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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttcctcctccgcctccatgacctcgtcgtcagagctcgggctccgactgtcacctcatcgccaccagcgctgccgtacttatcatgcgttggggttgacgggttttgatgtctggcagTATGCGGCGCTGCGGGACGCGTCGCCTAACGGGAGGCTGCGGATGCGGGACCTCCCCGCCGCCATCTCTGGCGTCCGCGGTGCGGCCAAGAGCAGGGACG

Basic information

species Zea mays
transcript GRMZM2G081380_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G081380_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g33080.1 (Oryza sativa), 3'ss of exon 1
gtatttcctcctccgcctccatgacctcgtcgtcagagctcgggctccgactgtcacctcatcgccaccagcgctgccgtacttatcatgcgttggggttgacg-ggttttgatgtctggcagTATGCGGCGCTGCGGGACGCGTCGCCTAACGGGAGGCTGCGGATGCGGGACCTCCCCGCCGCCATCTCTGGCGTCCGCGGTGCGGCCAAGAGCAGGGACG
    | |  |  ||   |||||| || || |   |    || | | ||  | | |    |  |||| |       |   | |   |     ||||| |||   | |||  || |||    ||||| |||||||||||||||||| |||| | ||||||||||||| |||||||||| || || ||  | ||   || | |||  | ||||  ||   | |  |
---gtacgacgaccctgtccatggccacggctcga----tccgccgcccgccgccgtgccgccgccgcattgatcgtgattcgcgtttctggttggtgtttgtgtggtggtggtgtt--acagTACGCGGCGCTGCGGGACGCGGCGCCGAGCGGGAGGCTGCGGCTGCGGGACCTGCCTGCGGCGCTATCATCCGCCGGCGTCGGGGCCGGGAAAGGAGGGG
















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|149096922|gb|EE182720.2|EE182720
EST:     ACCTGCAGCGCCGCTTCACGCAGGCCGAACTTCGCGCGCTCCAGGCCCAG                         TATGCGGCGCTGCGGGACGCGTCGCCTAACGGGAGGCTGCGGATGCGGGAC
genomic: ACCTGCAGCGCCGCTTCACGCAGGCCGAACTTCGCGCGCTCCAGGCCCAGgtatttcctc ... tgtctggcagTATGCGGCGCTGCGGGACGCGTCGCCTAACGGGAGGCTGCGGATGCGGGAC
EST: gi|71313366|gb|DR793232.1|DR793232
EST:     ACCTGCAGCGCCGCTTCACGCAGGCCGAACTTCGCGCGCTCCAGGCCCAG                         TATGCGGCGCTGCGGGACGCGTCGCCTAACGGGAGGCTGCGGATGCGGGAC
genomic: ACCTGCAGCGCCGCTTCACGCAGGCCGAACTTCGCGCGCTCCAGGCCCAGgtatttcctc ... tgtctggcagTATGCGGCGCTGCGGGACGCGTCGCCTAACGGGAGGCTGCGGATGCGGGAC
EST: gi|211325002|gb|FL127014.1|FL127014
EST:     ACCTGCTGCGTCGCTTCACGCAGGCCGAACTTCGCGCGCTCCAGGCCCAG                         TATGCGGCGCTGCGGGACGCGTCGCCTAACGGGAGGCTGCGGATGCGGGAT
genomic: ACCTGCAGCGCCGCTTCACGCAGGCCGAACTTCGCGCGCTCCAGGCCCAGgtatttcctc ... tgtctggcagTATGCGGCGCTGCGGGACGCGTCGCCTAACGGGAGGCTGCGGATGCGGGAC
EST: gi|91048165|gb|EB158583.1|EB158583
EST:     ACCTGCAGCGCCGCTTCACGCAGGCCGAACTTCGCGCGCTCCAGGCCCAG                         TATGCGGCGCTGCGGGACGCGTCGCCTAACGGGAGGCTGCGGATGCGGGAC
genomic: ACCTGCAGCGCCGCTTCACGCAGGCCGAACTTCGCGCGCTCCAGGCCCAGgtatttcctc ... tgtctggcagTATGCGGCGCTGCGGGACGCGTCGCCTAACGGGAGGCTGCGGATGCGGGAC
EST: gi|101398956|gb|EB821350.1|EB821350
EST:     ACCTGCAGCGCCGCTTCACGCAGGCCGAACTTCGCGCGCTCCAGGCCCAG                         TATGCGGCGCTGCGGGACGCGTCGCCTAACGGGAGGCTGCGGATGCGGGAC
genomic: ACCTGCAGCGCCGCTTCACGCAGGCCGAACTTCGCGCGCTCCAGGCCCAGgtatttcctc ... tgtctggcagTATGCGGCGCTGCGGGACGCGTCGCCTAACGGGAGGCTGCGGATGCGGGAC
EST: gi|148970201|gb|EE021132.2|EE021132
EST:     GCGCCGCTTCACGCAGGCCGAACTTCGCGCGCTCCAGGCCCAG                         TATGCGGCGCTGCGGGACGCGTCGCCTAACGGGAGGCTGCGGATGCGGGAC
genomic: GCGCCGCTTCACGCAGGCCGAACTTCGCGCGCTCCAGGCCCAGgtatttcctc ... tgtctggcagTATGCGGCGCTGCGGGACGCGTCGCCTAACGGGAGGCTGCGGATGCGGGAC
EST: gi|149081443|gb|EE170567.2|EE170567
EST:     ACCTGCAGCGCCGCTTCACGCAGGCCGAACTTCGCGCGCTCCAGGCCCAG                         TATGCGGCGCTGCGGGACGCGTCGCCTAACGGGAGGCTGCGGATGCGGGAC
genomic: ACCTGCAGCGCCGCTTCACGCAGGCCGAACTTCGCGCGCTCCAGGCCCAGgtatttcctc ... tgtctggcagTATGCGGCGCTGCGGGACGCGTCGCCTAACGGGAGGCTGCGGATGCGGGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccagcgctgccgtacttatcatgcgttggggttgacgggttttgatgtctggcagTATGCGGCGCTGCGGGACGCGTCGCCTAACGGGAGGCTGCGGATGCGGGACCTCCCCGCCGCCATCTCTGGCGTCCGCGGTGCGGCCAAGAGCAGGGACG
                                       ttttgat  putative branch site (score: 4)
            tacttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttcctcctccgcctccatgacctcgtcgtcagagctcgggctccgactgtcacctcatcgccaccagcgctgccgtacttatcatgcgttggggttgacgggttttgatgtctggcagTATGCGGCGCTGCGGGACGCGTCGCCTAACGGGAGGCTGCGGATGCGGGACCTCCCCGCCGCCATCTCTGGCGTCCGCGGTGCGGCCAAGAGCAGGGACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG