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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cacagtgcactagagagtagagactagactagcagcagcaagtgatgtctgatgactgagcaaaatgaatgggctggatgatctgttgcctatcttgcagTTGTCGTGGGGGCCGTTGCTGTACCAGGTGTCCCGGGTGGACGAGAAGGGCCTGCAGCAGTGCAACAGCGTGGCGGCCAAGATCAAGGAGCAGCTGGAGA

Basic information

species Zea mays
transcript GRMZM2G106165_T03
intron # 4
splice site 3'
intron type U2

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|148953881|gb|EC899259.2|EC899259
EST:     TCGCCGGCGTCGCCCTCGGGGATAGCTGGATCTCGCCGCTCGACTTCGTG                         TTGTCGTGGGGGCCGTTGCTG
genomic: TCGCCGGCGTCGCCCTCGGGGATAGCTGGATCTCGCCGCTCGACTTCGTGgtgagtttca ... tatcttgcagTTGTCGTGGGGGCCGTTGCTG
EST: gi|148978996|gb|EE026423.2|EE026423
EST:     TCGCCGGCGTCGCCCTCGGGGATAGCTGGATCTCGCCGCTCGACTTCGTG                         TTGTCGTGGGGGCCGTTGCTGTACCAGGTGTCCCGGGTGGACGAGAAGGGC
genomic: TCGCCGGCGTCGCCCTCGGGGATAGCTGGATCTCGCCGCTCGACTTCGTGgtgagtttca ... tatcttgcagTTGTCGTGGGGGCCGTTGCTGTACCAGGTGTCCCGGGTGGACGAGAAGGGC
EST: gi|32827593|gb|CD967271.1|CD967271
EST:     GATCTCGGCGGTCGACTTCGTG                         TTGTCGTGGGGGCCGTTGCTGTACCAGGTGTCCCGGGTGGACGAGAAGGGC
genomic: GATCTCGCCGCTCGACTTCGTGgtgagtttca ... tatcttgcagTTGTCGTGGGGGCCGTTGCTGTACCAGGTGTCCCGGGTGGACGAGAAGGGC
EST: gi|211078638|gb|FL013034.1|FL013034
EST:     TCGCCGGCGTCGCCCTCGGGGATAGCTGGATCTCGCCGCTCGACTTCTTG                         TTGTCGTGGGGGCCGTTGCTGTACCAGGTGTCCCGGTTGGACGAGAAGGGC
genomic: TCGCCGGCGTCGCCCTCGGGGATAGCTGGATCTCGCCGCTCGACTTCGTGgtgagtttca ... tatcttgcagTTGTCGTGGGGGCCGTTGCTGTACCAGGTGTCCCGGGTGGACGAGAAGGGC
EST: gi|149101726|gb|EE187863.2|EE187863
EST:     TCGCCGGCGTCGCCCTCGGGGATAGCTGGATCTCGCCGCTCGACTTCGTG                         TTGTCGTGGGGGCCGTTGCT
genomic: TCGCCGGCGTCGCCCTCGGGGATAGCTGGATCTCGCCGCTCGACTTCGTGgtgagtttca ... tatcttgcagTTGTCGTGGGGGCCGTTGCT
EST: gi|71775263|gb|DR973141.1|DR973141
EST:     TCGCCGGCGTCGCCCTCGGGGATAGCTGGATCTCGCCGCTCGACTTCGTG                         TTGTCGTGGGGGCCGTTGCTGTACCAGGTGTCCCGGGTGGACGAGAAGGGC
genomic: TCGCCGGCGTCGCCCTCGGGGATAGCTGGATCTCGCCGCTCGACTTCGTGgtgagtttca ... tatcttgcagTTGTCGTGGGGGCCGTTGCTGTACCAGGTGTCCCGGGTGGACGAGAAGGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtctgatgactgagcaaaatgaatgggctggatgatctgttgcctatcttgcagTTGTCGTGGGGGCCGTTGCTGTACCAGGTGTCCCGGGTGGACGAGAAGGGCCTGCAGCAGTGCAACAGCGTGGCGGCCAAGATCAAGGAGCAGCTGGAGA
 gtctgat  putative branch site (score: 4)
                                           cctatctt  putative PPT
                aaaatgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cacagtgcactagagagtagagactagactagcagcagcaagtgatgtctgatgactgagcaaaatgaatgggctggatgatctgttgcctatcttgcagTTGTCGTGGGGGCCGTTGCTGTACCAGGTGTCCCGGGTGGACGAGAAGGGCCTGCAGCAGTGCAACAGCGTGGCGGCCAAGATCAAGGAGCAGCTGGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA