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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCTGCGCTGTCGCTCCATGTCGGCCACCGCCGAGAGCGGTGGGGATCTGTCGGCGGCGCGCCGCCGGTGGGATCTCACCAACAAGGGGGCCGAGAGCACgtaatgcccactgccttctgctgcactcccttcgtttccgtgggttatgggtcggtctatccccggagcaatgtcgctgtcggagctcatcgtctagctc...

Basic information

species Zea mays
transcript GRMZM2G121176_T03
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G121176_T03 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os03g58480.1 (Oryza sativa), 5'ss of exon 1
----AGCTGCGCTGTCGCTCCATGTCGGCCACCGCCGAGAGCGGTGGGGATCTGTCGGCGGCGCGCCGCCGGTGGGATCTCACCAACAAGGGGGCCGAGAGCACgtaatgcccactgccttctgctgcactcccttcgtttccgtgggttatgggtcggtctatccccggagcaatgtcgctgtcggagctcatcgtctagctc-----
    ||||  |||  |   ||||| |||| |  | |||| | || || || |   ||||||||||  | ||||||||||| || |||||||| |||||||||| |||||| | | || |  | |||||| |    ||| ||   | | ||||   |   | | |     | |    |  |  |     |||| | || | ||       
CTGTAGCTA-GCTAGCTAGCCATGGCGGCGAATGGCGAGGGTGGCGGCGACC---CGGCGGCGCGGAGGCGGTGGGATCTGACGAACAAGGGTGCCGAGAGCATgtaatggc-agtggcaccagctgcatt----tcggtttgtttgtttattatttttttttttttttgggggggggggggggtttggctcgtggtgtggcgatgttc
















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|71441126|gb|DR822176.1|DR822176
EST:     TCGGCGGCGCGCCGCCGGTGGGATCTCACCAACAAGGGGGCCGAGAGCAC                         CCCAATTTTGAAAGATGCTGTGGAAATATCTACAGATGAAGAATCAGATGG
genomic: TCGGCGGCGCGCCGCCGGTGGGATCTCACCAACAAGGGGGCCGAGAGCACgtaatgccca ... ttttctgcagCCCAATTTTGAAAGATGCTGTGGAAATATCTACAGATGAAGAATCAGATGG
EST: gi|28873541|gb|CB329517.1|CB329517
EST:     TCGGCGGCGCGCCGCCGGTGGGATCTCACCAACAAGGGGGCCGAGAGCAC                         CCCAATTTTGAAAGATGCTGTGGAAATATCTACAGATGAAGAATCAGATGG
genomic: TCGGCGGCGCGCCGCCGGTGGGATCTCACCAACAAGGGGGCCGAGAGCACgtaatgccca ... ttttctgcagCCCAATTTTGAAAGATGCTGTGGAAATATCTACAGATGAAGAATCAGATGG
EST: gi|211077311|gb|FK959778.1|FK959778
EST:     TCGGCGGCGCGCCGCCGGTGGGATCTCACCAACAAGGGGGCCGAGAGCAC                         CCCAATTTTGAAAGATGCTGTGGAAATATCTACAGATGAAGAATCAGATGG
genomic: TCGGCGGCGCGCCGCCGGTGGGATCTCACCAACAAGGGGGCCGAGAGCACgtaatgccca ... ttttctgcagCCCAATTTTGAAAGATGCTGTGGAAATATCTACAGATGAAGAATCAGATGG
EST: gi|211080039|gb|FK959782.1|FK959782
EST:     TCGGCGGCGCGCCG-CGGTGGGATCTCACCAACAAGGGGGCCGAGAGCAC                         CCCAATTTTGAAAGATGCTGTGGAAATATCTACAGATGAAGAATCAGATGG
genomic: TCGGCGGCGCGCCGCCGGTGGGATCTCACCAACAAGGGGGCCGAGAGCACgtaatgccca ... ttttctgcagCCCAATTTTGAAAGATGCTGTGGAAATATCTACAGATGAAGAATCAGATGG
EST: gi|211077306|gb|FK959773.1|FK959773
EST:     TCGGCGGCGCGCCGCCGGTGGGATCTCACCAACAAGGGGGCCGAGAGCAC                         CCCAATTTTGAAAGATGCTGTGGAAATATCTACAGATGAAGAATCAGATGG
genomic: TCGGCGGCGCGCCGCCGGTGGGATCTCACCAACAAGGGGGCCGAGAGCACgtaatgccca ... ttttctgcagCCCAATTTTGAAAGATGCTGTGGAAATATCTACAGATGAAGAATCAGATGG
EST: gi|148982023|gb|EE028075.2|EE028075
EST:     TCGGCGGCGCGCCGCCGGTGGGATCTCACCAACAAGGGGGCCGAGAGCAC                         CCCAATTTTGAAAGATGCTGTGGAAATATCTACAGATGAAGAATCAGATGG
genomic: TCGGCGGCGCGCCGCCGGTGGGATCTCACCAACAAGGGGGCCGAGAGCACgtaatgccca ... ttttctgcagCCCAATTTTGAAAGATGCTGTGGAAATATCTACAGATGAAGAATCAGATGG
EST: gi|149112709|gb|EE295543.2|EE295543
EST:     TCGGCGGCGCGCCGCCGGTGGGATCTCACCAACAAGGGGGCCGAGAGCAC                         CCCAATTTTGAAAGATGCTGTGGAAATATCTACAGATGAAGAATCAGATGG
genomic: TCGGCGGCGCGCCGCCGGTGGGATCTCACCAACAAGGGGGCCGAGAGCACgtaatgccca ... ttttctgcagCCCAATTTTGAAAGATGCTGTGGAAATATCTACAGATGAAGAATCAGATGG
EST: gi|149073356|gb|EE161654.2|EE161654
EST:     TCGGCGGCGCGCCGCCGGTGGGATCTCACCAACAAGGGGGCCGAGAGCAC                         CCCAATTTTGAAAGATGCTGTGGAAATATCTACAGATGAAGAATCAGATGG
genomic: TCGGCGGCGCGCCGCCGGTGGGATCTCACCAACAAGGGGGCCGAGAGCACgtaatgccca ... ttttctgcagCCCAATTTTGAAAGATGCTGTGGAAATATCTACAGATGAAGAATCAGATGG
EST: gi|211077308|gb|FK959775.1|FK959775
EST:     TCGGCGGCGCGCCGCCGGTGGGATCTCACCAACAAGGGGGCCGAGAGCAC                         CCCAATTTTGAAAGATGCTGTGGAAATATCTACAGATGAAGAATCAGATGG
genomic: TCGGCGGCGCGCCGCCGGTGGGATCTCACCAACAAGGGGGCCGAGAGCACgtaatgccca ... ttttctgcagCCCAATTTTGAAAGATGCTGTGGAAATATCTACAGATGAAGAATCAGATGG
EST: gi|148942669|gb|EC887690.2|EC887690
EST:     TCGGCGGCGCGCCGCCGGTGGGATCTCACCAACAAGGGGGCCGAGAGCAC                         CCCAATTTTGAAAGATGCTGTGGAAATATCTACAGATGAAGAATCAGATGG
genomic: TCGGCGGCGCGCCGCCGGTGGGATCTCACCAACAAGGGGGCCGAGAGCACgtaatgccca ... ttttctgcagCCCAATTTTGAAAGATGCTGTGGAAATATCTACAGATGAAGAATCAGATGG
EST: gi|211077310|gb|FK959777.1|FK959777
EST:     TCGGCGGCGCGCCGCCGGTGGGATCTCACCAACAAGGGGGCCGAGAGCAC                         CCCAATTTTGAAAGATGCTGTGGAAATATCTACAGATGAAGAATCAGATGG
genomic: TCGGCGGCGCGCCGCCGGTGGGATCTCACCAACAAGGGGGCCGAGAGCACgtaatgccca ... ttttctgcagCCCAATTTTGAAAGATGCTGTGGAAATATCTACAGATGAAGAATCAGATGG
EST: gi|211077309|gb|FK959776.1|FK959776
EST:     TCGGCGGCGCGCCGCCGGTGGGATCTCACCAACAAGGGGGCCGAGAGCAC                         CCCAATTTTGAAAGATGCTGTGGAAATATCTACAGATGAAGAATCAGATGG
genomic: TCGGCGGCGCGCCGCCGGTGGGATCTCACCAACAAGGGGGCCGAGAGCACgtaatgccca ... ttttctgcagCCCAATTTTGAAAGATGCTGTGGAAATATCTACAGATGAAGAATCAGATGG
EST: gi|76912446|gb|DV164736.1|DV164736
EST:     TCGGCGGCGCGCCGCCGGTGGGATCTCACCAACAAGGGGGCCGAGAGCAC                         CCCAATTTTGAAAGATGCTGTGGAAATATCTACAGATGAAGAATCAGATGG
genomic: TCGGCGGCGCGCCGCCGGTGGGATCTCACCAACAAGGGGGCCGAGAGCACgtaatgccca ... ttttctgcagCCCAATTTTGAAAGATGCTGTGGAAATATCTACAGATGAAGAATCAGATGG
EST: gi|149095505|gb|EE181161.2|EE181161
EST:     TCGGCGGCGCGCCGCCGGTGGGATCTCACCAACAAGGGGGCCGAGAGCAC                         CCCAATTTTGAAAGATGCTGTGGAAATATCTACAGATGAAGAATCAGATGG
genomic: TCGGCGGCGCGCCGCCGGTGGGATCTCACCAACAAGGGGGCCGAGAGCACgtaatgccca ... ttttctgcagCCCAATTTTGAAAGATGCTGTGGAAATATCTACAGATGAAGAATCAGATGG
EST: gi|211077300|gb|FK959767.1|FK959767
EST:     TCGGCGGCGCGCCGCCGGTGGGATCTCACCAACAAGGGGGCCGAGAGCAC                         CCCAATTTTGAAAGATGCTGTGGAAATATCTACAGATGAAGAATCAGATGG
genomic: TCGGCGGCGCGCCGCCGGTGGGATCTCACCAACAAGGGGGCCGAGAGCACgtaatgccca ... ttttctgcagCCCAATTTTGAAAGATGCTGTGGAAATATCTACAGATGAAGAATCAGATGG
EST: gi|32826748|gb|CD966426.1|CD966426
EST:     GATCTCACCAACAAGGGGGCCGAGAGCAC                         CCCAATTTTGAAAGATGCTGTGGAAATATCTACAGATGAAGAATCAGATGG
genomic: GATCTCACCAACAAGGGGGCCGAGAGCACgtaatgccca ... ttttctgcagCCCAATTTTGAAAGATGCTGTGGAAATATCTACAGATGAAGAATCAGATGG
EST: gi|32827088|gb|CD966766.1|CD966766
EST:     GATCTTACCANCAAGGGGGCCGAGAGCAC                         CCCAATTTTGAAAGATGCTGTGGAAATATCTACAGATGAAGAATCAGATGG
genomic: GATCTCACCAACAAGGGGGCCGAGAGCACgtaatgccca ... ttttctgcagCCCAATTTTGAAAGATGCTGTGGAAATATCTACAGATGAAGAATCAGATGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCTGCGCTGTCGCTCCATGTCGGCCACCGCCGAGAGCGGTGGGGATCTGTCGGCGGCGCGCCGCCGGTGGGATCTCACCAACAAGGGGGCCGAGAGCACgtaatgcccactgccttctgctgcactcccttcgtttccgtgggttatgggtcggtctatccccggagcaatgtcgctgtcggagctcatcgtctagctc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA