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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgccaatacattccattcgactcatttgatggtttatagtgtttcctgaaaacttagtgccatggaaattttttgtttcagATTATGACACTCTGAGAGCATTGGATGCTGACAATAGCCCACATGCTCCATCTATGAGTGAAGAAGAAATAAATTCTCTTCCTGTCTTCAAATATAAAGT

Basic information

species Zea mays
transcript GRMZM2G337425_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G337425_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g16570.2 (Oryza sativa), 3'ss of exon 5
---gtgtgcca-atacattccattcgactcatttgatggtttatagtgtttcctgaaaacttagtgccatgga-aattttttgttt-cagATTATGACACTCTGAGAGCATTGGATGCTGACAATAGCCCACATGCTCCATCTATGAGTGAAGAAGAAATAAATTCTCTTCCTGTCTTCAAATATAAAGT
    |   |   || || |    |  | |||| |  || ||  || |   ||||| || | |       | |   || ||||| || ||||||||||  | || || || |||||||| ||||||||||| |||||||| || ||||||||||||||||||||| |||||||||| |||||||| || ||
gtgatacactttattcacttaggttaattcatatactgcttcttact--ctcctgcaagcattacattgtagctgatgttttgcttgcagATTATGATGCCCTTAGGGCCTTGGATGCAGACAATAGCCCTCATGCTCCTTCGATGAGTGAAGAAGAAATAAATGCTCTTCCTGTATTCAAATACAAGGT
















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|78109926|gb|DV528341.1|DV528341
EST:     GAGCCTTAGACTTCAACTGGCTCTTCTTGATCGTGAATTTGACGATTTAG                         ATTATGACACTCTGAGAGCATTGGATGCTGACAATAGCCCACATGCTCCAT
genomic: GAGCCTTAGACTTCAACTGGCTCTTCTTGATCGTGAATTTGACGATTTAGgtgtgccaat ... tttgtttcagATTATGACACTCTGAGAGCATTGGATGCTGACAATAGCCCACATGCTCCAT
EST: gi|50332883|gb|CO528009.1|CO528009
EST:     GAGCCTTAGACTTCAACTGGCTCTTCTTGATCGTGAATTTGACGATTTAG                         ATTATGACACTCTGAGAGCATTGGATGCTGACAATAGCCCACATGCTCCAT
genomic: GAGCCTTAGACTTCAACTGGCTCTTCTTGATCGTGAATTTGACGATTTAGgtgtgccaat ... tttgtttcagATTATGACACTCTGAGAGCATTGGATGCTGACAATAGCCCACATGCTCCAT
EST: gi|148931116|gb|EC873780.2|EC873780
EST:     GAGCCTTAGACTTCAACTGGCTCTTCTTGATCGTGAATTTGACGATTTAG                         ATTATGACACTCTGAGAGCATTGGATGCTGACAATAGCCCACATGCTCCAT
genomic: GAGCCTTAGACTTCAACTGGCTCTTCTTGATCGTGAATTTGACGATTTAGgtgtgccaat ... tttgtttcagATTATGACACTCTGAGAGCATTGGATGCTGACAATAGCCCACATGCTCCAT
EST: gi|78083979|gb|DV512372.1|DV512372
EST:     GAGCCTTAGACTTCAACTGGCTCTTCTTGATCGTGAATTTGACGATTTAG                         ATTATGACACTCTGAGAGCATTGGATGCTGACAATAGCCCACATGCTCCAT
genomic: GAGCCTTAGACTTCAACTGGCTCTTCTTGATCGTGAATTTGACGATTTAGgtgtgccaat ... tttgtttcagATTATGACACTCTGAGAGCATTGGATGCTGACAATAGCCCACATGCTCCAT
EST: gi|18164717|gb|BM334556.1|BM334556
EST:     GAGCCTTAGACTTCAACTGGCTCTTCTTGATCGTGAATTTGACGATTTAG                         ATTATGACACTCTGAGAGCATTGGATGCTGACAATAGCCCACATGCTCCAT
genomic: GAGCCTTAGACTTCAACTGGCTCTTCTTGATCGTGAATTTGACGATTTAGgtgtgccaat ... tttgtttcagATTATGACACTCTGAGAGCATTGGATGCTGACAATAGCCCACATGCTCCAT
EST: gi|91048354|gb|EB158772.1|EB158772
EST:     GAGCCTTAGACTTCAACTGGCTCTTCTTGATCGTGAATTTGACGATTTAG                         ATTATGACACTCTGAGAGCATTGGATGCTGACAATAGCCCACATGCTCCAT
genomic: GAGCCTTAGACTTCAACTGGCTCTTCTTGATCGTGAATTTGACGATTTAGgtgtgccaat ... tttgtttcagATTATGACACTCTGAGAGCATTGGATGCTGACAATAGCCCACATGCTCCAT
EST: gi|91876517|gb|EB406474.1|EB406474
EST:     GAGCCTTAGACTTCAACTGGCTCTTCTTGATCGTGAATTTGACGATTTAG                         ATTATGACACTCTGAGAGCATTGGATGCTGACAATAG
genomic: GAGCCTTAGACTTCAACTGGCTCTTCTTGATCGTGAATTTGACGATTTAGgtgtgccaat ... tttgtttcagATTATGACACTCTGAGAGCATTGGATGCTGACAATAG
EST: gi|76288198|gb|DV027766.1|DV027766
EST:     GAGCCTTAGACTTCAACTGGCTCTTCTTGATCGTGAATTTGACGATTTAG                         ATTATGACACTCTGAGAGCATTGGATGCTGACAATAGCCCACATGCTCCAT
genomic: GAGCCTTAGACTTCAACTGGCTCTTCTTGATCGTGAATTTGACGATTTAGgtgtgccaat ... tttgtttcagATTATGACACTCTGAGAGCATTGGATGCTGACAATAGCCCACATGCTCCAT
EST: gi|18166650|gb|BM336489.1|BM336489
EST:     GAGCCTTAGACTTCAACTGGCTCTTCTTGATCGTGAATTTGACGATTTAG                         ATTATGACACTCTGAGAGCATTGGATGCTGACAATAGCCCACATGCTCCAT
genomic: GAGCCTTAGACTTCAACTGGCTCTTCTTGATCGTGAATTTGACGATTTAGgtgtgccaat ... tttgtttcagATTATGACACTCTGAGAGCATTGGATGCTGACAATAGCCCACATGCTCCAT
EST: gi|78085073|gb|DV513466.1|DV513466
EST:     GAGCCTTAGACTTCAACTGGCTCTTCTTGATCGTGAATTTGACGATTTAG                         ATTATGACACTCTGAGAGCATTGGATGCTGACAATAGCCCACATGCTCCAT
genomic: GAGCCTTAGACTTCAACTGGCTCTTCTTGATCGTGAATTTGACGATTTAGgtgtgccaat ... tttgtttcagATTATGACACTCTGAGAGCATTGGATGCTGACAATAGCCCACATGCTCCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatggtttatagtgtttcctgaaaacttagtgccatggaaattttttgtttcagATTATGACACTCTGAGAGCATTGGATGCTGACAATAGCCCACATGCTCCATCTATGAGTGAAGAAGAAATAAATTCTCTTCCTGTCTTCAAATATAAAGT
 atttgat  putative branch site (score: 5)
                                          ttttttgtttc  putative PPT
                                       aaattttttgtttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgccaatacattccattcgactcatttgatggtttatagtgtttcctgaaaacttagtgccatggaaattttttgtttcagATTATGACACTCTGAGAGCATTGGATGCTGACAATAGCCCACATGCTCCATCTATGAGTGAAGAAGAAATAAATTCTCTTCCTGTCTTCAAATATAAAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA