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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGGCAGCATCAAATTGGACTGGTGAAGGATCTTTCCTGTTTACATCAAGTACAGCTCTGTATGATTGCAGTGACAACAGCATGTGCAACGAGgtactagagaaacacttattctgcagggattatatttgtctccactattttatctgtctcttttgggtgggtacaattgggaagattttaaaagtaacca...

Basic information

species Zea mays
transcript GRMZM2G017853_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017853_T01 (Zea mays), 5'ss of exon 4
lower sequence: 13113.m00225 (Oryza sativa), 5'ss of exon 4
ATTGGCAGCATCAAATTGGACTGGTGAAGGATCTTTCCTGTTTACATCAAGTACAGCTCTGTATGATTGCAGTGACAACAGCATGTGCAACGAGgta-ctagagaaacacttattctgcagggattatatttgtctccactattttatctgtctcttttgggtgggtacaattgggaagattttaaaagtaacca
| | || || |||||||||||||||||||| |||||| | |||||||||||||| |||||||| ||||| |||||||||    ||||||| |||||| |   | || |    |   || ||   | |  | | ||   ||| || | | || |||||||   |      | ||     ||  ||||||  || ||
AGTAGCTGCCTCAAATTGGACTGGTGAAGGCTCTTTCGTTTTTACATCAAGTACTGCTCTGTACGATTGTAGTGACAACGAATTGTGCAATGAGgtatccccacaagcctgcagattgtagctgtgaagtct-tccatacttttctttttggctcttttcatttatagaagttctagtgacattaaaaaaaaaca

upper sequence: GRMZM2G017853_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g26920.2 (Oryza sativa), 5'ss of exon 4
------ATTGGCAGCATCAAATTGGACTGGTGAAGGATCTTTCCTGTTTACATCAAGTACAGCTCTGTATGATTGCAGTGACAACAGCATGTGCAACGAGgta-ctagagaaacacttattctgcagggattatatttgtctccactattttatctgtctcttttgggtgggtacaattgggaagattttaaaagtaacca
      | | || || |||||||||||||||||||| |||||| | |||||||||||||| |||||||| ||||| |||||||||    ||||||| |||||| |   | || |    |   || ||   | |  | | ||   ||| || | | || |||||||   |      | ||     ||  ||||||  ||   
GTGCAGAGTAGCTGCCTCAAATTGGACTGGTGAAGGCTCTTTCGTTTTTACATCAAGTACTGCTCTGTACGATTGTAGTGACAACGAATTGTGCAATGAGgtatccccacaagcctgcagattgtagctgtgaagtct-tccatacttttctttttggctcttttcatttatagaagttctagtgacattaaaaaaaaaac

upper sequence: GRMZM2G017853_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g26920.1 (Oryza sativa), 5'ss of exon 4
ATTGGCAGCATCAAATTGGACTGGTGAAGGATCTTTCCTGTTTACATCAAGTACAGCTCTGTATGATTGCAGTGACAACAGCATGTGCAACGAGgta-ctagagaaacacttattctgcagggattatatttgtctccactattttatctgtctcttttgggtgggtacaattgggaagattttaaaagtaacca
| | || || |||||||||||||||||||| |||||| | |||||||||||||| |||||||| ||||| |||||||||    ||||||| |||||| |   | || |    |   || ||   | |  | | ||   ||| || | | || |||||||   |      | ||     ||  ||||||  ||   
AGTAGCTGCCTCAAATTGGACTGGTGAAGGCTCTTTCGTTTTTACATCAAGTACTGCTCTGTACGATTGTAGTGACAACGAATTGTGCAATGAGgtatccccacaagcctgcagattgtagctgtgaagtct-tccatacttttctttttggctcttttcatttatagaagttctagtgacattaaaaaaaaaac

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|74233405|gb|DT641319.1|DT641319
EST:     CATCAAGTACAGCTCTGTATGATTGCAGTGACAACAGCATGTGCAACGAG                         GATTGTCTGTCAGTGCCAATTGGCAGGAGCCCTCGTACTGATATTCTTCTA
genomic: CATCAAGTACAGCTCTGTATGATTGCAGTGACAACAGCATGTGCAACGAGgtactagaga ... ttttttgcagGATTGTCTGTCAGTGCCAATTGGCAGGAGCCCTCGTACTGATATTCTTCTA
EST: gi|91871463|gb|EB401433.1|EB401433
EST:     CATCAAGTACAGCTCTGTATGATTGCAGTGACAACAGCATGTGCAACGAG                         GATTGTCTGTCAGTGCCAATTGGCAGGAGCCCTCGTACTGATATTCTTCTA
genomic: CATCAAGTACAGCTCTGTATGATTGCAGTGACAACAGCATGTGCAACGAGgtactagaga ... ttttttgcagGATTGTCTGTCAGTGCCAATTGGCAGGAGCCCTCGTACTGATATTCTTCTA
EST: gi|211291636|gb|FL460652.1|FL460652
EST:     AGCTCTGTATGATTGCAGTGACAACAGCATGTGCAACGAG                         GATTGTCTGTCAGTGCCAATTGGCAGGAGCCCTCGTACTGATATTCTCCTA
genomic: AGCTCTGTATGATTGCAGTGACAACAGCATGTGCAACGAGgtactagaga ... ttttttgcagGATTGTCTGTCAGTGCCAATTGGCAGGAGCCCTCGTACTGATATTCTTCTA
EST: gi|71437097|gb|DR818147.1|DR818147
EST:     CATCAAGTACAGCTCTGTATGATTGCAGTGACAACAGCATGTGCAACGAG                         GATTGTCTGTCAGTGCCAATTGGCAGGAGCCCTCGTACTGATATTCTTCTA
genomic: CATCAAGTACAGCTCTGTATGATTGCAGTGACAACAGCATGTGCAACGAGgtactagaga ... ttttttgcagGATTGTCTGTCAGTGCCAATTGGCAGGAGCCCTCGTACTGATATTCTTCTA
EST: gi|76927174|gb|DV171165.1|DV171165
EST:     CATCAAGTACAGCTCTGTATGATTGCAGTGACAACAGCATGTGCAACGAG                         GATTGTCTGTCAGTGCCAATTGGCAGGAGCCCTCGTACTGATATTCTTCTA
genomic: CATCAAGTACAGCTCTGTATGATTGCAGTGACAACAGCATGTGCAACGAGgtactagaga ... ttttttgcagGATTGTCTGTCAGTGCCAATTGGCAGGAGCCCTCGTACTGATATTCTTCTA
EST: gi|71310881|gb|DR791743.1|DR791743
EST:     CATCAAGTACAGCTCTGTATGATTGCAGTGACAACAGCATGTGCAACGAG                         GATTGTCTGTCAGTGCCAATTGGCAGGAGCCCTCGTACTGATATTCTTCTA
genomic: CATCAAGTACAGCTCTGTATGATTGCAGTGACAACAGCATGTGCAACGAGgtactagaga ... ttttttgcagGATTGTCTGTCAGTGCCAATTGGCAGGAGCCCTCGTACTGATATTCTTCTA
EST: gi|78089273|gb|DV517647.1|DV517647
EST:     CATCAAGTACAGCTCTGTATGATTGCAGTGACAACAGCATGTGCAACGAG                         GATTGTCTGTCAGTGCCAATTGGCAGGAGCCCTCGTACTGATATTCTTCTA
genomic: CATCAAGTACAGCTCTGTATGATTGCAGTGACAACAGCATGTGCAACGAGgtactagaga ... ttttttgcagGATTGTCTGTCAGTGCCAATTGGCAGGAGCCCTCGTACTGATATTCTTCTA
EST: gi|78082079|gb|DV510491.1|DV510491
EST:     CATCAAGTACAGCTCTGTATGATTGCAGTGACAACAGCATGTGCAACGAG                         GATTGTCTGTCAGTGCCAATTGGCAGGAGCCCTCGTACTGATATTCTTCTA
genomic: CATCAAGTACAGCTCTGTATGATTGCAGTGACAACAGCATGTGCAACGAGgtactagaga ... ttttttgcagGATTGTCTGTCAGTGCCAATTGGCAGGAGCCCTCGTACTGATATTCTTCTA
EST: gi|71310883|gb|DR791744.1|DR791744
EST:     CATCAAGTACAGCTCTGTATGATTGCAGTGACAACAGCATGTGCAACGAG                         GATTGTCTGTCAGTGCCAATTGGCAGGAGCCCTCGTACTGATATTCTTCTA
genomic: CATCAAGTACAGCTCTGTATGATTGCAGTGACAACAGCATGTGCAACGAGgtactagaga ... ttttttgcagGATTGTCTGTCAGTGCCAATTGGCAGGAGCCCTCGTACTGATATTCTTCTA
EST: gi|74233404|gb|DT641318.1|DT641318
EST:     CATCAAGTACAGCTCTGTATGATTGCAGTGACAACAGCATGTGCAACGAG                         GATTGTCTGTCAGTGCCAATTGGCAGGAGCCCTCGTACTGATATTCTTCTA
genomic: CATCAAGTACAGCTCTGTATGATTGCAGTGACAACAGCATGTGCAACGAGgtactagaga ... ttttttgcagGATTGTCTGTCAGTGCCAATTGGCAGGAGCCCTCGTACTGATATTCTTCTA
EST: gi|148975423|gb|EE025724.2|EE025724
EST:     CATCAAGTACAGCTCTGTATGATTGCAGTGACAACAGCATGTGCAACGAG                         GATTGTCTGTCAGTGCCAATTGGCAGGAGCCCTCGTACTGATATTCTTCTA
genomic: CATCAAGTACAGCTCTGTATGATTGCAGTGACAACAGCATGTGCAACGAGgtactagaga ... ttttttgcagGATTGTCTGTCAGTGCCAATTGGCAGGAGCCCTCGTACTGATATTCTTCTA
EST: gi|78085442|gb|DV513835.1|DV513835
EST:     CATCAAGTACAGCTCTGTATGATTGCAGTGACAACAGCATGTGCAACGAG                         GATTGTCTGTCAGTGCCAATTGGCAGGAGCCCTCGTACTGATATTCTTCTA
genomic: CATCAAGTACAGCTCTGTATGATTGCAGTGACAACAGCATGTGCAACGAGgtactagaga ... ttttttgcagGATTGTCTGTCAGTGCCAATTGGCAGGAGCCCTCGTACTGATATTCTTCTA
EST: gi|50336042|gb|CO531168.1|CO531168
EST:     CATCAAGTACAGCTCTGTATGATTGCAGTGACAACAGCATGTGCAACGAG                         GATTGTCTGTCAGTGCCAATTGGCAGGAGCCCTCGTACTGATATTCTTCTA
genomic: CATCAAGTACAGCTCTGTATGATTGCAGTGACAACAGCATGTGCAACGAGgtactagaga ... ttttttgcagGATTGTCTGTCAGTGCCAATTGGCAGGAGCCCTCGTACTGATATTCTTCTA
EST: gi|101382998|gb|EB813552.1|EB813552
EST:     CATCAAGTACAGCTCTGTATGATTGCAGTGACAACAGCATGTGCAACGAG                         GATTGTCTGTCAGTGCCAATTGGCAGGAGCCCTCGTACTGATATTCTTCTA
genomic: CATCAAGTACAGCTCTGTATGATTGCAGTGACAACAGCATGTGCAACGAGgtactagaga ... ttttttgcagGATTGTCTGTCAGTGCCAATTGGCAGGAGCCCTCGTACTGATATTCTTCTA
EST: gi|78089274|gb|DV517648.1|DV517648
EST:     CATCAAGTACAGCTCTGTATGATTGCAGTGACAACAGCATGTGCAACGAG                         GATTGTCTGTCAGTGCCAATTGGCAGGAGCCCTCGTACTGATATTCTTCTA
genomic: CATCAAGTACAGCTCTGTATGATTGCAGTGACAACAGCATGTGCAACGAGgtactagaga ... ttttttgcagGATTGTCTGTCAGTGCCAATTGGCAGGAGCCCTCGTACTGATATTCTTCTA
EST: gi|76927172|gb|DV171164.1|DV171164
EST:     CATCAAGTACAGCTCTGTATGATTGCAGTGACAACAGCATGTGCAACGAG                         GATTGTCTGTCAGTGCCAATTGGCAGGAGCCCTCGTACTGATATTCTTTTA
genomic: CATCAAGTACAGCTCTGTATGATTGCAGTGACAACAGCATGTGCAACGAGgtactagaga ... ttttttgcagGATTGTCTGTCAGTGCCAATTGGCAGGAGCCCTCGTACTGATATTCTTCTA
EST: gi|71764490|gb|DR962427.1|DR962427
EST:     CATCAAGTACAGCTCTGTATGATTGCAGTGACAACAGCATGTGCAACGAG                         GATTGTCTGTCAGTGCCAATTGGCAGGAGCCCTCGTACTGATATTCTTCTA
genomic: CATCAAGTACAGCTCTGTATGATTGCAGTGACAACAGCATGTGCAACGAGgtactagaga ... ttttttgcagGATTGTCTGTCAGTGCCAATTGGCAGGAGCCCTCGTACTGATATTCTTCTA
EST: gi|89251154|gb|DY622940.1|DY622940
EST:     CATCAAGTACAGCTCTGTATGATTGCAGTGACAACAGCATGTGCAACGAG                         GATTGTCTGTCAGTGCAAATTGGCAGGAGCCCTCGTACTGATATTCTTCTA
genomic: CATCAAGTACAGCTCTGTATGATTGCAGTGACAACAGCATGTGCAACGAGgtactagaga ... ttttttgcagGATTGTCTGTCAGTGCCAATTGGCAGGAGCCCTCGTACTGATATTCTTCTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTGGCAGCATCAAATTGGACTGGTGAAGGATCTTTCCTGTTTACATCAAGTACAGCTCTGTATGATTGCAGTGACAACAGCATGTGCAACGAGgtactagagaaacacttattctgcagggattatatttgtctccactattttatctgtctcttttgggtgggtacaattgggaagattttaaaagtaacca

- - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC