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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAGGAGGCAAGCTGAGGCTAACCGCATCAGGGAGAAATACCCTGACAGAATCCCTgtaagccttaattaatttttacccatgtcctctgattatttccatgatagcttttgtgttcattcaaacctgctttcttgtaatatag

Basic information

species Zea mays
transcript GRMZM2G134613_T05
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G134613_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os08g09240.1 (Oryza sativa), 5'ss of exon 3
AAAGGAGGCAAGCTGAGGCTAACCGCATCAGGGAGAAATACCCTGACAGAATCCCTgtaagcc--ttaattaatttttacccatgtcctctgattatttc--catgatagcttttgtgttcattcaaacctgctttct----tgtaatatag
|||||||||| |||||||| ||||||||||||||||| || || || ||||| ||||||||     |   |  || || |   ||   |  | ||| ||   ||||||   ||||||  | ||   || |  ||| ||    |  |||||||
AAAGGAGGCAGGCTGAGGCCAACCGCATCAGGGAGAAGTATCCCGATAGAATTCCTgtaagttggatggattcttgttgcttgtggtgttcgcttactttgtcatgatta-ttttgttcttatgtgaagcaacttcctgtgattaaatatag
















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|7162618|gb|AW520240.1|AW520240
EST:     CGCATCAGGGAGAAATACCCTG-CAGAATCCCT                         GTCATTGTTGAGAAGGCCGAGAGGAGTGACATCCCAGACATTGACAAGAAA
genomic: CGCATCAGGGAGAAATACCCTGACAGAATCCCTgtaagcctta ... tgtaatatagGTCATTGTTGAGAAGGCCGAGAGGAGTGACATCCCAGACATTGACAAGAAA
EST: gi|211028099|gb|FK976175.1|FK976175
EST:     GGCAAGCTGAGGCTAACCGCATCAGGGAGAAATACCCTGACAGAATCCCT                         GTCATTGTTGAGAAGGCCGAGAGGAGTGACATCCCAGACATTGACAAGAAA
genomic: GGCAAGCTGAGGCTAACCGCATCAGGGAGAAATACCCTGACAGAATCCCTgtaagcctta ... tgtaatatagGTCATTGTTGAGAAGGCCGAGAGGAGTGACATCCCAGACATTGACAAGAAA
EST: gi|5761920|gb|AI966893.1|AI966893
EST:     GGCAAGCTGAGGCTAACCGCATCAGGGAGAAATACCCTGACAGAATCCCT                         GTCATTGTTGAGAAGGCCGAGAGGAGTGACATCCCAGACATTGACAAGAAA
genomic: GGCAAGCTGAGGCTAACCGCATCAGGGAGAAATACCCTGACAGAATCCCTgtaagcctta ... tgtaatatagGTCATTGTTGAGAAGGCCGAGAGGAGTGACATCCCAGACATTGACAAGAAA
EST: gi|7227531|gb|AW566172.1|AW566172
EST:     ATACCCTGACAGAATCCCT                         GTCATTGCTGAGAAGGCCGAGAGGAGTGACATCCCAGACATTGACAAGAAA
genomic: ATACCCTGACAGAATCCCTgtaagcctta ... tgtaatatagGTCATTGTTGAGAAGGCCGAGAGGAGTGACATCCCAGACATTGACAAGAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAGGAGGCAAGCTGAGGCTAACCGCATCAGGGAGAAATACCCTGACAGAATCCCTgtaagccttaattaatttttacccatgtcctctgattatttccatgatagcttttgtgttcattcaaacctgctttcttgtaatatag

- - - - CAAGCT
- - - -  AAGCTG
- - - - - AGCTGA
- - - - - - - - - - - - - - -  GGAGAA