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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaatggcttctgcgccatttcttctttactgtcatggttgcatatttcttatcactagtgtgttgattgtgcaatttcttactctgtgaaacatacgcagGAGAGCTTCTGTGGCATTAAACGTATGGCAACCACAAGTTGTTCGTGGTCGTCAGAAGCAGTTGGTTCAGCAATGCACAGTTCCTGTTGATTCCCGTCTT

Basic information

species Zea mays
transcript GRMZM2G155285_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G155285_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g59910.2 (Oryza sativa), 3'ss of exon 2
aaatggcttctgcgccatttcttctttactgtcatggttgcatatt-tcttatcactagtgtgttgattgtgcaatttcttactctgtgaaacatacgcagGAGAGCTTCTGTGGCATTAAACGTATGGCAACCACAAGTTGTTCGTGGTCGTCAGAAGCAGTTGGTTCAGCAATGCACAGTTCCTGTTGATTCCCGTCTT
  ||    | |   | |  ||| |     |  | || ||   |  | || |          |  |   |   |||||  ||    | |||    |   |||||||||||| ||||||||||| |||||||||||||||||||||||||| ||||| || || |||||||| || ||||||||||| |||||||||||||||
-tatcatctttttccaagctctacagccattccttgattatgtgctatcatgggttctcgctactatattctcaattcattgtcatttgagttgtctacagGAGAGCTTCAGTGGCATTAAATGTATGGCAACCACAAGTTGTTCGTGGACGTCAAAAACAATTGGTTCAACAGTGCACAGTTCCAGTTGATTCCCGTCTT
















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|91878136|gb|EB408093.1|EB408093
EST:     GAGAGGATGAAGACGGCTGCGCAGGAGCTCGACAACCTCGAGAGGGTCAG                         GAGAGCTTCTGTGGCATTAAACGTATGGCAAC
genomic: GAGAGGATGAAGACGGCTGCGCAGGAGCTCGACAACCTCGAGAGGGTCAGgtgggcttgc ... acatacgcagGAGAGCTTCTGTGGCATTAAACGTATGGCAAC
EST: gi|78091970|gb|DV520344.1|DV520344
EST:     GAGAGGATGAAGACGGCTGCGCAGGAGCTCGACAACCTCGAGAGGGTCAG                         GAGAGCTTCTGTGGCATTAAACGTATGGCAACCACAAGTTGTTCGTGGTCG
genomic: GAGAGGATGAAGACGGCTGCGCAGGAGCTCGACAACCTCGAGAGGGTCAGgtgggcttgc ... acatacgcagGAGAGCTTCTGTGGCATTAAACGTATGGCAACCACAAGTTGTTCGTGGTCG
EST: gi|101390955|gb|EB817413.1|EB817413
EST:     GAGAGGATGAAGACGGCTGCGCAGGAGCTCGACAACCTCGAGAGGGTCAG                         GAGAGCTTCTG
genomic: GAGAGGATGAAGACGGCTGCGCAGGAGCTCGACAACCTCGAGAGGGTCAGgtgggcttgc ... acatacgcagGAGAGCTTCTG
EST: gi|71772037|gb|DR969974.1|DR969974
EST:     GAGAGGATGAAGACGGCTGCGCAGGAGCTCGACAACCTCGAGAGGGTCAG                         GAGAGCTTCTGTGGCATTAAACGTATGGCAACCACAAGTTGTTCGGGGTCG
genomic: GAGAGGATGAAGACGGCTGCGCAGGAGCTCGACAACCTCGAGAGGGTCAGgtgggcttgc ... acatacgcagGAGAGCTTCTGTGGCATTAAACGTATGGCAACCACAAGTTGTTCGTGGTCG
EST: gi|89252865|gb|DY624651.1|DY624651
EST:     GAGAGGATGAAGACGGCTGCGCAGGAGCTCGACAACCTCGAGAGGGTCAG                         GAGAGCTTCTGTGGCATTAAACGTATGGCAACCACAAGTTGTTCGTGGTCG
genomic: GAGAGGATGAAGACGGCTGCGCAGGAGCTCGACAACCTCGAGAGGGTCAGgtgggcttgc ... acatacgcagGAGAGCTTCTGTGGCATTAAACGTATGGCAACCACAAGTTGTTCGTGGTCG
EST: gi|76018025|gb|DT945195.1|DT945195
EST:     GAGAGGATGAAGACGGCTGCGCAGGAGCTCGACAACCTCGAGAGGGTCAG                         GAGAGCTTCTGTGGCATTAAACGTATGGCAACCACAAGTTGTTCGTGGTCG
genomic: GAGAGGATGAAGACGGCTGCGCAGGAGCTCGACAACCTCGAGAGGGTCAGgtgggcttgc ... acatacgcagGAGAGCTTCTGTGGCATTAAACGTATGGCAACCACAAGTTGTTCGTGGTCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttatcactagtgtgttgattgtgcaatttcttactctgtgaaacatacgcagGAGAGCTTCTGTGGCATTAAACGTATGGCAACCACAAGTTGTTCGTGGTCGTCAGAAGCAGTTGGTTCAGCAATGCACAGTTCCTGTTGATTCCCGTCTT
                              ttcttac  putative branch site (score: 2)
                           aatttctta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaatggcttctgcgccatttcttctttactgtcatggttgcatatttcttatcactagtgtgttgattgtgcaatttcttactctgtgaaacatacgcagGAGAGCTTCTGTGGCATTAAACGTATGGCAACCACAAGTTGTTCGTGGTCGTCAGAAGCAGTTGGTTCAGCAATGCACAGTTCCTGTTGATTCCCGTCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC