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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tccatgtatctggacagtgatgtcctcctcatctagttaaaactattcacaagttgaattacgacttaattttatgctaatatttctttatattttcaagGAGTGAGGAATTGGAAACTGCTTTGATGGAGATGGTCGAGCATGACAACAGACGTATGTTGAGTGCAAAG

Basic information

species Zea mays
transcript GRMZM2G154883_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G154883_T02 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os03g17540.3 (Oryza sativa), 3'ss of exon 10
--tccatgtatctggaca--gtgatgtcctcctcatctagttaaaactattcacaagttgaattacgacttaattttatgctaatatttctttatattttcaagGAGTGAGGAATTGGAAACTGCTTTGATGGAGATGGTCGAGCATGACAACAGACGTATGTTGAGTGCAAAG
  | ||| ||  | | |   || ||||  |   |   ||  | |   |  |     ||  || | | |      | |||  ||| |  | |  ||  | ||| | || ||||| |||||||||||||||||||| |||||| |||| |||||||||| |||||||||||| |||
ctttcatctaagttgtcgctgtaatgttttgggccattaacttagttttgtactgtgtccaactcctatcatgatctat--taacacatgtc-atgctctca-gAAGCGAGGAGTTGGAAACTGCTTTGATGGAAATGGTCAAGCAGGACAACAGACATATGTTGAGTGCTAAG
















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|21432349|gb|BQ547839.1|BQ547839
EST:     AAGGTTGAACTATGCATGCTGCTCGAGGAGAAAAGATCAGCTGATCTCAG                         GAGTGAGGAATTGGAAACTGCTTTGATGGAGATGGTCGAGCATGACAACAG
genomic: AAGGTTGAACTATGCAAGCTGCTCGAGGAGAAAAGATCAGCTGATCTCAGgtttgggtta ... tattttcaagGAGTGAGGAATTGGAAACTGCTTTGATGGAGATGGTCGAGCATGACAACAG
EST: gi|211179247|gb|FL124466.1|FL124466
EST:     AAGGTTGAACTATGCAAGCTGCTCGAGGAGAAAAGATCAGCTGATCTCAG                         GAGTGAGGAATTGGAAACTGCTTTGATGGAGATGGTCGAGCATGACAACAG
genomic: AAGGTTGAACTATGCAAGCTGCTCGAGGAGAAAAGATCAGCTGATCTCAGgtttgggtta ... tattttcaagGAGTGAGGAATTGGAAACTGCTTTGATGGAGATGGTCGAGCATGACAACAG
EST: gi|5895871|gb|AW037117.1|AW037117
EST:     AGAAAAGA-CAGCTGATCTCAG                         GAGNGAGGAATTGGAAACTGCTTTGATGGAGATGGTCGAGCATGACAACAG
genomic: AGAAAAGATCAGCTGATCTCAGgtttgggtta ... tattttcaagGAGTGAGGAATTGGAAACTGCTTTGATGGAGATGGTCGAGCATGACAACAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcacaagttgaattacgacttaattttatgctaatatttctttatattttcaagGAGTGAGGAATTGGAAACTGCTTTGATGGAGATGGTCGAGCATGACAACAGACGTATGTTGAGTGCAAAG
                             tgctaat  putative branch site (score: 2)
                                     tttctttatattttc  CT-rich tract
                  acttaattttatgcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tccatgtatctggacagtgatgtcctcctcatctagttaaaactattcacaagttgaattacgacttaattttatgctaatatttctttatattttcaagGAGTGAGGAATTGGAAACTGCTTTGATGGAGATGGTCGAGCATGACAACAGACGTATGTTGAGTGCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- catgtat
- - - - -ctggaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgctaa