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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTAATGATGACGACGACCATGTAAAAAAGAAGATTCGGCTGGGTGCTCCTGCAACACAGTGGATTTCAGTATACAATTCAAGGCAACCTATGAAGCAGAGgttaatgttatttctcaagttaatttcttcctgtagactgtatatcctgtttcgagtatccatccagagttatattatcgtagtgtgttctgtatcgttc...

Basic information

species Zea mays
transcript GRMZM2G017835_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017835_T01 (Zea mays), 5'ss of exon 10
lower sequence: Vv06s0004g01090.t01 (Vitis vinifera), 5'ss of exon 11
TTAATGATGACGACGACCATGTAAAAAAGAAGATTCGGCTGGGTGCTCCTGCAACACAGTGGATTTCAGTATACAATTCAAGGCAACCTATGAAGCAGAGgttaa-tgttatttctcaagttaatttcttcctgtagactgtatatcctgtttcgagtatc-catccagagttata-ttatcgtagtgtgttctgtatcgttc
   | || || || |  ||    || || ||| ||||  ||||   |||||| || ||||||||||||||||||||| | |||| ||| ||||| ||||||| |  |||  | |      ||| ||| | | | |      || ||||||  |    |||  | |||| |    || |||||      |  || | |  | | 
AGGAAGAAGAAGATGGGCAACCCAAGAAAAAGGTTCGATTGGGAATTCCTGCTACCCAGTGGATTTCAGTATACAATGCTAGGCTACCGATGAAACAGAGgtgagctgtcttgtgcttcattactttgtacttctt--tcatacatcctgcatgttttatttcttccacatgggtaattatcaggagataatcaggaaggat-
















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|6020774|gb|AW065582.1|AW065582
EST:     TCAGTATACAATTCAAGGCAACCTATGAAGCAGAG                         GTACCACTATAATGTGGCTGATGCAAGGTTAGCGCAACATGTGGAGAAAGG
genomic: TCAGTATACAATTCAAGGCAACCTATGAAGCAGAGgttaatgtta ... cccttgatagGTACCACTATAATGTGGCTGATGCAAGGTTAGCGCAACATGTGGAGAAAGG
EST: gi|67011551|gb|CO440300.1|CO440300
EST:     GCAACCTATGAAGCAGAG                         GTACCACTATAATGTGGCTGATGCAAGGTTAGCGCAACATGTGGAGAAAGG
genomic: GCAACCTATGAAGCAGAGgttaatgtta ... cccttgatagGTACCACTATAATGTGGCTGATGCAAGGTTAGCGCAACATGTGGAGAAAGG
EST: gi|6020754|gb|AW065562.1|AW065562
EST:     TCAGTATACAATTCAAGGCAACCTATGAAGCAGAG                         GTACCACTATAATGTGGCTGATGCAAGGTTAGCGCAACATGTGGAGAAAGG
genomic: TCAGTATACAATTCAAGGCAACCTATGAAGCAGAGgttaatgtta ... cccttgatagGTACCACTATAATGTGGCTGATGCAAGGTTAGCGCAACATGTGGAGAAAGG
EST: gi|76285883|gb|DV025451.1|DV025451
EST:     GCAACACAGTGGATTTCAGTATACAATTCAAGGCAACCTATGAAGCAGAG                         GTACCACTATAATGTGGCTGATGCAAGGTTAGCGCAACATGTGGAGAAAGG
genomic: GCAACACAGTGGATTTCAGTATACAATTCAAGGCAACCTATGAAGCAGAGgttaatgtta ... cccttgatagGTACCACTATAATGTGGCTGATGCAAGGTTAGCGCAACATGTGGAGAAAGG
EST: gi|38568968|gb|CF974853.1|CF974853
EST:     GCAACACAGTGGATTTCAGTATACAATTCAAGGCAACCTATGAAGCAGAG                         GTACCACTATAATGTGGCTGATGCAAGGTTAGCGCAACATGTGGAGAAAGG
genomic: GCAACACAGTGGATTTCAGTATACAATTCAAGGCAACCTATGAAGCAGAGgttaatgtta ... cccttgatagGTACCACTATAATGTGGCTGATGCAAGGTTAGCGCAACATGTGGAGAAAGG
EST: gi|67025680|gb|CO454429.1|CO454429
EST:     GCAACACAGTGGATTTCAGTATACAATTCAAGGCAACCTATGAAGCAGAG                         GTACCACTATAATGTGGCTGATGCAAGGTTAGCGCAACATGTGGAGAAAGG
genomic: GCAACACAGTGGATTTCAGTATACAATTCAAGGCAACCTATGAAGCAGAGgttaatgtta ... cccttgatagGTACCACTATAATGTGGCTGATGCAAGGTTAGCGCAACATGTGGAGAAAGG
EST: gi|67011858|gb|CO440607.1|CO440607
EST:     GCAACACAGTGGATTTCAGTATACAATTCAAGGCAACCTATGAAGCAGAG                         GTACCACTATAATGTGGCTGATGCAAGGTTAGCGCAACATGTGGAGAAAGG
genomic: GCAACACAGTGGATTTCAGTATACAATTCAAGGCAACCTATGAAGCAGAGgttaatgtta ... cccttgatagGTACCACTATAATGTGGCTGATGCAAGGTTAGCGCAACATGTGGAGAAAGG
EST: gi|14204221|gb|BG837898.1|BG837898
EST:     GCAACACAGTGGATTTCAGTATACAATTCAAGGCAACCTATGAAGCAGAG                         GTACCACTATAATGTGGCTGATGCAAGGTTAGCGCAACATGTGGAGAAAGG
genomic: GCAACACAGTGGATTTCAGTATACAATTCAAGGCAACCTATGAAGCAGAGgttaatgtta ... cccttgatagGTACCACTATAATGTGGCTGATGCAAGGTTAGCGCAACATGTGGAGAAAGG
EST: gi|31359524|gb|CD443881.1|CD443881
EST:     GCAACACAGTGGATTTCAGTATACAATTCAAGGCAACCTATGAAGCAGAG                         GTACCACTATAATGTGGCTGATGCAAGGTTAGCGCAACATGTGGAGAAAGG
genomic: GCAACACAGTGGATTTCAGTATACAATTCAAGGCAACCTATGAAGCAGAGgttaatgtta ... cccttgatagGTACCACTATAATGTGGCTGATGCAAGGTTAGCGCAACATGTGGAGAAAGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTAATGATGACGACGACCATGTAAAAAAGAAGATTCGGCTGGGTGCTCCTGCAACACAGTGGATTTCAGTATACAATTCAAGGCAACCTATGAAGCAGAGgttaatgttatttctcaagttaatttcttcctgtagactgtatatcctgtttcgagtatccatccagagttatattatcgtagtgtgttctgtatcgttc

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC