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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attgaaatttcttgggaactcttgtaatatatttttgtttcttccatttattttctaatattcttttattgtgcttacatgtgtcacctggaatatgtagTTCTTCTGCTCAGAAATATTTCAGGAGGGCAACACGTTTAAATTGGCCTGAAGGTGCTGTTTCAAGAGAAAGCATCAGAGCTGTGAAGAAACTGGATCGA

Basic information

species Zea mays
transcript GRMZM2G366935_T07
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G366935_T09 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os01g40840.1 (Oryza sativa), 3'ss of exon 10
attgaaatttcttgggaactcttgtaatatatttttgtttcttccatttattttctaatattcttttat-tgtgc-ttacatgtgtcacctggaatatgtagTTCTTCTGCTCAGAAATATTTCAGGAGGGCAACACGTTTAAATTGGCCTGAAGGTGCTGTTTCAAGAGAAAGCATCAGAGCTGTGAAGAAACTGGATCGA
  |    | |  |   |  |  |||  |  | |  |   |||||  || ||||| || |  | ||  || | ||| |    | ||||| |||||||||| ||||| || |||||||||||||| ||  | | | | ||| ||||||||||||||||||||||||||||||| || |||||||| || || ||||| ||||| 
gctatggtatgctaccatttactgtcttgcaatgatcaatcttc--ttcattttatactgattttccatatttgcatcgtgtatgtcaactggaatatgcagTTCATCAGCTCAGAAATATTTTAGACGAGGAGCGCGTCTAAATTGGCCTGAAGGTGCTGTTTCAAGAGAGAGTATCAGAGCAGTCAAAAAACTAGATCGG

upper sequence: GRMZM2G366935_T09 (Zea mays), 3'ss of exon 9
lower sequence: Vv04s0008g04220.t01 (Vitis vinifera), 3'ss of exon 10
----attgaaatttcttgggaactcttgtaatatatttttgtttcttccatttattttctaatattcttttattgtgcttacatgtgtcacctggaatatgtagTTCTTCTGCTCAGAAATATTTCAGGAGGGCAACACGTTTAAATTGGCCTGAAGGTGCTGTTTCAAGAGAAAGCATCAGAGCTGTGAAGAAACTGGATCGA
    ||      |        | | ||||| |  || |    |||    ||  || ||   ||||     | |  |||    || | ||       || || ||      || | | || ||||||||| | | | |||| || |||||||||||||| || ||||| || ||||| |||||||| |||||||| || || || 
cttgatcattgctgtccctctatttttgta-tgcatctaaaattcgagaatg-atgtttcgatatcaccctttaatgccattatatatc--tgtatatttgcagCCGAAGTGTTGAAAAGTATTTCAGGGGAGGATCACGGTTGAATTGGCCTGAAGGAGCAGTTTCTAGGGAAAGTATCAGAGCAGTGAAGAAGCTTGACCGT
















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|71766680|gb|DR964617.1|DR964617
EST:     ATGGAGAGAGTTTTGGGACCTCTACCAGAGCATATGATACGGAAATCAAG                         TTCTTCTGCTCAGAAATATTTCAGGAGGGCAACACGTTTAAATTGGCCTGA
genomic: ATGGAGAGAGTTTTGGGACCTCTACCAGAGCATATGATACGGAAATCAAGgtgtgttatt ... gaatatgtagTTCTTCTGCTCAGAAATATTTCAGGAGGGCAACACGTTTAAATTGGCCTGA
EST: gi|76915207|gb|DV165881.1|DV165881
EST:     ATGGAGAGAGTTTTGGGACCTCTACCAGAGCATATGATACGGAAATCAAG                         TTCTTCTGCTCAGAAATATTTCAGGAGGGCAACACGTTTAAATTGGCCTGA
genomic: ATGGAGAGAGTTTTGGGACCTCTACCAGAGCATATGATACGGAAATCAAGgtgtgttatt ... gaatatgtagTTCTTCTGCTCAGAAATATTTCAGGAGGGCAACACGTTTAAATTGGCCTGA
EST: gi|24765506|gb|CA400665.1|CA400665
EST:     ATGGAGAGAGTTTTGGGACCTCTACCAGAGCATATGATACGGAAAGCAAG                         TTCTTCTGCTCAGAAATATTTCAGGAGGGCAACACGTTTAAATTGGCCTGA
genomic: ATGGAGAGAGTTTTGGGACCTCTACCAGAGCATATGATACGGAAATCAAGgtgtgttatt ... gaatatgtagTTCTTCTGCTCAGAAATATTTCAGGAGGGCAACACGTTTAAATTGGCCTGA
EST: gi|71760328|gb|DR958265.1|DR958265
EST:     ATGGAGAGAGTTTTGGGACCTCTACCAGAGCATATGATACGGAAATCAAG                         TTCTTCTGCTCAGAAATATTTCAGGAGGGCAACACGTTTAAATTGGCCTGA
genomic: ATGGAGAGAGTTTTGGGACCTCTACCAGAGCATATGATACGGAAATCAAGgtgtgttatt ... gaatatgtagTTCTTCTGCTCAGAAATATTTCAGGAGGGCAACACGTTTAAATTGGCCTGA
EST: gi|21331443|gb|BQ486824.1|BQ486824
EST:     ATGGAGAGAGTTTTGGGACCTCTACCAGAGCATATGATACGGAAAGCAAG                         TTCTTCTGCTCAGAAATATTTCAGGAGGGCAACACGTTTAAATTGGCCTGA
genomic: ATGGAGAGAGTTTTGGGACCTCTACCAGAGCATATGATACGGAAATCAAGgtgtgttatt ... gaatatgtagTTCTTCTGCTCAGAAATATTTCAGGAGGGCAACACGTTTAAATTGGCCTGA
EST: gi|71426269|gb|DR807319.1|DR807319
EST:     ATGGAGAGAGTTTTGGGACCTCTACCAGAGCATATGATACGGAAATCAAG                         TTCTTCTGTTCAGAAATATTTCAGGAGGGCAACACGTTTAAATTGGCCTGA
genomic: ATGGAGAGAGTTTTGGGACCTCTACCAGAGCATATGATACGGAAATCAAGgtgtgttatt ... gaatatgtagTTCTTCTGCTCAGAAATATTTCAGGAGGGCAACACGTTTAAATTGGCCTGA
EST: gi|60345840|gb|DN212813.1|DN212813
EST:     ATGGAGAGAGTTTTGGGACCTCTACCAGAGCATATGATACGGAAAGCAAG                         TTCTTCTGCTCAGAAATATTTCAGGAGGGCAACACGTTTAAATTGGCCTGA
genomic: ATGGAGAGAGTTTTGGGACCTCTACCAGAGCATATGATACGGAAATCAAGgtgtgttatt ... gaatatgtagTTCTTCTGCTCAGAAATATTTCAGGAGGGCAACACGTTTAAATTGGCCTGA
EST: gi|74242829|gb|DT650743.1|DT650743
EST:     ATGGAGAGAGTTTTGGGACCTCTACCAGAGCATATGATACGGAAATCAAG                         TTCTTCTGCTCAGAAATATTTCAGGAGGGCAACACGTTTAAATTGGCCTGA
genomic: ATGGAGAGAGTTTTGGGACCTCTACCAGAGCATATGATACGGAAATCAAGgtgtgttatt ... gaatatgtagTTCTTCTGCTCAGAAATATTTCAGGAGGGCAACACGTTTAAATTGGCCTGA
EST: gi|71775054|gb|DR972932.1|DR972932
EST:     ATGGAGAGAGTTTTGGGACCTCTACCAGAGCATATGATACGGAAATCAAG                         TTCTTCTGTTCAGAAATATTTCAGGAGGGCAACACGTTTAAATTGGCCTGA
genomic: ATGGAGAGAGTTTTGGGACCTCTACCAGAGCATATGATACGGAAATCAAGgtgtgttatt ... gaatatgtagTTCTTCTGCTCAGAAATATTTCAGGAGGGCAACACGTTTAAATTGGCCTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttattttctaatattcttttattgtgcttacatgtgtcacctggaatatgtagTTCTTCTGCTCAGAAATATTTCAGGAGGGCAACACGTTTAAATTGGCCTGAAGGTGCTGTTTCAAGAGAAAGCATCAGAGCTGTGAAGAAACTGGATCGA
                          tgcttac  putative branch site (score: 2)
     ttttctaatattcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attgaaatttcttgggaactcttgtaatatatttttgtttcttccatttattttctaatattcttttattgtgcttacatgtgtcacctggaatatgtagTTCTTCTGCTCAGAAATATTTCAGGAGGGCAACACGTTTAAATTGGCCTGAAGGTGCTGTTTCAAGAGAAAGCATCAGAGCTGTGAAGAAACTGGATCGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA