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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGTCGCGGATGGTGGGCACTATGACTACGATCTCTTCGTCATCGGGGCGGGCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAGgttcgttgcttccccacaccccaccagctcctatgcctgacgtgatgcctcctagccgtgatacccgagcccatctactgtcgcctcgctgctctatccg...

Basic information

species Zea mays
transcript GRMZM5G806449_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G806449_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g56850.1 (Oryza sativa), 5'ss of exon 2
CGTCGCGGATGGTGGGCACTATGACTACGATCTCTTCGTCATCGGGGCGGGCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAGgttcgttgcttccccacaccccaccagctcctatgcctgacgtgatgcctcctagccgtgatacccgagcccatctactgtcgcctcgctgctctatccg------
|||| | || || |||  ||| |||||||| || ||||| ||||| || || ||||||||||| || |||||||||||| |||| |||||||| ||||||||| |    ||| || | ||||  |    || ||   ||    ||  | |  | |   |  ||        | | |  | | |  ||| ||       ||      
CGTCACCGACGGCGGGAGCTACGACTACGACCTGTTCGTGATCGGCGCCGGGAGCGGCGGCGTCCGGGGCTCTCGCACCTCCGCGTCCTTCGGGGCTAAGgtttgacttttctcctctcccc--cgctccccatttttgcgaggaaacgtgttggatttt-tattttttttcgtgtgat-ttgattcggtgtgtggcgcggttcag
















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|211339791|gb|FK980807.1|FK980807
EST:     GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAG                         GTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
genomic: GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAGgttcgttgct ... tttctggcagGTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
EST: gi|149077608|gb|EE166308.2|EE166308
EST:     GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAG                         GTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
genomic: GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAGgttcgttgct ... tttctggcagGTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
EST: gi|29577206|gb|CB617318.1|CB617318
EST:     GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAG                         GTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
genomic: GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAGgttcgttgct ... tttctggcagGTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
EST: gi|31611942|gb|CD568564.1|CD568564
EST:     GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAG                         GTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
genomic: GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAGgttcgttgct ... tttctggcagGTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
EST: gi|31664370|gb|CD573095.1|CD573095
EST:     GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAG                         GTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
genomic: GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAGgttcgttgct ... tttctggcagGTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
EST: gi|211426647|gb|FL071975.1|FL071975
EST:     GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAG                         GTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
genomic: GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAGgttcgttgct ... tttctggcagGTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
EST: gi|211426649|gb|FL071977.1|FL071977
EST:     GCAGCGGCGGCGATCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAG                         GTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
genomic: GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAGgttcgttgct ... tttctggcagGTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
EST: gi|31405875|gb|CD484607.1|CD484607
EST:     GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAG                         GCTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
genomic: GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAGgttcgttgct ... tttctggcagGTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
EST: gi|30306583|gb|CD001256.1|CD001256
EST:     GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAG                         GTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
genomic: GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAGgttcgttgct ... tttctggcagGTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
EST: gi|211337400|gb|FK980798.1|FK980798
EST:     GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAG                         GTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
genomic: GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAGgttcgttgct ... tttctggcagGTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
EST: gi|28910264|gb|CB331352.1|CB331352
EST:     GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAG                         GCTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
genomic: GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAGgttcgttgct ... tttctggcagGTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
EST: gi|211341005|gb|FL266234.1|FL266234
EST:     GCAGCGGCGGTGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAG                         GTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
genomic: GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAGgttcgttgct ... tttctggcagGTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
EST: gi|31611973|gb|CD568595.1|CD568595
EST:     GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCT-AG                         GTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
genomic: GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAGgttcgttgct ... tttctggcagGTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
EST: gi|211337405|gb|FK980803.1|FK980803
EST:     GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAG                         GTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
genomic: GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAGgttcgttgct ... tttctggcagGTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
EST: gi|76012767|gb|DT939937.1|DT939937
EST:     GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAG                         GTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
genomic: GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAGgttcgttgct ... tttctggcagGTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
EST: gi|148994377|gb|EE034060.2|EE034060
EST:     GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAG                         GTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
genomic: GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAGgttcgttgct ... tttctggcagGTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
EST: gi|149108741|gb|EE292941.2|EE292941
EST:     GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAG                         GTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
genomic: GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAGgttcgttgct ... tttctggcagGTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGTCGCGGATGGTGGGCACTATGACTACGATCTCTTCGTCATCGGGGCGGGCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAGgttcgttgcttccccacaccccaccagctcctatgcctgacgtgatgcctcctagccgtgatacccgagcccatctactgtcgcctcgctgctctatccg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT