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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gggaatgtgtagtctttggaatgagctgcactaataaataacttgtgaaacaacatttgtggtttattaagaatattttatattcttgtattgtttgtagGCTGTGGAGCGGGCAGCTGGTACTGATGGCCAAAAGATAACATACGGTGTCATAAAACACCGTTTGGGCGATCTATTTTATCGCCTAGT

Basic information

species Zea mays
transcript GRMZM2G128877_T03
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G128877_T02 (Zea mays), 3'ss of exon 17
lower sequence: LOC_Os02g07870.1 (Oryza sativa), 3'ss of exon 17
gggaatgtgtagtctttggaatgagctgcactaataaataact-tgtgaaa-caacatttgtggtttattaagaatattttatattcttgtattgttt-gtagGCTGTGGAGCGGGCAGCTGGTACTGATGGCCAAAAGATAACATACGGTGTCATAAAACACCGTTTGGGCGATCTATTTTATCGCCTAGT
  |  |    | |  |    || |     | ||  | ||  |  |   |||  | |||  ||  | | |||| |||    | ||| ||| ||||||||  ||||| |||||||||||||||||| ||||||| || ||||| |||||| |||||||||| || ||  ||||||||||||| || ||||||||
ttgtttactcattactcaatataattacaaataggatattcccatacaaaagtagcataagtactattttaataat---ctgtatgcttttattgttttatagGCGGTGGAGCGGGCAGCTGGTGCTGATGGACAGAAGATTACATACAGTGTCATAAAGCATCGCATGGGCGATCTATTCTACCGCCTAGT
















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|32929207|gb|CF034019.1|CF034019
EST:     CCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAG                         GCTGTGGAGCGGGCAGCTGGTA
genomic: CCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAGgtaagctctc ... ttgtttgtagGCTGTGGAGCGGGCAGCTGGTA
EST: gi|60338201|gb|DN205174.1|DN205174
EST:     CCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAG                         GCTGTGGAGCGGGCAGCTGGTACTGATGGCCAAAAGATAACATACGGTGTC
genomic: CCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAGgtaagctctc ... ttgtttgtagGCTGTGGAGCGGGCAGCTGGTACTGATGGCCAAAAGATAACATACGGTGTC
EST: gi|5770168|gb|AI973342.1|AI973342
EST:     CCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAG                         GCTGTGGAGCGGGCAGCTGGTACTGATGGCCAAAAGATAACATACGGTGTC
genomic: CCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAGgtaagctctc ... ttgtttgtagGCTGTGGAGCGGGCAGCTGGTACTGATGGCCAAAAGATAACATACGGTGTC
EST: gi|13149764|gb|BG320086.1|BG320086
EST:     CCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAG                         GCTGTGGAGCGGGCAGCTGGTACTGATGGCCAAAAGATAACATACGGTGTC
genomic: CCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAGgtaagctctc ... ttgtttgtagGCTGTGGAGCGGGCAGCTGGTACTGATGGCCAAAAGATAACATACGGTGTC
EST: gi|32831320|gb|CD970998.1|CD970998
EST:     CCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAG                         GCTGTGGAGCGGGCAGCTGGT
genomic: CCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAGgtaagctctc ... ttgtttgtagGCTGTGGAGCGGGCAGCTGGT
EST: gi|67018748|gb|CO447497.1|CO447497
EST:     CCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAG                         GCTGTGGAGCGGGCAGCTGGTACTGATGGCCAAAAGATAACATACGGTGTC
genomic: CCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAGgtaagctctc ... ttgtttgtagGCTGTGGAGCGGGCAGCTGGTACTGATGGCCAAAAGATAACATACGGTGTC
EST: gi|4646572|gb|AI491316.2|AI491316
EST:     CCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAG                         GCTGTGGAGCGGGCAGCTGGTACTGATGGCCAAAAGATAACATACGGTGTC
genomic: CCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAGgtaagctctc ... ttgtttgtagGCTGTGGAGCGGGCAGCTGGTACTGATGGCCAAAAGATAACATACGGTGTC
EST: gi|32928400|gb|CF033212.1|CF033212
EST:     CCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAG                         GCTGTGGAGCGGGCAGCTGGTA
genomic: CCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAGgtaagctctc ... ttgtttgtagGCTGTGGAGCGGGCAGCTGGTA
EST: gi|32837774|gb|CD977452.1|CD977452
EST:     CCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAG                         GCTGTGGAGCGGGCAGCTGGTAC
genomic: CCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAGgtaagctctc ... ttgtttgtagGCTGTGGAGCGGGCAGCTGGTAC
EST: gi|5296280|gb|AI783050.1|AI783050
EST:     CCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAG                         GCTGTGGAGCGGGCAGCTGGTACTGATGGCCAAAAGATAACATACGGTGTC
genomic: CCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAGgtaagctctc ... ttgtttgtagGCTGTGGAGCGGGCAGCTGGTACTGATGGCCAAAAGATAACATACGGTGTC
EST: gi|5846764|gb|AI999847.1|AI999847
EST:     CCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAG                         GCTGTGGAGCGGGCAGCTGGTACTGATGGCCAAAAGATAACATACGGTGTC
genomic: CCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAGgtaagctctc ... ttgtttgtagGCTGTGGAGCGGGCAGCTGGTACTGATGGCCAAAAGATAACATACGGTGTC
EST: gi|32939925|gb|CF044744.1|CF044744
EST:     CCGTTTGGATGATGC-CAATATTATTCACTTCAACACATTGGCAAATCAG                         GCTGTGGAGCGGGCAGCTGGTACTGATGGCCAAAAGATAACATACGGTGTC
genomic: CCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAGgtaagctctc ... ttgtttgtagGCTGTGGAGCGGGCAGCTGGTACTGATGGCCAAAAGATAACATACGGTGTC
EST: gi|211152801|gb|FL123511.1|FL123511
EST:     CCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAG                         GCTGTGGAGCGGGCAGCTGGTACTGATGGCCAAAAGATAACATACGGTGTC
genomic: CCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAGgtaagctctc ... ttgtttgtagGCTGTGGAGCGGGCAGCTGGTACTGATGGCCAAAAGATAACATACGGTGTC
EST: gi|5871663|gb|AW018134.1|AW018134
EST:     CCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAG                         GCTGTGGAGCGGGCAGCTGGTACTGATGGCCAAAAGATAACATACGGTGTC
genomic: CCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAGgtaagctctc ... ttgtttgtagGCTGTGGAGCGGGCAGCTGGTACTGATGGCCAAAAGATAACATACGGTGTC
EST: gi|4630580|gb|AI621454.1|AI621454
EST:     ATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAG                         GCTGTGGAGCGGGCAGCTGGTACTGATGGCCAAAAGATAACATACGGTGTC
genomic: ATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAGgtaagctctc ... ttgtttgtagGCTGTGGAGCGGGCAGCTGGTACTGATGGCCAAAAGATAACATACGGTGTC
EST: gi|5847131|gb|AW000210.1|AW000210
EST:     CCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAG                         GCTGTGGAGCGGGCAGCTGGTACTGATGGCCAAAAGATAACATACGGTGTC
genomic: CCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAGgtaagctctc ... ttgtttgtagGCTGTGGAGCGGGCAGCTGGTACTGATGGCCAAAAGATAACATACGGTGTC
EST: gi|5804554|gb|AI979524.1|AI979524
EST:     CCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAG                         GCTGTGGAGCGGGCAGCTGGTACTGATGGCCAAAAGATAACATACGGTGTC
genomic: CCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAGgtaagctctc ... ttgtttgtagGCTGTGGAGCGGGCAGCTGGTACTGATGGCCAAAAGATAACATACGGTGTC
EST: gi|33092495|gb|CF052489.1|CF052489
EST:     CCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAG                         GCTGTGGAGCGGGCAGCTGGT
genomic: CCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAGgtaagctctc ... ttgtttgtagGCTGTGGAGCGGGCAGCTGGT
EST: gi|5846817|gb|AI999900.1|AI999900
EST:     CCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAG                         GCTGTGGAGCGGGCAGCTGGTACTGATGGCCAAAAGATAACATACGGTGTC
genomic: CCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAGgtaagctctc ... ttgtttgtagGCTGTGGAGCGGGCAGCTGGTACTGATGGCCAAAAGATAACATACGGTGTC
EST: gi|4572998|gb|AI586647.1|AI586647
EST:     CCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAG                         GCTGTGGAGCGGGCAGCTGGTACTGATGGCCAAAAGATAACATACGGTGTC
genomic: CCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAGgtaagctctc ... ttgtttgtagGCTGTGGAGCGGGCAGCTGGTACTGATGGCCAAAAGATAACATACGGTGTC
EST: gi|5846863|gb|AI999946.1|AI999946
EST:     CCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAG                         GCTGTGGAGCGGGCAGCTGGTACTGATGGCCAAAAGATAACATACGGTGTC
genomic: CCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAGgtaagctctc ... ttgtttgtagGCTGTGGAGCGGGCAGCTGGTACTGATGGCCAAAAGATAACATACGGTGTC
EST: gi|67040096|gb|CO466351.1|CO466351
EST:     CCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAG                         GCTGTGGAGCGGGCAGCTGGTACTGATGGCCAAAAGATAACATACGGTGTC
genomic: CCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAGgtaagctctc ... ttgtttgtagGCTGTGGAGCGGGCAGCTGGTACTGATGGCCAAAAGATAACATACGGTGTC
EST: gi|149076737|gb|EE165383.2|EE165383
EST:     CCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAG                         GCTGTGGAGCGGGCAGCTGGTACTGATGGCCAAAAGATAACATACGGTGTC
genomic: CCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAGgtaagctctc ... ttgtttgtagGCTGTGGAGCGGGCAGCTGGTACTGATGGCCAAAAGATAACATACGGTGTC
EST: gi|32836684|gb|CD976362.1|CD976362
EST:     CCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAG                         GCTGTGGAGCGGGCAGCTGGT
genomic: CCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAGgtaagctctc ... ttgtttgtagGCTGTGGAGCGGGCAGCTGGT
EST: gi|83278503|gb|DV942511.1|DV942511
EST:     CCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAG                         GCTGTGGAGCGGGCAGCTGGTACTGATGGCCAAAAGATAACATACGGTGTC
genomic: CCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAGgtaagctctc ... ttgtttgtagGCTGTGGAGCGGGCAGCTGGTACTGATGGCCAAAAGATAACATACGGTGTC
EST: gi|5343199|gb|AI795384.1|AI795384
EST:     CCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAG                         GCTGTGGAGCGGGCAGCTGGTACTGATGGCCAAAAGATAACATACGGTGTC
genomic: CCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAGgtaagctctc ... ttgtttgtagGCTGTGGAGCGGGCAGCTGGTACTGATGGCCAAAAGATAACATACGGTGTC
EST: gi|5296225|gb|AI782905.1|AI782905
EST:     CCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAG                         GCTGTGGAGCGGGCAGCTGGTACTGATGGCCAAAAGATAACATACGGTGTC
genomic: CCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAGgtaagctctc ... ttgtttgtagGCTGTGGAGCGGGCAGCTGGTACTGATGGCCAAAAGATAACATACGGTGTC
EST: gi|5325051|gb|AI783242.1|AI783242
EST:     CCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAG                         GCTGTGGAGCGGGCAGCTGGTACTGATGGCCAAAAGATAACATACGGTGTC
genomic: CCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAGgtaagctctc ... ttgtttgtagGCTGTGGAGCGGGCAGCTGGTACTGATGGCCAAAAGATAACATACGGTGTC
EST: gi|211156008|gb|FL123543.1|FL123543
EST:     CCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAG                         GCTGTGGAGCGGGCAGCTGGTACTGATGGCCAAAAGATAACATACGGTGTC
genomic: CCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAGgtaagctctc ... ttgtttgtagGCTGTGGAGCGGGCAGCTGGTACTGATGGCCAAAAGATAACATACGGTGTC
EST: gi|32910829|gb|CF015641.1|CF015641
EST:     CCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAG                         GCTGTGGAGCGGGCAGCTGGTACTGATGGCCAAAAGATAACATACGGTGTC
genomic: CCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAGgtaagctctc ... ttgtttgtagGCTGTGGAGCGGGCAGCTGGTACTGATGGCCAAAAGATAACATACGGTGTC
EST: gi|67025855|gb|CO454604.1|CO454604
EST:     CCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAG                         GCTGTGGAGCGGGCAGCTGGTACTGATGGCCAAAAGATAACATACGGTGTC
genomic: CCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAGgtaagctctc ... ttgtttgtagGCTGTGGAGCGGGCAGCTGGTACTGATGGCCAAAAGATAACATACGGTGTC
EST: gi|61236472|gb|DN586224.1|DN586224
EST:     TGGC-AATCAG                         GCTGTGGAGCGGGCAGCTGGTACTGATGGCCAAAAGATAACATACGGTGTC
genomic: TGGCAAATCAGgtaagctctc ... ttgtttgtagGCTGTGGAGCGGGCAGCTGGTACTGATGGCCAAAAGATAACATACGGTGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaacaacatttgtggtttattaagaatattttatattcttgtattgtttgtagGCTGTGGAGCGGGCAGCTGGTACTGATGGCCAAAAGATAACATACGGTGTCATAAAACACCGTTTGGGCGATCTATTTTATCGCCTAGT
                 tttattaagaatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gggaatgtgtagtctttggaatgagctgcactaataaataacttgtgaaacaacatttgtggtttattaagaatattttatattcttgtattgtttgtagGCTGTGGAGCGGGCAGCTGGTACTGATGGCCAAAAGATAACATACGGTGTCATAAAACACCGTTTGGGCGATCTATTTTATCGCCTAGT

- gaatgtg
- - - - - - - - - - - - gctgcac
- - - - - - - - - - - - - - - - - -aaataac
- - - - - - - - - - - - - - - - - - - - - - - - aacaaca