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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcatttgtgggtgacaattctcatgtttttagcgaggttccattatttttactgtgcacgatttacagGTGGATGTTACCGGGCTTGTTGATGGCCATTCTTCGTACCTGTCAGCTGCCCAGCAGATCCTGGAGCACCTTGAACTGAATACCTACTATCCTGTTTTTG

Basic information

species Zea mays
transcript GRMZM2G092776_T07
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G092776_T03 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os03g02170.2 (Oryza sativa), 3'ss of exon 14
gtaagcatttgtgggtgacaattctcatgttttta-gcgaggttccattat-ttttac-------tgtgca-----cgatttacagGTGGATGTTACCGGGCTTGTTGATGGCCATTCTTCGTACCTGTCAGCTGCCCAGCAGATCCTGGAGCACCTTGAACTGAATACCTACTATCCTGTTTTTG
|||||||| || ||||| || ||||  |||| ||| | ||  |||   ||| ||||||       |||| |     | |||||||||| |||||||| | |||||| ||||||||||| || |||||||| || || || ||||| |||||||| |||||||| |||||||||||||| |||||||
gtaagcatctg-gggtgcca-ttcttgtgttcttacgtgattttcatctatcttttacacgtctttgtgtacaatgcaatttacagGTCGATGTTACGGAGCTTGTCGATGGCCATTCGTCTTACCTGTCGGCAGCACAACAGATACTGGAGCATCTTGAACTAAATACCTACTATCCGGTTTTTG
















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|110536646|gb|EE040761.1|EE040761
EST:     CCCAAGGACTGGCTGGCATCCAGGCCATTGATGTGCCTGGTGTTGAGAAC                         GTGGATGTTACCGGGCTTGTTGATGGCCATTTTTTGTACCTGTCAGCTGCC
genomic: CCCAAGGACTGGCTGGCATCCAGGCCATTGATGTGCCTGGTGTTGAGAACgtaagcattt ... cgatttacagGTGGATGTTACCGGGCTTGTTGATGGCCATTCTTCGTACCTGTCAGCTGCC
EST: gi|89252188|gb|DY623974.1|DY623974
EST:     CCCAAGGACTGGCTGGCATCCAGGCCATTGATGTGCCTGGTGTTGAGAAC                         GTGGATGTTACCGGGCTTGTTGATGGCCATTTTTTGTACCTGTCAGCTGCC
genomic: CCCAAGGACTGGCTGGCATCCAGGCCATTGATGTGCCTGGTGTTGAGAACgtaagcattt ... cgatttacagGTGGATGTTACCGGGCTTGTTGATGGCCATTCTTCGTACCTGTCAGCTGCC
EST: gi|110960194|gb|EE180246.1|EE180246
EST:     CCCAAGGACTGGCTGGCATCCAGGCCATTGATGTGCCTGGTGTTGAGAAC                         GTGGATGTTACCGGGCTTGTTGATGGCCATTCTTCGTACCTGTCAGCTGCC
genomic: CCCAAGGACTGGCTGGCATCCAGGCCATTGATGTGCCTGGTGTTGAGAACgtaagcattt ... cgatttacagGTGGATGTTACCGGGCTTGTTGATGGCCATTCTTCGTACCTGTCAGCTGCC
EST: gi|149106666|gb|EE188560.2|EE188560
EST:     CCCAAGGACTGGCTGGCATCCAGGCCATTGATGTGCCTGGTGTTGAGAAC                         GTGGATGTTGCCGGGCTTGTTGATGGCCATTTTTTGTACCTGTCAGCTGCC
genomic: CCCAAGGACTGGCTGGCATCCAGGCCATTGATGTGCCTGGTGTTGAGAACgtaagcattt ... cgatttacagGTGGATGTTACCGGGCTTGTTGATGGCCATTCTTCGTACCTGTCAGCTGCC
EST: gi|148966542|gb|EE017566.2|EE017566
EST:     CCCAAGGACTGGGTGGCATTCAGGCCATTGATGTGCCTGGTGTTGAGAAC                         GTGGATGTTACCGGGCTTGTTGATGGCCATTTTTTGTTCCTGTCAGCTGCC
genomic: CCCAAGGACTGGCTGGCATCCAGGCCATTGATGTGCCTGGTGTTGAGAACgtaagcattt ... cgatttacagGTGGATGTTACCGGGCTTGTTGATGGCCATTCTTCGTACCTGTCAGCTGCC
EST: gi|74233198|gb|DT641112.1|DT641112
EST:     CCCAAGGACTGGCTGGCATCCAGGCCATTGATGTACCTGGTGTTGAGAAC                         GTGGATGTTACCGAGCTTGTTGATGGTCATTCTTCGTACCTGTCAGCTGCC
genomic: CCCAAGGACTGGCTGGCATCCAGGCCATTGATGTGCCTGGTGTTGAGAACgtaagcattt ... cgatttacagGTGGATGTTACCGGGCTTGTTGATGGCCATTCTTCGTACCTGTCAGCTGCC
EST: gi|91877534|gb|EB407491.1|EB407491
EST:     CCCAAGGACTGGCTGGCATCCAGGCCATTGATGTGCCTGGTGTTGAGAAC                         GTGGATGTTACCGGGCTTGTTGATGGCCATTCTTCGTACCTGTCAGCTGCC
genomic: CCCAAGGACTGGCTGGCATCCAGGCCATTGATGTGCCTGGTGTTGAGAACgtaagcattt ... cgatttacagGTGGATGTTACCGGGCTTGTTGATGGCCATTCTTCGTACCTGTCAGCTGCC
EST: gi|211299421|gb|FL314585.1|FL314585
EST:     CCCAAGGACTGGCTGGCATCCAGGCCATTGATGTACCTGGTGTTGAGAAC                         GTGGATGTTACCGAGCTTGTTGATGGTCATTCTTCGTACCTGTCAGCTGCC
genomic: CCCAAGGACTGGCTGGCATCCAGGCCATTGATGTGCCTGGTGTTGAGAACgtaagcattt ... cgatttacagGTGGATGTTACCGGGCTTGTTGATGGCCATTCTTCGTACCTGTCAGCTGCC
EST: gi|91877535|gb|EB407492.1|EB407492
EST:     CCCAAGGACTGGCTGGCATCCAGGCCATTGATGTGCCTGGTGTTGAGAAC                         GTGGATGTTACCGGG
genomic: CCCAAGGACTGGCTGGCATCCAGGCCATTGATGTGCCTGGTGTTGAGAACgtaagcattt ... cgatttacagGTGGATGTTACCGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaattctcatgtttttagcgaggttccattatttttactgtgcacgatttacagGTGGATGTTACCGGGCTTGTTGATGGCCATTCTTCGTACCTGTCAGCTGCCCAGCAGATCCTGGAGCACCTTGAACTGAATACCTACTATCCTGTTTTTG
                        ttccattattttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcatttgtgggtgacaattctcatgtttttagcgaggttccattatttttactgtgcacgatttacagGTGGATGTTACCGGGCTTGTTGATGGCCATTCTTCGTACCTGTCAGCTGCCCAGCAGATCCTGGAGCACCTTGAACTGAATACCTACTATCCTGTTTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA