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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggactgaaagagagtcacatttctttttatctgtacatatatatgtattgtgactataatatcacctttatgcttaatggctactgttgcaatcaccagGTTATGCAATATGGACATCATCTCTAAGGTCCAACAGGTAATCTGCTTCGCGTTCCACGACAGCAAACTGCTGATGGAAACATGCCAGGAGGCCATGAAC

Basic information

species Zea mays
transcript GRMZM2G081653_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G081653_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g23680.3 (Oryza sativa), 3'ss of exon 4
--tggactgaaagagagtcacattt-ctttttatctgtacatatatatgtattgtgactataatatcacctttatgcttaatggctactgttgcaatcaccagGTTATGCAATATGGACATCATCTCTAAGGTCCAACAGGTAATCTGCTTCGCGTTCCACGACAGCAAACTGCTGATGGAAACATGCCAGGAGGCCATGAAC
  |  |   |  |       |||   |     ||    | |  ||   ||    | |  || |       ||  ||||||||   ||   |  ||||   |||||||||||| |||||||||||||| |||||||||||||| || || || || ||||| |||||||| ||||||||||| || ||||||||||||| ||| 
ccttaatccactggctcctgcataaacaaaacattctaatagctactggtgcaattagaattagcagctattggtgcttaatatgta---tcacaatattcagGTTATGCAACATGGACATCATCTCGAAGGTCCAACAGGTGATTTGTTTTGCATTCCATGACAGCAAGCTGCTGATGGAGACCTGCCAGGAGGCCAAGAAT
















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|89764107|gb|DY691035.1|DY691035
EST:     TTACTCGAGAAACCACAGTATGATCATTTGCCACTGATTGAGGCTAGCAG                         GTTATGCAATATGGACATCATCTCTAAGGTCCAACAGGTAATCTGCTTCGC
genomic: TTACTCGAGAAACCACAGTATGATCATTTGCCACTAATTGAGGCTAGCAGgtcagtgagc ... caatcaccagGTTATGCAATATGGACATCATCTCTAAGGTCCAACAGGTAATCTGCTTCGC
EST: gi|149090139|gb|EE179439.2|EE179439
EST:     TTACTCGAGAAACCACAGTATGATCATTTGCCACTAATTGAGGCTAGCAG                         GTTATGCAATATGGACATCATCTCTAAGGTCCAACAGGTAATCTGCTTCGC
genomic: TTACTCGAGAAACCACAGTATGATCATTTGCCACTAATTGAGGCTAGCAGgtcagtgagc ... caatcaccagGTTATGCAATATGGACATCATCTCTAAGGTCCAACAGGTAATCTGCTTCGC
EST: gi|148973267|gb|EE024347.2|EE024347
EST:     TTACTCGAGAAACCACAGTATGATCATTTGCCACTAATTGAGGCTAGCAG                         GTTATGCAATATGGACATCATCT
genomic: TTACTCGAGAAACCACAGTATGATCATTTGCCACTAATTGAGGCTAGCAGgtcagtgagc ... caatcaccagGTTATGCAATATGGACATCATCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtattgtgactataatatcacctttatgcttaatggctactgttgcaatcaccagGTTATGCAATATGGACATCATCTCTAAGGTCCAACAGGTAATCTGCTTCGCGTTCCACGACAGCAAACTGCTGATGGAAACATGCCAGGAGGCCATGAAC
                           gcttaat  putative branch site (score: 4)
        actataatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tggactgaaagagagtcacatttctttttatctgtacatatatatgtattgtgactataatatcacctttatgcttaatggctactgttgcaatcaccagGTTATGCAATATGGACATCATCTCTAAGGTCCAACAGGTAATCTGCTTCGCGTTCCACGACAGCAAACTGCTGATGGAAACATGCCAGGAGGCCATGAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
tggactg
- - - -aaagagag
- - - - - - - - - - - - - - - -ctgtaca
- - - - - - - - - - - - - - - - - - - - -atatgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcttaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctactg