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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCATGGCTGGACCTGCTGTTCTCAATGAGCGTATCCTTTCTTCCATGTCCCAGAAACATGTTGCTGCTCACCCATGGCATGATTTGGAGATAGgtactaaacacttcttccctcatcaaggacatgctcccctcattttgctatcctttgtttcatagactatgatattgtcacctttgcattccctgattccctcatggcgtaagaatatcaaattgcactagtgctctgctctataagcgatttgctgttttgtatttcccttaccgtgtacactttcaaatgcag

Basic information

species Zea mays
transcript GRMZM2G046587_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G046587_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g47600.2 (Oryza sativa), 5'ss of exon 2
------CCATGGC-TGGACCTGCTGTTCTCAATGAGCGTATCCTTTCTTCCATGTCCCAGAAACATGTTGCTGCTCACCCATGGCATGATTTGGAGATAGgtactaaacacttcttccctcatcaaggacatgctcccctcattttgctatcctttgtttcatagactatgatattgtcacctttgcattccctgattccctcatggcgtaagaatatcaaattgcactagtgctctgctct-ataagcgatttgctgttttgtatttcccttaccgtgtacactttcaaatgcag
       || |       ||||||| |||||| ||||| ||||||||||||||||| || ||||||||||||||||| |||||||| ||| |||||||||||||    || |  ||| ||||    | | ||  |    ||  ||   | |  |   || | ||  || ||| ||| |   || |||  |   ||||| | |   |    ||   | ||  |||| |    |  | | |||| | | ||                                               
CTGGGATCAAGATACCCCCCTGCTGCTCTCAACGAGCGCATCCTTTCTTCCATGTCTCAAAAACATGTTGCTGCTCATCCATGGCACGATCTGGAGATAGgtaccttgcaatgtttcactca----gaatatatttttttctgttcagtcttttcc-ttgcttatgct-tga-attatt--ctgtgctctgaatgatttctt---gttccaaatttgtcttattggatgcctattgtcctcttaaatgcag---------------------------------------------
















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|211537734|gb|FL105292.1|FL105292
EST:     CATGTCCCAGAAACATGTTGCTGCTCACCCATGGCATGATTTGGAGATAG                         GACCAGGGGCTCCTGAATTCTTCAATTGT
genomic: CATGTCCCAGAAACATGTTGCTGCTCACCCATGGCATGATTTGGAGATAGgtactaaaca ... tcaaatgcagGACCAGGGGCTCCTGAATTCTTCAATTGT
EST: gi|88756535|gb|DY540676.1|DY540676
EST:     CATGTCCCAGAAACATGTTGCTGCTCACCCATGGCATGATTTGGAGATAG                         GACCAGGGGCTCCTGAATTCTTCAATTGT
genomic: CATGTCCCAGAAACATGTTGCTGCTCACCCATGGCATGATTTGGAGATAGgtactaaaca ... tcaaatgcagGACCAGGGGCTCCTGAATTCTTCAATTGT
EST: gi|13126709|gb|BG317279.1|BG317279
EST:     CATGTCCCAGAAACATGTTGCTGCTCACCCATGGCATGATTTGGAGATAG                         GACCAGGGGCTCCTGAATTCTTCAATTGT
genomic: CATGTCCCAGAAACATGTTGCTGCTCACCCATGGCATGATTTGGAGATAGgtactaaaca ... tcaaatgcagGACCAGGGGCTCCTGAATTCTTCAATTGT
EST: gi|13126289|gb|BG316859.1|BG316859
EST:     CATGTCCCAGAAACATGTTGCTGCTCACCCATGGCATGATTTGGAGATAG                         GACCAGGGGCTCCTGAATTCTTCAATTGT
genomic: CATGTCCCAGAAACATGTTGCTGCTCACCCATGGCATGATTTGGAGATAGgtactaaaca ... tcaaatgcagGACCAGGGGCTCCTGAATTCTTCAATTGT
EST: gi|13491080|gb|BG517844.1|BG517844
EST:     CATGTCCCAGAAACATGTTGCTGCTCATTTATGGCATGATTTGGAGATAG                         GACCAGGGGCTCCTGAATTCTTCAATTGT
genomic: CATGTCCCAGAAACATGTTGCTGCTCACCCATGGCATGATTTGGAGATAGgtactaaaca ... tcaaatgcagGACCAGGGGCTCCTGAATTCTTCAATTGT
EST: gi|74244615|gb|DT652529.1|DT652529
EST:     CATGTCCCAGAAACATGTTGCTGCTCACCCATGGCATGATTTGGAGATAG                         GACCAGGGGCTCCTGAATTCTTCAATTGT
genomic: CATGTCCCAGAAACATGTTGCTGCTCACCCATGGCATGATTTGGAGATAGgtactaaaca ... tcaaatgcagGACCAGGGGCTCCTGAATTCTTCAATTGT
EST: gi|9732830|gb|BE511582.1|BE511582
EST:     ATGA-TTGGAGATAG                         GACCAGGGGCTCCTGAATTCTTCAATTGT
genomic: ATGATTTGGAGATAGgtactaaaca ... tcaaatgcagGACCAGGGGCTCCTGAATTCTTCAATTGT
EST: gi|32851273|gb|CD990954.1|CD990954
EST:     CATGTCCCAGAAACATGTTGCTGCTCACCCATGGCATGATTTGGAGATAG                         GACCAGGGGCTCCTGAATTCTTCAATTGT
genomic: CATGTCCCAGAAACATGTTGCTGCTCACCCATGGCATGATTTGGAGATAGgtactaaaca ... tcaaatgcagGACCAGGGGCTCCTGAATTCTTCAATTGT
EST: gi|60354612|gb|DN221585.1|DN221585
EST:     GGCATGATTTGGAGATAG                         GACCAGGGGCTCCTGAATTCTTCAATTGT
genomic: GGCATGATTTGGAGATAGgtactaaaca ... tcaaatgcagGACCAGGGGCTCCTGAATTCTTCAATTGT
EST: gi|149099849|gb|EE185901.2|EE185901
EST:     CATGTCCCAGAAACATGTTGCTGCTCACCCATGGCATGATTTGGAGATAG                         GACCAGGGGCTCCTGAATTCTTCAATTGT
genomic: CATGTCCCAGAAACATGTTGCTGCTCACCCATGGCATGATTTGGAGATAGgtactaaaca ... tcaaatgcagGACCAGGGGCTCCTGAATTCTTCAATTGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCATGGCTGGACCTGCTGTTCTCAATGAGCGTATCCTTTCTTCCATGTCCCAGAAACATGTTGCTGCTCACCCATGGCATGATTTGGAGATAGgtactaaacacttcttccctcatcaaggacatgctcccctcattttgctatcctttgtttcatagactatgatattgtcacctttgcattccctgattccctcatggcgtaagaatatcaaattgcactagtgctctgctctataagcgatttgctgttttgtatttcccttaccgtgtacactttcaaatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT