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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctggtcaatttccctagttcatctaaataaaattttcaggcagattttaccattcatttgagctggacactaacaaaaaaaattgttatccatgtgcagAGGCTTGTGATGAAATACGGGTCACTTGTGTCTGTTGTCTCTTTTGTTGGACTGTTTATCTACCTTGTCGCGAGCCCGTCGAAGAGCAGCTCAAAGGCAA

Basic information

species Zea mays
transcript GRMZM2G067476_T03
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G067476_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g01307.2 (Oryza sativa), 3'ss of exon 5
tctggtcaatttccctagttcatctaaataaaattttcaggcagattttaccattcatttgagctggacactaacaaaaaaaattgttatccatgtgcagAGGCTTGTGATGAAATACGGGTCACTTGTGTCTGTTGTCTCTTTTGTTGGACTGTTTATCTACCTTGTCGCGAGCCCGTCGAAG---AGCAGCTCAAAGGCAA
    || ||||| |    ||  | | | |  |        |||  ||||    | ||| |  | | ||    |  |   | ||   |||||||| ||||||||||||||  ||| |||||||| || ||||| |||||    || |||||| ||||||||||||| || || |||||||| ||    ||| |  |||| |   
----gtaaatttactc--tttgttttattcta--caaggagcaacttttctagtgcatctatggtagaagaaattactgagaa--attatccatttgcagAGGCTTGTGGCGAAGTACGGGTCGCTGGTGTCCGTTGTTGGCTTGGTTGGAGTGTTTATCTACCTGGTTGCAAGCCCGTCAAAATCCAGCGGTGCAAAAG---
















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|15426866|gb|BI542688.1|BI542688
EST:     AGAGAAGAAGTTTGAATGGGCTAAG                         AGGCTTGTGATGAAATACGGGTCACTTGTGTCTGTTGTCTCTTTTGTTGG
genomic: AGAGAAGAAGTTTGAATGGG-TAA-gtaagcatgc ... ccatgtgcagAGGCTTGTGATGAAATACGGGTCACTTGTGTCTGTTGTCTCTTTTGTTGG
EST: gi|15426866|gb|BI542688.1|BI542688
EST:     AGAGAAGAAGTTTGAATGGGCTAAG                         AGGCTTGTGATGAAATACGGGTCACTTGTGTCTGTTGTCTCTTTTGTTGG
genomic: AGAGAAGAAGTTTGAATGGG-TAA-gtaagcatgc ... ccatgtgcagAGGCTTGTGATGAAATACGGGTCACTTGTGTCTGTTGTCTCTTTTGTTGG
EST: gi|15053686|gb|BI359231.1|BI359231
EST:     AGAGAAGAAGTTTGAATGGGCTAAG                         AGGCTTGTGATGAAATACGGGTCACTTGTGTCTGTTGTCTCTTTTGTTGG
genomic: AGAGAAGAAGTTTGAATGGG-TAA-gtaagcatgc ... ccatgtgcagAGGCTTGTGATGAAATACGGGTCACTTGTGTCTGTTGTCTCTTTTGTTGG
EST: gi|15053686|gb|BI359231.1|BI359231
EST:     AGAGAAGAAGTTTGAATGGGCTAAG                         AGGCTTGTGATGAAATACGGGTCACTTGTGTCTGTTGTCTCTTTTGTTGG
genomic: AGAGAAGAAGTTTGAATGGG-TAA-gtaagcatgc ... ccatgtgcagAGGCTTGTGATGAAATACGGGTCACTTGTGTCTGTTGTCTCTTTTGTTGG
EST: gi|101397131|gb|EB820489.1|EB820489
EST:     AGAGAAGAAGTTTGAATGGGTTAAG                         AGGCTTGTGATGAAATACGGGTCACTTGTGTCTGTTGTCTCTTTTGTTGG
genomic: AGAGAAGAAGTTTGAATGGG-TAA-gtaagcatgc ... ccatgtgcagAGGCTTGTGATGAAATACGGGTCACTTGTGTCTGTTGTCTCTTTTGTTGG
EST: gi|101397131|gb|EB820489.1|EB820489
EST:     AGAGAAGAAGTTTGAATGGGTTAAG                         AGGCTTGTGATGAAATACGGGTCACTTGTGTCTGTTGTCTCTTTTGTTGG
genomic: AGAGAAGAAGTTTGAATGGG-TAA-gtaagcatgc ... ccatgtgcagAGGCTTGTGATGAAATACGGGTCACTTGTGTCTGTTGTCTCTTTTGTTGG
EST: gi|78026101|gb|DV494488.1|DV494488
EST:     AGAGAAGAAGTTTGAATGGGCTAAG                         AGGCTTGTGATGAAATACGGGTCACTTGTGTCTGTTGTCTCTTTTGTTGG
genomic: AGAGAAGAAGTTTGAATGGG-TAA-gtaagcatgc ... ccatgtgcagAGGCTTGTGATGAAATACGGGTCACTTGTGTCTGTTGTCTCTTTTGTTGG
EST: gi|78026101|gb|DV494488.1|DV494488
EST:     AGAGAAGAAGTTTGAATGGGCTAAG                         AGGCTTGTGATGAAATACGGGTCACTTGTGTCTGTTGTCTCTTTTGTTGG
genomic: AGAGAAGAAGTTTGAATGGG-TAA-gtaagcatgc ... ccatgtgcagAGGCTTGTGATGAAATACGGGTCACTTGTGTCTGTTGTCTCTTTTGTTGG
EST: gi|18176005|gb|BM351115.1|BM351115
EST:     AGAGAAGAAGTTTGAATGGGCTAAG                         AGGCTTGTGATGAAATACGGGTCACTTGTGTCTGTTGTCTCTTTTGTTGG
genomic: AGAGAAGAAGTTTGAATGGG-TAA-gtaagcatgc ... ccatgtgcagAGGCTTGTGATGAAATACGGGTCACTTGTGTCTGTTGTCTCTTTTGTTGG
EST: gi|18176005|gb|BM351115.1|BM351115
EST:     AGAGAAGAAGTTTGAATGGGCTAAG                         AGGCTTGTGATGAAATACGGGTCACTTGTGTCTGTTGTCTCTTTTGTTGG
genomic: AGAGAAGAAGTTTGAATGGG-TAA-gtaagcatgc ... ccatgtgcagAGGCTTGTGATGAAATACGGGTCACTTGTGTCTGTTGTCTCTTTTGTTGG
EST: gi|78105566|gb|DV523984.1|DV523984
EST:     AGAGAAGAAGTTTGATTGGGTTAAG                         AGGCTTGTGATGAAATACGGGTCACTGGTGTCTGTTGTCTCTTTTGTTGG
genomic: AGAGAAGAAGTTTGAATGGG-TAA-gtaagcatgc ... ccatgtgcagAGGCTTGTGATGAAATACGGGTCACTTGTGTCTGTTGTCTCTTTTGTTGG
EST: gi|78105566|gb|DV523984.1|DV523984
EST:     AGAGAAGAAGTTTGATTGGGTTAAG                         AGGCTTGTGATGAAATACGGGTCACTGGTGTCTGTTGTCTCTTTTGTTGG
genomic: AGAGAAGAAGTTTGAATGGG-TAA-gtaagcatgc ... ccatgtgcagAGGCTTGTGATGAAATACGGGTCACTTGTGTCTGTTGTCTCTTTTGTTGG
EST: gi|6742602|gb|AW313417.1|AW313417
EST:     AGAGAAGAAGTTTGAATGGGCTAAG                         AGGCTTGTGATGAAATACGGGTCACTTGTGTCTGTTGTCTCTTTTGTTGG
genomic: AGAGAAGAAGTTTGAATGGG-TAA-gtaagcatgc ... ccatgtgcagAGGCTTGTGATGAAATACGGGTCACTTGTGTCTGTTGTCTCTTTTGTTGG
EST: gi|6742602|gb|AW313417.1|AW313417
EST:     AGAGAAGAAGTTTGAATGGGCTAAG                         AGGCTTGTGATGAAATACGGGTCACTTGTGTCTGTTGTCTCTTTTGTTGG
genomic: AGAGAAGAAGTTTGAATGGG-TAA-gtaagcatgc ... ccatgtgcagAGGCTTGTGATGAAATACGGGTCACTTGTGTCTGTTGTCTCTTTTGTTGG
EST: gi|51592511|gb|CV071657.1|CV071657
EST:     AGAGAAGAAGTTTGAATGGGCTAAG                         AGGCTTGTGATGAAATACGGGTCACTTGTGTCTGTTGTCTCTTTTGTTGG
genomic: AGAGAAGAAGTTTGAATGGG-TAA-gtaagcatgc ... ccatgtgcagAGGCTTGTGATGAAATACGGGTCACTTGTGTCTGTTGTCTCTTTTGTTGG
EST: gi|51592511|gb|CV071657.1|CV071657
EST:     AGAGAAGAAGTTTGAATGGGCTAAG                         AGGCTTGTGATGAAATACGGGTCACTTGTGTCTGTTGTCTCTTTTGTTGG
genomic: AGAGAAGAAGTTTGAATGGG-TAA-gtaagcatgc ... ccatgtgcagAGGCTTGTGATGAAATACGGGTCACTTGTGTCTGTTGTCTCTTTTGTTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttaccattcatttgagctggacactaacaaaaaaaattgttatccatgtgcagAGGCTTGTGATGAAATACGGGTCACTTGTGTCTGTTGTCTCTTTTGTTGGACTGTTTATCTACCTTGTCGCGAGCCCGTCGAAGAGCAGCTCAAAGGCAA
                       cactaac  putative branch site (score: 1)
                        actaacaaaaaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctggtcaatttccctagttcatctaaataaaattttcaggcagattttaccattcatttgagctggacactaacaaaaaaaattgttatccatgtgcagAGGCTTGTGATGAAATACGGGTCACTTGTGTCTGTTGTCTCTTTTGTTGGACTGTTTATCTACCTTGTCGCGAGCCCGTCGAAGAGCAGCTCAAAGGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - -gttcatc
- - - - - - - - - - - - -aaataaa
- - - - - - - - - - - - - - - - - - -caggcag
- - - - - - - - - - - - - - - - - - - - - - - - - - -ttcattt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctggac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaaa