTAGGG
genomic: CCTTCGAAGGTCATTGGACTAGCCACCATGAACTCTTTTACCAAAACAAGgtatggtaca ... atgttttcagGTCATTGATCTGGCAAGATTGAATCATGAGAACATAGCAAAGTTCTTAGGG
EST: gi|149074933|gb|EE163389.2|EE163389
EST:     CCTTCGAAGGTCATTGGACTAGCCACCATGAACTCTTTTACCAAAACAAG                         GTCATTGATCTGGCAAGATTGAATCATGAGAACATAGCAAAGTTCTTAGGG
genomic: CCTTCGAAGGTCATTGGACTAGCCACCATGAACTCTTTTACCAAAACAAGgtatggtaca ... atgttttcagGTCATTGATCTGGCAAGATTGAATCATGAGAACATAGCAAAGTTCTTAGGG
EST: gi|94474040|gb|EB702998.1|EB702998
EST:     CCTTCGAAGGTCATTGGACTAGCCACCATGAACTCTTTTACCAAAACAAG                         GTCATTGATCTGGCAAGATTGAATCATGAGAACATAGCAAAGTTCTTAGGG
genomic: CCTTCGAAGGTCATTGGACTAGCCACCATGAACTCTTTTACCAAAACAAGgtatggtaca ... atgttttcagGTCATTGATCTGGCAAGATTGAATCATGAGAACATAGCAAAGTTCTTAGGG
EST: gi|149089831|gb|EE179109.2|EE179109
EST:     CCTTCGAAGGTCATTGGACTAGCCACCATGAACTCTTTTACCAAAACAAG                         GTCATTGATCTGGCAAGATTGAATCATGAGAACATAGCAAAGTTCTTAGGG
genomic: CCTTCGAAGGTCATTGGACTAGCCACCATGAACTCTTTTACCAAAACAAGgtatggtaca ... atgttttcagGTCATTGATCTGGCAAGATTGAATCATGAGAACATAGCAAAGTTCTTAGGG
EST: gi|149111973|gb|EE191133.2|EE191133
EST:     AGGTCATTGGACTAGCCACCATG-ACTTCTTTTACCAAAACAAG                         GTCATTGATCTGGCAAGATTGAATCATGAGAACATAGCAAAGTTCTTAGGG
genomic: AGGTCATTGGACTAGCCACCATGAAC-TCTTTTACCAAAACAAGgtatggtaca ... atgttttcagGTCATTGATCTGGCAAGATTGAATCATGAGAACATAGCAAAGTTCTTAGGG
EST: gi|148999085|gb|EE024226.2|EE024226
EST:     CCTTCGAAGGTCATTGGACTAGCCACCATGAACTCTTTTACCAAAACAAG                         GTCATTGATCTGGCAAGATTGAATCATGAGAACATAGCAAAGTTCTTAGGG
genomic: CCTTCGAAGGTCATTGGACTAGCCACCATGAACTCTTTTACCAAAACAAGgtatggtaca ... atgttttcagGTCATTGATCTGGCAAGATTGAATCATGAGAACATAGCAAAGTTCTTAGGG
EST: gi|91875214|gb|EB405171.1|EB405171
EST:     CCTTGGAGGGTCATTGGACTAGCCACCATGAACTCTTTTACCAAAACAAG                         GTCATTGATCTGGCAAGATTGAATCATGAGAACATAGCAAAGTTCTTAGGG
genomic: CCTTCGAAGGTCATTGGACTAGCCACCATGAACTCTTTTACCAAAACAAGgtatggtaca ... atgttttcagGTCATTGATCTGGCAAGATTGAATCATGAGAACATAGCAAAGTTCTTAGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaaacacttgtttttttttcttcccctggatactaaacggggtgatgttttcagGTCATTGATCTGGCAAGATTGAATCATGAGAACATAGCAAAGTTCTTAGGGTACTGCAGGGAGAGTGATCCATTCTCTCGGATGCTAGTCTTCGAGTACG
                               tactaaa  putative branch site (score: 1)
 tgttttc  putative PPT
 ttgtttttttttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggtacatgacaccaagggattcaaacacttgtttttttttcttcccctggatactaaacggggtgatgttttcagGTCATTGATCTGGCAAGATTGAATCATGAGAACATAGCAAAGTTCTTAGGGTACTGCAGGGAGAGTGATCCATTCTCTCGGATGCTAGTCTTCGAGTACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG