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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaaacaaagaaagagacaaagaaaattaaaagatacctactttacaccagagtttgtgtcctacatggctacatcacagtgttgtaatcatatttctagGTGTACCTTCGCTGAAACGATCAGAGCTGGAAACGGCATGCGAGGATTTCAGCAACATAATTGGTTCTACCTCTACCTGCATGCTGTACAAGGGAACTTT

Basic information

species Zea mays
transcript GRMZM2G135359_T04
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G135359_T04 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g18370.1 (Oryza sativa), 3'ss of exon 4
agaaacaaagaaagagacaaagaaaattaaaagatacctactt-tacaccagagtttgtgtcctacatggctacatcacagtgttgtaatcatatttctagGTGTACCTTCGCTGAAACGATCAGAGCTGGAAACGGCATGCGAGGATTTCAGCAACATAATTGGTTCTACCTCTACCTGCATGCTGTACAAGGGAACTTT
                           |     || |||||||  | |    ||| | |   |    |  | |   ||       | |||  ||| | ||||||| ||| |  |||||||||||||||||||||| || ||||||||||| ||||| |||||||||| ||| |||||||| |  |||||||||||||||||
------------------------gtatgctttattcctacttgcatatataagtatctcggcagttttccgaatccatcacacagcaattgtatctatagGTGTGCCTGCATTGAAACGATCAGAGCTGGAAACAGCGTGCGAGGATTTTAGCAATATAATTGGTTGTACATCTACCTGTACACTGTACAAGGGAACTTT
















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|50328044|gb|CO523170.1|CO523170
EST:     GCCATGGGCGACAGGTCTAAGTGGACAATTGCAGAAAGCTTTTGTAACTG                         GTGTACCTTCGCTGAAACGATCAGAGCTGGAAACGGCATGCGAGGATTTCA
genomic: GCCATGGGCGACAGGTCTAAGTGGACAATTGCAGAAAGCTTTTGTAACTGgtatggcttt ... atatttctagGTGTACCTTCGCTGAAACGATCAGAGCTGGAAACGGCATGCGAGGATTTCA
EST: gi|211161240|gb|FL160681.1|FL160681
EST:     GCCATGGGCGACAGGTCTAAGTGGACAATTGCAGAAAGCTTTTGTAACTG                         GTGTACCTTCGCTG
genomic: GCCATGGGCGACAGGTCTAAGTGGACAATTGCAGAAAGCTTTTGTAACTGgtatggcttt ... atatttctagGTGTACCTTCGCTG
EST: gi|211161241|gb|FL160682.1|FL160682
EST:     GCCATGGGCGACAGGTCTAAGTGGACAATTGCAGAAAGCTTTTGTAACTG                         GTGTACCTTCGCTGAAACGATCAGAGCTGGAAACGGCATGCGAGGAT
genomic: GCCATGGGCGACAGGTCTAAGTGGACAATTGCAGAAAGCTTTTGTAACTGgtatggcttt ... atatttctagGTGTACCTTCGCTGAAACGATCAGAGCTGGAAACGGCATGCGAGGAT
EST: gi|211161242|gb|FL160683.1|FL160683
EST:     GCCATGGGCGACAGGTCTAAGTGGACAATTGCAGAAAGCTTTTGTAACTG                         GTGTACCTTCGCTGAAACGATCAGAGCTG
genomic: GCCATGGGCGACAGGTCTAAGTGGACAATTGCAGAAAGCTTTTGTAACTGgtatggcttt ... atatttctagGTGTACCTTCGCTGAAACGATCAGAGCTG
EST: gi|149070912|gb|EE159319.2|EE159319
EST:     GCCATGGGCGACAGGTCTAAGTGGACAATTGCAGAAAGCTTTTGTAACTG                         GTGTACCTTCGCTGAAACGATCAGAGCTGGAAACGGCATGCGAGGATTTCA
genomic: GCCATGGGCGACAGGTCTAAGTGGACAATTGCAGAAAGCTTTTGTAACTGgtatggcttt ... atatttctagGTGTACCTTCGCTGAAACGATCAGAGCTGGAAACGGCATGCGAGGATTTCA
EST: gi|76012816|gb|DT939986.1|DT939986
EST:     GCCATGGGCGACAGGTCTAAGTGGACAATTGCAGAAAGCTTTTGTAACTG                         GTGTACCTTCGCTGAAACGATCAGAGCTGGAAACGGCATGCGAGGATTTCA
genomic: GCCATGGGCGACAGGTCTAAGTGGACAATTGCAGAAAGCTTTTGTAACTGgtatggcttt ... atatttctagGTGTACCTTCGCTGAAACGATCAGAGCTGGAAACGGCATGCGAGGATTTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caccagagtttgtgtcctacatggctacatcacagtgttgtaatcatatttctagGTGTACCTTCGCTGAAACGATCAGAGCTGGAAACGGCATGCGAGGATTTCAGCAACATAATTGGTTCTACCTCTACCTGCATGCTGTACAAGGGAACTTT
                                              tatttct  CT-rich tract
                                     ttgtaatcatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agaaacaaagaaagagacaaagaaaattaaaagatacctactttacaccagagtttgtgtcctacatggctacatcacagtgttgtaatcatatttctagGTGTACCTTCGCTGAAACGATCAGAGCTGGAAACGGCATGCGAGGATTTCAGCAACATAATTGGTTCTACCTCTACCTGCATGCTGTACAAGGGAACTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG