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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caattagtcatttgctatcacggaactaggagagcacactaatctaaattcttgtttcttgtgttttgaaaatatttttaatgaatgaataattttgcagAAGCAACACCAAAAACTATCTTAAGGACGATGGGTGTCAAGGGTCTTACTCTTTTCCACTTGAAGAGTCATCTTCAG

Basic information

species Zea mays
transcript GRMZM2G064197_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G064197_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os09g12750.2 (Oryza sativa), 3'ss of exon 1
-caattagtcatttgctatcacggaactaggagagcacactaatctaaattcttgtttcttgtgttttgaaaatatttttaatgaatgaataattttgcagAAGCAACACCAAAAACTATCTTAAGGACGATGGGTGTCAAGGGTCTTACTCTTTTCCACTTGAAGAGTCATCTTCAG
  ||   || |           | | | || | | ||   |||  |    | |  ||   | | |||  |     |  | |||| |||| || | |||||||||||||||| ||||||||||| ||||| |||||||| ||||| || ||||||||||||||||||||||||||||||
ctaaaatgtgaaaaatccaggggaatccagtaaaacagtttaagatttgatttcattatatatttttaaattgagtactcaatgcatgatta-tcttgcagAAGCAACACCTAAAACTATCTTGAGGACAATGGGTGTGAAGGGGCTCACTCTTTTCCACTTGAAGAGTCATCTTCAG

upper sequence: GRMZM2G064197_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA09G02030.1 (Glycine max), 3'ss of exon 1
-----caattagtcat--ttgctatcacggaactaggagagcacactaatctaaattcttgtttcttgtgttttgaaaatatttttaatgaatgaataattttgcagAAGCAACACCAAAAACTATCTTAAGGACGATGGGTGTCAAGGGTCTTACTCTTTTCCACTTGAAGAGTCATCTTCAG
      ||| |  | |  || |  |  |  | |  | |     ||    | |||||| |  |         |||   | ||  ||   || |||  ||  | ||||||||| ||||||||| | ||| |  |||| |||  |||||||||| | ||||| || || ||||||||||||||||||
gtagttaataaagcctgatttccttttcttatcctgaaatcttcat--gtgtaaattatcatcagcatcactttctgactaggttc--tggatgt-ta--tctgcagAAGCTACACCAAAAGCAATCATGCGGACTATGAATGTCAAGGGTTTGACTCTGTTTCATTTGAAGAGTCATCTTCAG

upper sequence: GRMZM2G064197_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA15G12930.2 (Glycine max), 3'ss of exon 2
-caattagtca--tttgctatcacggaactaggagagcacactaatc--taaattcttgtttcttgtgttttgaaaatatttttaatgaatgaataattttgcagAAGCAACACCAAAAACTATCTTAAGGACGATGGGTGTCAAGGGTCTTACTCTTTTCCACTTGAAGAGTCATCTTCAG
  | ||| | |    |||| ||       ||       |   | ||   |||||| |  |         |||   | ||  ||   || |||  ||  | ||||||||| ||||||||| | ||| |  |||| |||  |||||||||| | ||||| || || ||||||||||||||||||
gtagttaataaagcctgctttccttttcttatcctgaaatcttcatgcgtaaattatcatcaacatcactttctgactaggttc--tggatgt-ta--tctgcagAAGCTACACCAAAAGCAATCATGCGGACCATGAATGTCAAGGGTTTGACTCTGTTTCATTTGAAGAGTCATCTTCAG

upper sequence: GRMZM2G064197_T02 (Zea mays), 3'ss of exon 1
lower sequence: PP1S25_131V6.1 (Physcomitrella patens), 3'ss of exon 1
caattagtcatttgctatcacggaactaggagagcacactaatctaaattcttgtttcttgtgttttgaaaata-----tttttaatgaatgaata-attttgcagAAGCAACACCAAAAACTATCTTAAGGACGATGGGTGTCAAGGGTCTTACTCTTTTCCACTTGAAGAGTCATCTTCAG
      |   ||    |  | |    ||| | |    |    |        ||  |  | |    |  ||| ||     | | | ||   ||   | | |   |||| || ||||| ||| || |  | ||    ||||| || |||||||||||||||| ||| |||||||| |||||||||
------gatgttgctgactaagttggtagtaaaatgtatgtcttcgtgggattagtattaggtcatcaaaactaactcgtctgtcattgttgttcacaatggacagAGGCTACACCGAAATCTGTAATGAGAGTCATGGGAGTGAAGGGTCTTACTCTTTACCATTTGAAGAGCCATCTTCAG

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|76292621|gb|DV032189.1|DV032189
EST:     CCTCCACGAGCGTTTCGTCGACGCCGTGGCCCAGCTCGGCGGACCCGAGA                         AAGCAACACCAAAAACTATCTTAAGGACGATGGGTGTCAAGGGTCTTACTC
genomic: CCTCCACGAGCGTTTCGTCGACGCCGTGGCCCAGCTCGGCGGACCCGAGAgtgagctacc ... aattttgcagAAGCAACACCAAAAACTATCTTAAGGACGATGGGTGTCAAGGGTCTTACTC
EST: gi|50333124|gb|CO528250.1|CO528250
EST:     CCTCCACGAGCGTTTCGTCGACGCCGTGGCCCAGCTCGGCGGACCCGAGA                         AAGCAACACCAAAAACTATCTTAAGGACGATGGGTGTCAAGGGTCTTACTC
genomic: CCTCCACGAGCGTTTCGTCGACGCCGTGGCCCAGCTCGGCGGACCCGAGAgtgagctacc ... aattttgcagAAGCAACACCAAAAACTATCTTAAGGACGATGGGTGTCAAGGGTCTTACTC
EST: gi|211244393|gb|FL238844.1|FL238844
EST:     CCTCCACGAGCGTTTCGTCGACGCCGTGGCCCAGCTCGGCGGACCCGAGA                         AAGCAACACCAAAAACTATCTTAAGGACGATGGGTGTCAAGGGTCTTACTC
genomic: CCTCCACGAGCGTTTCGTCGACGCCGTGGCCCAGCTCGGCGGACCCGAGAgtgagctacc ... aattttgcagAAGCAACACCAAAAACTATCTTAAGGACGATGGGTGTCAAGGGTCTTACTC
EST: gi|101397100|gb|EB820474.1|EB820474
EST:     CCTCCACGAGCGTTTCGTCGACGCCGTGGCCCAGCTCGGCGGACCCGAGA                         AAGTCA-CACCAAAAACTATCTTAAGGACGATGGGTGTCAAGGGTCTTACT
genomic: CCTCCACGAGCGTTTCGTCGACGCCGTGGCCCAGCTCGGCGGACCCGAGAgtgagctacc ... aattttgcagAAG-CAACACCAAAAACTATCTTAAGGACGATGGGTGTCAAGGGTCTTACT
EST: gi|87156993|gb|DY401782.1|DY401782
EST:     CCTCCACGAGCGTTTCGTCGACGCCGTGGCCCAGCTCGGCGGACCCGAGA                         AAGCAACACCAAAAACTATCTTAAGGACGATGGGTGTCAAGGGTCTTACTC
genomic: CCTCCACGAGCGTTTCGTCGACGCCGTGGCCCAGCTCGGCGGACCCGAGAgtgagctacc ... aattttgcagAAGCAACACCAAAAACTATCTTAAGGACGATGGGTGTCAAGGGTCTTACTC
EST: gi|22473367|gb|BU037847.1|BU037847
EST:     CCTCCACGAGCGTTTCGTCGACGCCGTGGCCCAGCTCGGCGGACCCGAGA                         AAGCAACACCAAAAACTATCTTAAGGACGATGGGTGTCAAGGGTCTTACTC
genomic: CCTCCACGAGCGTTTCGTCGACGCCGTGGCCCAGCTCGGCGGACCCGAGAgtgagctacc ... aattttgcagAAGCAACACCAAAAACTATCTTAAGGACGATGGGTGTCAAGGGTCTTACTC
EST: gi|26558692|gb|CA830927.1|CA830927
EST:     CCTCCACGAGCGTTTCGTCGACGCCGTGGCCCAGCTCGGCGGACCCGAGA                         AAGCAACACCAAAAACTATCTTAAGGACGATGGGTGTCAAGGGTCTTACTC
genomic: CCTCCACGAGCGTTTCGTCGACGCCGTGGCCCAGCTCGGCGGACCCGAGAgtgagctacc ... aattttgcagAAGCAACACCAAAAACTATCTTAAGGACGATGGGTGTCAAGGGTCTTACTC
EST: gi|76918384|gb|DV167269.1|DV167269
EST:     CCTCCACGAGCGTTTCGTCGACGCCGTGGCCCAGCTCGGCGGACCCGAGA                         AAGCAACACCAAAAACTATCTTAAGGACGATGGGTGTCAAGGGTCTTACTC
genomic: CCTCCACGAGCGTTTCGTCGACGCCGTGGCCCAGCTCGGCGGACCCGAGAgtgagctacc ... aattttgcagAAGCAACACCAAAAACTATCTTAAGGACGATGGGTGTCAAGGGTCTTACTC
EST: gi|76292002|gb|DV031570.1|DV031570
EST:     CCTCCACGAGCGTTTCGTCGACGCCGTGGCCCAGCTCGGCGGACCCGAGA                         AAGCAACACCAAAAACTATCTTAAGGACGATGGGTGTCAAGGGTCTTACTC
genomic: CCTCCACGAGCGTTTCGTCGACGCCGTGGCCCAGCTCGGCGGACCCGAGAgtgagctacc ... aattttgcagAAGCAACACCAAAAACTATCTTAAGGACGATGGGTGTCAAGGGTCTTACTC
EST: gi|91051798|gb|EB162216.1|EB162216
EST:     CCTCCACGAGCGTTTCGTCGACGCCGTGGCCCAGCTCGGCGGACCCGAGA                         AAGCAACACCAAAAACTATCTTAAGGACGATGGGTGTCAAGGGTCTTACTC
genomic: CCTCCACGAGCGTTTCGTCGACGCCGTGGCCCAGCTCGGCGGACCCGAGAgtgagctacc ... aattttgcagAAGCAACACCAAAAACTATCTTAAGGACGATGGGTGTCAAGGGTCTTACTC
EST: gi|74233858|gb|DT641772.1|DT641772
EST:     CCTCCACGAGCGTTTCGTCGACGCCGTGGCCCAGCTCGGCGGACCCGAGA                         AAGCAACACCAAAAACTATCTTAAGGACGATGGGTGTCAAGGGTCTTACTC
genomic: CCTCCACGAGCGTTTCGTCGACGCCGTGGCCCAGCTCGGCGGACCCGAGAgtgagctacc ... aattttgcagAAGCAACACCAAAAACTATCTTAAGGACGATGGGTGTCAAGGGTCTTACTC
EST: gi|71436515|gb|DR817565.1|DR817565
EST:     CCTCCACGAGCGTTTCGTCGACGCCGTGGCCCAGCTCGGCGGACCCGAGA                         AAGCAACACCAAAAACTATCTTAAGGACGATGGGTGTCAAGGGTCTTACTC
genomic: CCTCCACGAGCGTTTCGTCGACGCCGTGGCCCAGCTCGGCGGACCCGAGAgtgagctacc ... aattttgcagAAGCAACACCAAAAACTATCTTAAGGACGATGGGTGTCAAGGGTCTTACTC
EST: gi|88755721|gb|DY539862.1|DY539862
EST:     CCTCCACGAGCGTTTCGTCGACGCCGTGGCCCAGCTCGGCGGACCCGAGA                         AAGCAACACCAAAAACTATCTTAAGGACGATGGGTGTCAAGGGTCTTACTC
genomic: CCTCCACGAGCGTTTCGTCGACGCCGTGGCCCAGCTCGGCGGACCCGAGAgtgagctacc ... aattttgcagAAGCAACACCAAAAACTATCTTAAGGACGATGGGTGTCAAGGGTCTTACTC
EST: gi|74232735|gb|DT640649.1|DT640649
EST:     CCTCCACGAGCGTTTCGTCGACGCCGTGGCCCAGCTCGGCGGACCCGAGA                         AAGCAACACCAAAAACTATCTTAAGGACGATGGGTGTCAAGGGTCTTACTC
genomic: CCTCCACGAGCGTTTCGTCGACGCCGTGGCCCAGCTCGGCGGACCCGAGAgtgagctacc ... aattttgcagAAGCAACACCAAAAACTATCTTAAGGACGATGGGTGTCAAGGGTCTTACTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaattcttgtttcttgtgttttgaaaatatttttaatgaatgaataattttgcagAAGCAACACCAAAAACTATCTTAAGGACGATGGGTGTCAAGGGTCTTACTCTTTTCCACTTGAAGAGTCATCTTCAG
                              ttttaat  putative branch site (score: 3)
             ttgtgttttgaaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caattagtcatttgctatcacggaactaggagagcacactaatctaaattcttgtttcttgtgttttgaaaatatttttaatgaatgaataattttgcagAAGCAACACCAAAAACTATCTTAAGGACGATGGGTGTCAAGGGTCTTACTCTTTTCCACTTGAAGAGTCATCTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA