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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgatccgaacaccagatgaaagtcttctttgaaatagataaccatattcgcctcactttttttgttcaccacaactacctgagatttccttggcctgcagCTTGTGAAGCTACCACGATCACCTACTGTTGATGATATTCTAAAGAAGTACTTGGAACACCGGGCAAAGAAGGATGGCAA

Basic information

species Zea mays
transcript GRMZM2G484880_T03
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G484880_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os04g01130.1 (Oryza sativa), 3'ss of exon 7
-----------tgatccgaacaccagatgaaagtcttctttgaaataga--taaccatattc---gcctcact-ttttttgttcaccacaactac----ctgag---atttccttggcctgcagCTTGTGAAGCTACCACGATCACCTACTGTTGATGATATTCTAAAGAAGTACTTGGAACACCGGGCAAAGAAGGATGGCAA
             | |   | |   |||||   | | ||  |  ||     || |  ||| |      | ||| ||| |  ||| |  || || |    |||||   |||||||||  |||||||||||||||||||| ||||| || ||||| |||||||||||||||||||||||||| |||||  |||||||||||  |||
gtacttgttataaaactacaaatacgatgagtttgtcctcagttatcactttatcagtatgccaaagttaactgtttatcattctcaccagcttctttcctgagccaatttccttgttctgcagCTTGTGAAGCTACCTCGATCCCCCACTGTCGATGATATTCTAAAGAAGTACTTGGAGCACCGAACAAAGAAGGATAACAA

upper sequence: GRMZM2G484880_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os11g34300.2 (Oryza sativa), 3'ss of exon 7
tgatccgaacaccagatgaaagtcttctttgaaatagataaccatattcgcc-tcact-ttttttgttc-accacaac--tacctgag---atttccttggcctgcagCTTGTGAAGCTACCACGATCACCTACTGTTGATGATATTCTAAAGAAGTACTTGGAACACCGGGCAAAGAAGGATGGCAA
      ||| ||  |||||   | | ||  |  ||  ||  | |  ||  |  | ||| ||| |  ||| ||||   |  | ||||||   |||||||||  |||||||||||||||||||| || || || || || |||||||||||||||||||||||||| |||||| |||||||||||  |||
------gaatac--gatgagtttgtcctcagtgatgtatgccaaagttaactgtaactgtttatcattctaccagttcctttcctgagccaatttccttgtactgcagCTTGTGAAGCTACCTCGGTCCCCCACGGTCGATGATATTCTAAAGAAGTACTTGGAGCACCGGACAAAGAAGGATAACAA
















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|60343282|gb|DN210255.1|DN210255
EST:     TGAAGAAGCAACTTGTGGATGATTGGGAGTTTGTTACGCAGATGGGTAAG                         CTTGTGAAGCTACCACGATCACCTACTGTTGATGATATTCTAAAGAAGTAC
genomic: TGAAGAAGCAACTTGTGGATGATTGGGAGTTTGTTACGCAGATGGGTAAGgtatttagtt ... tggcctgcagCTTGTGAAGCTACCACGATCACCTACTGTTGATGATATTCTAAAGAAGTAC
EST: gi|78544095|gb|DV621593.1|DV621593
EST:     TGAAGAAGCAACTTGTGGATGATTGGGAGTTTGTTACGCAGATGGGTAAG                         CTTGTGAAGCTACCACGATCACCTACTGTTGATGATATTCTAAAGAAGTAC
genomic: TGAAGAAGCAACTTGTGGATGATTGGGAGTTTGTTACGCAGATGGGTAAGgtatttagtt ... tggcctgcagCTTGTGAAGCTACCACGATCACCTACTGTTGATGATATTCTAAAGAAGTAC
EST: gi|31997933|gb|CD661838.1|CD661838
EST:     TACGCAGATGGGTAAG                         CTTGTGAAGCTACCACGATCACCTACTGTTGATGATATTCTAAAGAAGTAC
genomic: TACGCAGATGGGTAAGgtatttagtt ... tggcctgcagCTTGTGAAGCTACCACGATCACCTACTGTTGATGATATTCTAAAGAAGTAC
EST: gi|37386752|gb|CF630565.1|CF630565
EST:     AAGAAGCAACTTGTGGATGATTGGGAGTTTGTTACGCAGAT--G---G                         CTTGTGAAGCTACCACGATCACCTACTGTTGATGATATTCTAAAGAAGTAC
genomic: AAGAAGCAACTTGTGGATGATTGGGAGTTTGTTACGCAGATGGGTAAGgtatttagtt ... tggcctgcagCTTGTGAAGCTACCACGATCACCTACTGTTGATGATATTCTAAAGAAGTAC
EST: gi|22546503|gb|BU098814.1|BU098814
EST:     TGAAGAAGCAACTTGTGGATGATTGGGAGTTTGTTACGCAGATGGGTAAG                         CTTGTGAAGCTACCACGATCACCTACTGTTGATGATATTCTAAAGAAGTAC
genomic: TGAAGAAGCAACTTGTGGATGATTGGGAGTTTGTTACGCAGATGGGTAAGgtatttagtt ... tggcctgcagCTTGTGAAGCTACCACGATCACCTACTGTTGATGATATTCTAAAGAAGTAC
EST: gi|93284202|gb|EB676466.1|EB676466
EST:     TGAAGAAGCAACTTGTGGATGATTGGGAGTTTGTTACGCAGATGGGTAAG                         CTTGTGAAGCTACCACGATCACCTACTGTTGATGATATTCTAAAGAAGTAC
genomic: TGAAGAAGCAACTTGTGGATGATTGGGAGTTTGTTACGCAGATGGGTAAGgtatttagtt ... tggcctgcagCTTGTGAAGCTACCACGATCACCTACTGTTGATGATATTCTAAAGAAGTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcgcctcactttttttgttcaccacaactacctgagatttccttggcctgcagCTTGTGAAGCTACCACGATCACCTACTGTTGATGATATTCTAAAGAAGTACTTGGAACACCGGGCAAAGAAGGATGGCAA
    gcctcac  putative branch site (score: 3)
                                       tttcctt  putative PPT
           tttttttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgatccgaacaccagatgaaagtcttctttgaaatagataaccatattcgcctcactttttttgttcaccacaactacctgagatttccttggcctgcagCTTGTGAAGCTACCACGATCACCTACTGTTGATGATATTCTAAAGAAGTACTTGGAACACCGGGCAAAGAAGGATGGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - -aacacca
- - - - - - - - - - - - - - - gaaataga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccacaac