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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgcttttcttcctcaagataccgtttcaaattccagagttttttcgggtttatgattacgacatacacggtgactctttatgcatgttcggtgttgcagATCTATGTAGTTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCTGAATTTCAG

Basic information

species Zea mays
transcript GRMZM2G106795_T03
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G106795_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g47110.1 (Oryza sativa), 3'ss of exon 3
ctgcttttcttcctcaagataccgtttcaaattccagagttttttcgggtttatgattacgac--atacacggtgactctttatgcatgttcggtgttgcagATCTATGTAGTTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCTGAATTTCAG
 | ||    |||      || |     || |  | |     |||     ||  | ||  | ||  || |        | ||| |||| |||| |  |||||||||||||||||||||||||||||| | ||||| || |||||||| ||||| || ||||||
-tactgaaattcggatgtattcatgagcatacccaactacatttataaatt-gtaatagcaacttattcctatatgttatttttgcacgttctgatttgcagATCTATGTAGTTGATTCATTGGATAGAGAGAGAATCGGAAAAGCGAAAGCGGAGTTTCAG

upper sequence: GRMZM2G106795_T03 (Zea mays), 3'ss of exon 3
lower sequence: Vv16s0039g02240.t01 (Vitis vinifera), 3'ss of exon 3
ctgcttttcttcctcaagataccgtttcaaattccagagttttttcgggttt-atgattacgacatacacggtgactctttatgcatgttcggtgt-tgcagATCTATGTAGTTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCTGAATTTCAG
   | |   ||| |  |  || | | |  | ||      | | || || |||  | |  | ||    | |      | || |   ||| ||  | | ||||||||||||| |||||||| |||||||| ||||||||||||||||| || || || ||||||
-aacatactttcttagaagtatcttgttcatttttttcttctatttggtttttgtaacaatgaagccctcaacctatgttga-aaatggtctatatatgcagATCTATGTTGTTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCAGAGTTTCAG
















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|211091310|gb|FL335551.1|FL335551
EST:     AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCTTG                         ATCTATGTAGTTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCT
genomic: AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCTTGgtatgtttat ... ggtgttgcagATCTATGTAGTTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCT
EST: gi|74241061|gb|DT648975.1|DT648975
EST:     AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCTTG                         ATCTATGTAGTTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCT
genomic: AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCTTGgtatgtttat ... ggtgttgcagATCTATGTAGTTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCT
EST: gi|101398288|gb|EB821017.1|EB821017
EST:     AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCTTG                         ATCTATGTAGTTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCT
genomic: AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCTTGgtatgtttat ... ggtgttgcagATCTATGTAGTTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCT
EST: gi|211076278|gb|FL377992.1|FL377992
EST:     AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCTTG                         ATCTATGTAGTTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCT
genomic: AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCTTGgtatgtttat ... ggtgttgcagATCTATGTAGTTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCT
EST: gi|211066463|gb|FL305323.1|FL305323
EST:     AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCTTG                         ATCTATGTAGTTGATTCATTGGATCGGGAGAGGATTGGAAAAAGCTAAAGC
genomic: AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCTTGgtatgtttat ... ggtgttgcagATCTATGTAGTTGATTCATTGGATCGGGAGAGGATTGGAAAA-GCTAAAGC
EST: gi|211069201|gb|FL305331.1|FL305331
EST:     AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAAT-CTGATGGCTTG                         ATCTATGTAGTTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCT
genomic: AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCTTGgtatgtttat ... ggtgttgcagATCTATGTAGTTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCT
EST: gi|211497259|gb|FL426008.1|FL426008
EST:     AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCTTG                         ATCTATGTAGTTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCT
genomic: AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCTTGgtatgtttat ... ggtgttgcagATCTATGTAGTTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCT
EST: gi|211066466|gb|FL305326.1|FL305326
EST:     AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCTTG                         ATCTATGTAGTTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCT
genomic: AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCTTGgtatgtttat ... ggtgttgcagATCTATGTAGTTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCT
EST: gi|211066470|gb|FL305330.1|FL305330
EST:     AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCTTG                         ATCTATGTAGTTGA
genomic: AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCTTGgtatgtttat ... ggtgttgcagATCTATGTAGTTGA
EST: gi|211066462|gb|FL305322.1|FL305322
EST:     AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCTTG                         ATCTATGTAGTTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCT
genomic: AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCTTGgtatgtttat ... ggtgttgcagATCTATGTAGTTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCT
EST: gi|211066467|gb|FL305327.1|FL305327
EST:     AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCTTG                         ATCTATGTAGTTGATTCATTGGATCGGGAGATGATTGGA
genomic: AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCTTGgtatgtttat ... ggtgttgcagATCTATGTAGTTGATTCATTGGATCGGGAGAGGATTGGA
EST: gi|211069202|gb|FL305332.1|FL305332
EST:     AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCTTG                         ATCTATGTAGTTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCT
genomic: AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCTTGgtatgtttat ... ggtgttgcagATCTATGTAGTTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgggtttatgattacgacatacacggtgactctttatgcatgttcggtgttgcagATCTATGTAGTTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCTGAATTTCAG
     ttatgatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgcttttcttcctcaagataccgtttcaaattccagagttttttcgggtttatgattacgacatacacggtgactctttatgcatgttcggtgttgcagATCTATGTAGTTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCTGAATTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
ctgcttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catacac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcatgtt