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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGAGCCTTTTGCTAGCCTTTGTCGACATTTATGCACTTCTTGTCAAGCGATCGTTGAGAAATGCCCGAGCTGTATGTATATTTACTATCGGAGATGGGgtgagtaatatcatttcattctaccctgtaaaaaaactctgttttgtaaaatatataacactgttgtactttttttcactcatttgactattcgtctatt...

Basic information

species Zea mays
transcript GRMZM2G136901_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G136901_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os10g20250.1 (Oryza sativa), 5'ss of exon 2
GTGGAGCCTTTTGCTAGCCTTTGTCGACATTTATGCACTTCTTGTCAAGCGATCGTTGAGAAATGCCCGAGCTGTATGTATATTTACTATCGGAGATGGGgtgagtaatatcatttcattctaccctgtaaaaaaactctgttttgtaaaatatataacactgttgtactttttttcactcatttgactattcgtctatt----------------
|||||||||||  |||||| |||| || ||||||||||||||||| ||||| || ||| | ||| | |  ||||| ||||||||||| |||||||||||||| |||       ||| ||  | |  |  | ||     |  |||||  ||    ||  |  | ||    |||   | | |    |  |||||   | |                  
GTGGAGCCTTTCACTAGCCGTTGTTGATATTTATGCACTTCTTGTGAAGCGTTCTTTGCGGAATCCACAGGCTGTGTGTATATTTACCATCGGAGATGGGgttagtg------ttttatctttctataaataaggggccatttttgctaag---attccttttttactttttgcataaatagaatacctattgaacaacgttattgatttttgtag
















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|8516225|gb|BE122953.1|BE122953
EST:     GATCGTTGAGAAATGCCCGAGCTGTATGTATATTTACTATCGGAGATGGG                         ATCACAGGTACAATAACCTTGGGCGCGGCATGTGCTTCAGCAGGAATCACT
genomic: GATCGTTGAGAAATGCCCGAGCTGTATGTATATTTACTATCGGAGATGGGgtgagtaata ... ttatttgtagATCACAGGTACAATAACCTTGGGCGCGGCATGTGCTTCAGCAGGAATCACT
EST: gi|166571205|gb|EG067630.1|EG067630
EST:     ATTTACTATCGGAGATGGG                         ATCACAGGTACAATAACCTTGGGCGCGGCATGTGACTTCAGCAGGAATCAC
genomic: ATTTACTATCGGAGATGGGgtgagtaata ... ttatttgtagATCACAGGTACAATAACCTTGGGCGCGGCATGTG-CTTCAGCAGGAATCAC
EST: gi|211165529|gb|FL456872.1|FL456872
EST:     GATCGTTGAGAAATGCCCGAGCTGTATGTATATTTACTATCGGAGATGGG                         ATCACAGGTACAATAACCTTGGGCGCGGCATGTGCTTCAGCAGGAATCACT
genomic: GATCGTTGAGAAATGCCCGAGCTGTATGTATATTTACTATCGGAGATGGGgtgagtaata ... ttatttgtagATCACAGGTACAATAACCTTGGGCGCGGCATGTGCTTCAGCAGGAATCACT
EST: gi|8516346|gb|BE123072.1|BE123072
EST:     GATCGTTGAGAAATGCCCGAGCTGTATGTATATTTACTATCGGAGATGGG                         ATCACAGGTACAATAACCTTGGGCGCGGCATGTGCTTCAGCAGGAATCACT
genomic: GATCGTTGAGAAATGCCCGAGCTGTATGTATATTTACTATCGGAGATGGGgtgagtaata ... ttatttgtagATCACAGGTACAATAACCTTGGGCGCGGCATGTGCTTCAGCAGGAATCACT
EST: gi|78022291|gb|DV490678.1|DV490678
EST:     GATCGTTGAGAAATGCCCGAGCTGTATGTATATTTACTATCGGAGATGGG                         ATCACAGGTACAATAACCTTGGGCGCGGCATGTGCTTCAGCAGGAATCACT
genomic: GATCGTTGAGAAATGCCCGAGCTGTATGTATATTTACTATCGGAGATGGGgtgagtaata ... ttatttgtagATCACAGGTACAATAACCTTGGGCGCGGCATGTGCTTCAGCAGGAATCACT
EST: gi|211372489|gb|FL433669.1|FL433669
EST:     GATCGTTGAGAAATGCCCGAGCTGTATGTATATTTACTATCGGAGATGGG                         ATCACAGGTACAATAACCTTGGGCGCGGCATGTGCTTCAGCAGGAATCACT
genomic: GATCGTTGAGAAATGCCCGAGCTGTATGTATATTTACTATCGGAGATGGGgtgagtaata ... ttatttgtagATCACAGGTACAATAACCTTGGGCGCGGCATGTGCTTCAGCAGGAATCACT
EST: gi|33096686|gb|CF056680.1|CF056680
EST:     GATCGTTGAGAAATGCCCGAGCTGTATGTATATTTACTATCGGAGATGGG                         ATCACAGGTACAATAACCTTGGGCGCGGCATGTGCTTCAGCAGGAATCACT
genomic: GATCGTTGAGAAATGCCCGAGCTGTATGTATATTTACTATCGGAGATGGGgtgagtaata ... ttatttgtagATCACAGGTACAATAACCTTGGGCGCGGCATGTGCTTCAGCAGGAATCACT
EST: gi|8516703|gb|BE123427.1|BE123427
EST:     GATCGTTGAGAAATGCCCGAGCTGTATGTATATTTACTATCGGAGATGGG                         ATCCCAGGTACAATAACCTTGGGCGCGGCATGTGCTTCAGCAGGAATCCCT
genomic: GATCGTTGAGAAATGCCCGAGCTGTATGTATATTTACTATCGGAGATGGGgtgagtaata ... ttatttgtagATCACAGGTACAATAACCTTGGGCGCGGCATGTGCTTCAGCAGGAATCACT
EST: gi|166534918|gb|EG239696.1|EG239696
EST:     ATTTACTATCGGAGATGGG                         ATCACAGGTACAATAACCTTGGGCGCGGCATGTGCTTCAGCAGGAATCACT
genomic: ATTTACTATCGGAGATGGGgtgagtaata ... ttatttgtagATCACAGGTACAATAACCTTGGGCGCGGCATGTGCTTCAGCAGGAATCACT
EST: gi|14883584|gb|BI273433.1|BI273433
EST:     TATCGGAGATGGG                         ATCACAGGTACAATAACCTTGGGCGCGGCATGTGCTTCAGCAGGAATCACT
genomic: TATCGGAGATGGGgtgagtaata ... ttatttgtagATCACAGGTACAATAACCTTGGGCGCGGCATGTGCTTCAGCAGGAATCACT
EST: gi|88747491|gb|DY531632.1|DY531632
EST:     GATCGTTGAGAAATGCCCGAGCTGTATGTATATTTACTATCGGAGATGGG                         ATCACAGGTACAATAACCTTGGGCGCGGCATGTGCTTCAGCAGGAATCACT
genomic: GATCGTTGAGAAATGCCCGAGCTGTATGTATATTTACTATCGGAGATGGGgtgagtaata ... ttatttgtagATCACAGGTACAATAACCTTGGGCGCGGCATGTGCTTCAGCAGGAATCACT

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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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGAGCCTTTTGCTAGCCTTTGTCGACATTTATGCACTTCTTGTCAAGCGATCGTTGAGAAATGCCCGAGCTGTATGTATATTTACTATCGGAGATGGGgtgagtaatatcatttcattctaccctgtaaaaaaactctgttttgtaaaatatataacactgttgtactttttttcactcatttgactattcgtctatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG