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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatccatccatacttaattcaaggattccacaagactattctatgttatttcttaagatattcattaggaattgtaggttgtatgtgcagcttggatttccttaatgaagcttcagTGCGGATGCTCATAGGAAGCAGCAGAAGGATAAGCAAGAAAAGTCAGAGACGGAGGATGCGGCACCCAAAAACATGGCAGCCTCTAGCAACCAGGATCAG

Basic information

species Zea mays
transcript GRMZM2G075551_T03
intron # 5
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G075551_T03 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os04g02500.2 (Oryza sativa), 3'ss of exon 5
gtatccatcc-atacttaattcaaggatt-ccacaagactattctatgttatttcttaagatattcattaggaattgtaggttgtatgtgcagcttggatttccttaatgaagcttcagTGCGGATGCTCATAGGAAGCAGCAGAAGGATAAGCAAGAAAAGTCAGAGA------CGGAGGATGCGGCACCCAAAAACATGGCAGCCTCTAGCAACCAGGATCAG
|||||||||| ||  || | ||||  |     | ||  | ||  | || ||  | | || | ||    |      |||   ||| |  ||||      ||||||||||||   ||||||||| ||||||||||| ||||||||| || | |||||||||   |||||||      | |||       ||   || ||| || |   | ||   || |||      
gtatccatcccatgttttagtcaataacaatgataactcaatgatgtgctaactatgaacaaatgtgctgaa---tgtttattgaacttgca------atttccttaatgggacttcagTGCTGATGCTCATAGAAAGCAGCAGCAGCAGAAGCAAGAACCATCAGAGAGCTCATCAGAGAGAATTACAATGAAGAACTTGCCTAACCCTTCAAATCAG------
















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|76285589|gb|DV025157.1|DV025157
EST:     AAACGTGAACAACAACGAGAAGAGAAGGAGCTGGCAAAAATTGCTCAACT                         TGCGGATGCTCATAGGAAGCAGCAGAAGGATAAGCAAGAAAAGTCAGAGAC
genomic: AAACGTGAACAACAACGAGAAGAGAAGGAGCTGGCAAAAATTGCTCAACTgtatccatcc ... gaagcttcagTGCGGATGCTCATAGGAAGCAGCAGAAGGATAAGCAAGAAAAGTCAGAGAC
EST: gi|78121467|gb|DV539851.1|DV539851
EST:     AAACGTGAACAACAACGAGAAGAGAAGGAGCTGGCAAAAATTGCTCAACT                         TGCGGATGCTCATAGGAAGCAGCAGAAGGATAAGCAAGAAAAGTCAGAGAC
genomic: AAACGTGAACAACAACGAGAAGAGAAGGAGCTGGCAAAAATTGCTCAACTgtatccatcc ... gaagcttcagTGCGGATGCTCATAGGAAGCAGCAGAAGGATAAGCAAGAAAAGTCAGAGAC
EST: gi|76282171|gb|DV021739.1|DV021739
EST:     AACGTGAACAACAACGAGAAGAGAAAGGAGCTGGCAAAAATTGCTCAACT                         TGCGGATGCTCATAGGAAGCAGCAGAAGGATAAGCAAGAAAAGTCAGAGAC
genomic: AACGTGAACAACAACGAGAAGAG-AAGGAGCTGGCAAAAATTGCTCAACTgtatccatcc ... gaagcttcagTGCGGATGCTCATAGGAAGCAGCAGAAGGATAAGCAAGAAAAGTCAGAGAC
EST: gi|74244524|gb|DT652438.1|DT652438
EST:     AACGTGAAACA-CAACGAGAAGAGAAGGAGCTGGCAAAAATTGCTCAACT                         TGCGGATGCTCATAGGAAGCAGC
genomic: AACGTGAA-CAACAACGAGAAGAGAAGGAGCTGGCAAAAATTGCTCAACTgtatccatcc ... gaagcttcagTGCGGATGCTCATAGGAAGCAGC
EST: gi|60358695|gb|DN225668.1|DN225668
EST:     AAACGTGAACAACAACGAGAAGAGAAGGAGCTGGCAAAAATTGCTCAACT                         TGCGGATGCTCATAGGAAGCAGCAGAAGGATAAGCAAGAAAAGTCAGAGAC
genomic: AAACGTGAACAACAACGAGAAGAGAAGGAGCTGGCAAAAATTGCTCAACTgtatccatcc ... gaagcttcagTGCGGATGCTCATAGGAAGCAGCAGAAGGATAAGCAAGAAAAGTCAGAGAC
EST: gi|71324315|gb|DR798858.1|DR798858
EST:     AAACGTGAACAACAACGAGAAGAGAAGGAGCTGGCAAAAATTGCTCAACT                         TGCGGATGCTCATAGGAAGCAGCAGAAGGATAAGCAAGAAAAGTCAGAGAC
genomic: AAACGTGAACAACAACGAGAAGAGAAGGAGCTGGCAAAAATTGCTCAACTgtatccatcc ... gaagcttcagTGCGGATGCTCATAGGAAGCAGCAGAAGGATAAGCAAGAAAAGTCAGAGAC
EST: gi|71324316|gb|DR798859.1|DR798859
EST:     AAACGTGAACAACAACGAGAAGAGAAGGAGCTGGCAAAAATTGCTCAACT                         TGCGGATGCTCATAG
genomic: AAACGTGAACAACAACGAGAAGAGAAGGAGCTGGCAAAAATTGCTCAACTgtatccatcc ... gaagcttcagTGCGGATGCTCATAG
EST: gi|71422269|gb|DR805671.1|DR805671
EST:     AAACGTGAACAACAACGAGAAGAGAAGGAGCTGGCAAAAATTGCTCAACT                         TGCGGATGCTCATAGGAAGCAGCAGAAGGATAAGCAAGAAAAGTCAGAGAC
genomic: AAACGTGAACAACAACGAGAAGAGAAGGAGCTGGCAAAAATTGCTCAACTgtatccatcc ... gaagcttcagTGCGGATGCTCATAGGAAGCAGCAGAAGGATAAGCAAGAAAAGTCAGAGAC
EST: gi|71433464|gb|DR814514.1|DR814514
EST:     AAACGTGAACAACAACGAGAAGAGAAGGAGCTGGCAAAAATTGCTCAACT                         TGCGGATGCTCATAGGAAGCAGCAGAAGGATAAGCAAGAAAAGTCAGAGAC
genomic: AAACGTGAACAACAACGAGAAGAGAAGGAGCTGGCAAAAATTGCTCAACTgtatccatcc ... gaagcttcagTGCGGATGCTCATAGGAAGCAGCAGAAGGATAAGCAAGAAAAGTCAGAGAC
EST: gi|93281363|gb|EB673627.1|EB673627
EST:     AAACGTGAACAACAACGAGAAGAGAAGGAGCTGGCAAAAATTGCTCAACT                         TGCGGATGCTCATAGGAAGCAGCAGAAGGATAAGCAAGAAAAGTCAGAGAC
genomic: AAACGTGAACAACAACGAGAAGAGAAGGAGCTGGCAAAAATTGCTCAACTgtatccatcc ... gaagcttcagTGCGGATGCTCATAGGAAGCAGCAGAAGGATAAGCAAGAAAAGTCAGAGAC
EST: gi|71322954|gb|DR798154.1|DR798154
EST:     AAACGTGAACAACAACGAGAAGAGAAGGAGCTGGCAAAAATTGCTCAACT                         TGCGGATGCTCATAGGAAGCAGCAGAAGGATAAGCAAGAAAAGTCAGAGAC
genomic: AAACGTGAACAACAACGAGAAGAGAAGGAGCTGGCAAAAATTGCTCAACTgtatccatcc ... gaagcttcagTGCGGATGCTCATAGGAAGCAGCAGAAGGATAAGCAAGAAAAGTCAGAGAC
EST: gi|86470692|gb|DY237062.1|DY237062
EST:     AAACGTGAACAACAACGAGAAGAGAAGGAGCTGGCAAAAATTGCTCAACT                         TGCGGATGCTCATAGGAAGCAGCAGAAGGATAAGCAAGAAAAGTCAGAGAC
genomic: AAACGTGAACAACAACGAGAAGAGAAGGAGCTGGCAAAAATTGCTCAACTgtatccatcc ... gaagcttcagTGCGGATGCTCATAGGAAGCAGCAGAAGGATAAGCAAGAAAAGTCAGAGAC
EST: gi|76283407|gb|DV022975.1|DV022975
EST:     AAACGTGAACAACAACGAGAAGAGAAGGAGGTGGCAAAAATTGCTCAACT                         TGCGGATGCTCATAGGAAGCAGCAGAAGGATAAGCAAGAAAAGTCAGAGAC
genomic: AAACGTGAACAACAACGAGAAGAGAAGGAGCTGGCAAAAATTGCTCAACTgtatccatcc ... gaagcttcagTGCGGATGCTCATAGGAAGCAGCAGAAGGATAAGCAAGAAAAGTCAGAGAC
EST: gi|76011266|gb|DT938436.1|DT938436
EST:     AAACGTGAACAACAACGAGAAGAGAAGGAGCTGGCAAAAATTGCTCAACT                         TGCGGATGCTCATAGGAAGCAGCAGAAGGATAAGCAAGAAAAGTCAGAGAC
genomic: AAACGTGAACAACAACGAGAAGAGAAGGAGCTGGCAAAAATTGCTCAACTgtatccatcc ... gaagcttcagTGCGGATGCTCATAGGAAGCAGCAGAAGGATAAGCAAGAAAAGTCAGAGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcattaggaattgtaggttgtatgtgcagcttggatttccttaatgaagcttcagTGCGGATGCTCATAGGAAGCAGCAGAAGGATAAGCAAGAAAAGTCAGAGACGGAGGATGCGGCACCCAAAAACATGGCAGCCTCTAGCAACCAGGATCAG
 ttccttaat  putative branch site 
                                        ttaatgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatccatccatacttaattcaaggattccacaagactattctatgttatttcttaagatattcattaggaattgtaggttgtatgtgcagcttggatttccttaatgaagcttcagTGCGGATGCTCATAGGAAGCAGCAGAAGGATAAGCAAGAAAAGTCAGAGACGGAGGATGCGGCACCCAAAAACATGGCAGCCTCTAGCAACCAGGATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG