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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAGgtcattgttcatcatgccattgattcttccagcgcctcatgtgaaaaactcaattacagaatttatttttgaattgcag

Basic information

species Zea mays
transcript GRMZM2G165357_T02
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G165357_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os03g16980.4 (Oryza sativa), 5'ss of exon 6
ACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAGgtcattgttcatc--atgcc-attgattcttccagcgc--ctcatgtgaaaaactcaattacagaatttattt---ttgaattgcag
|||||||||||||| ||||| || |||||||||||||| |||||||| |||||||||||||||||||   ||||  |   ||||  ||| | |  |||   ||  || ||| |||  |   ||| |  | |  | |||   ||| | |||||
ACCATCAAGACAAACGTTATCGGAACCCTGAACATGCTTGGACTTGCCAAGAGAGTTGGAGCTAGgttggtgtttttttaatgctgattaacttgtcctatgcaacttatgagaactatataatgaagggaggtttttatgttgtactgcag

upper sequence: GRMZM2G165357_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA11G15020.1 (Glycine max), 5'ss of exon 6
ACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAGgtcattgt-tcatcat--gccattgattcttccagcgcctcatgtgaaaaactcaattacagaatttattttt----gaattgcag------------------
|| || ||||||||||| ||||| || ||||||||||| || ||||||||  ||||||| || ||||       |  || |  |  | ||||  || ||||  ||    | |     ||  |||     ||| |||||    || |   ||                  
ACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTTGCAAAACGAGTTGGGGCAAGgttggaaaattgtctttggaaaatgataatttcagcttctatcatcatttggtct-ttattctttttctttttagtagagtcttagttcttattttattggcag

upper sequence: GRMZM2G165357_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA12G06990.1 (Glycine max), 5'ss of exon 6
ACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAGgtcattgt-tcatcat--gccattgattcttccagcgcctcatgtgaaaaactcaattacagaatttatttttg--aattgcag------------------
|| || ||||||||||| |||||||| ||||||||||| || ||||| ||| ||||||| || ||||   |   |  || |  |  | ||||  || ||||  ||    | |     ||  |||     ||| || |||  | |   ||                  
ACAATAAAGACAAATGTGATTGGTACACTGAACATGCTTGGGCTTGCCAAGCGAGTTGGGGCAAGgttggtaaattgtctttggaaaatgataatttcagcttctatcatcagttggtct-ttattctttttcttcttgttagtcttagttcttattttattggcag

upper sequence: GRMZM2G165357_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA13G40960.1 (Glycine max), 5'ss of exon 7
ACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAGgtc---attgttcatcatgccattgattcttccagcgcctcatgtgaaaaactcaattacagaatttatttttgaattgcag
|| || ||||||||||| ||||| || ||||||||||| || ||||||||| |||| ||||| ||||    ||  ||  | |  | ||    ||  |    |||  ||  |     || |||||     | || |||| | |  |||
ACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTTGCAAAGCGAGTAGGAGCAAGgttgggatattttcttaaacaataatctcaactgctgcc--attagttggtcttaatta---gttctaatttt-attgacag

upper sequence: GRMZM2G165357_T02 (Zea mays), 5'ss of exon 5
lower sequence: Vv13s0019g00840.t01 (Vitis vinifera), 5'ss of exon 6
ACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAGgtcattgttcatcatgccattgattcttccagcgcctcatgtgaaaaactcaattacagaatttatttttgaattgcag------------
|| || ||||||||||| ||||| ||| |||||||| | || ||||| |||||||||||||| ||||        |     || |   |  ||   ||   |  | | | ||||  |||| | |   ||| || |    || |             
ACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCCAGgttggaaactacttgcccgtc--tctttgttgcattttgt-ttataaacataatt-ctggtcttacttatagcatgtaataatggctacag

upper sequence: GRMZM2G165357_T02 (Zea mays), 5'ss of exon 5
lower sequence: PP1S189_118V6.1 (Physcomitrella patens), 5'ss of exon 6
ACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAGgt--------cattgttcatcatgccattgattcttccagcgcctcatgtga---aaaactcaattacagaatttatttt---tgaattgcag-------
||||||||||||||||| |||||||| || |||||||| ||||| || ||  ||||||| || ||||        | ||||  ||| |||  || | | |  |    |  || |  |     | ||  | |   || || || ||   |  | ||||        
ACCATCAAGACAAATGTGATTGGTACGCTCAACATGCTTGGACTCGCTAAACGAGTTGGTGCAAGgtgcaaaattctttgtatatcttgctctttaatttctcttgtcaccaggaaactggcagctggacttacgatttcatgttatgtatactgcaagtagctc

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|149070503|gb|EE158907.2|EE158907
EST:     GTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAG                         GATTTTGTTGACATCAACCTCTGAAGTTTATGGTGATCCACTTGAGCATCC
genomic: GTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAGgtcattgttc ... tgaattgcagGATTTTGTTGACATCAACCTCTGAAGTTTATGGTGATCCACTTGAGCATCC
EST: gi|211182716|gb|FL410032.1|FL410032
EST:     GTTATTGGTACCCTGAACATGCTTGGACTTGCAAAGAGAGTTGGAGCTAG                         GATTTTGTTGACATCAACCTCTGAAGTTTATGGTGATCCACTTGAGCATCC
genomic: GTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAGgtcattgttc ... tgaattgcagGATTTTGTTGACATCAACCTCTGAAGTTTATGGTGATCCACTTGAGCATCC
EST: gi|32838870|gb|CD978551.1|CD978551
EST:     ACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAG                         GATTTTGTTGACATCAACCTCTGAAGTTTATGGTGATCCACTTGAGCATCC
genomic: ACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAGgtcattgttc ... tgaattgcagGATTTTGTTGACATCAACCTCTGAAGTTTATGGTGATCCACTTGAGCATCC
EST: gi|32850602|gb|CD990283.1|CD990283
EST:     TACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAG                         GATTTTGTTGACATCAACCTCTGAAGTTTATGGTGATCCACTTGAGCATCC
genomic: TACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAGgtcattgttc ... tgaattgcagGATTTTGTTGACATCAACCTCTGAAGTTTATGGTGATCCACTTGAGCATCC
EST: gi|149082965|gb|EE172201.2|EE172201
EST:     GTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAG                         GATTTTGTTGACATCAACCTCTGAAGTTTATGGTGATCCACTTGAGCATCC
genomic: GTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAGgtcattgttc ... tgaattgcagGATTTTGTTGACATCAACCTCTGAAGTTTATGGTGATCCACTTGAGCATCC
EST: gi|60394382|gb|DN227252.1|DN227252
EST:     GTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAG                         GATTTTGTTGACATCAACCTCTGAAGTTTATGGTGATCCACTTGAGCATCC
genomic: GTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAGgtcattgttc ... tgaattgcagGATTTTGTTGACATCAACCTCTGAAGTTTATGGTGATCCACTTGAGCATCC
EST: gi|149070980|gb|EE159385.2|EE159385
EST:     GTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAG                         GATTTTGTTGACATCAACCTCTGAAGTTTATGGTGATCCACTTGAGCATCC
genomic: GTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAGgtcattgttc ... tgaattgcagGATTTTGTTGACATCAACCTCTGAAGTTTATGGTGATCCACTTGAGCATCC
EST: gi|32914071|gb|CF018883.1|CF018883
EST:     GTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAG                         GATTTTGTTGACATCAACCTCTGAAGTTTATGGTGATCCACTTGAGCGTTC
genomic: GTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAGgtcattgttc ... tgaattgcagGATTTTGTTGACATCAACCTCTGAAGTTTATGGTGATCCACTTGAGCATCC
EST: gi|71444250|gb|DR825300.1|DR825300
EST:     GTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAG                         GATTTTGTTGACATCAACCTCTGAAGTTTATGGTGATCCACTTGAGCATCC
genomic: GTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAGgtcattgttc ... tgaattgcagGATTTTGTTGACATCAACCTCTGAAGTTTATGGTGATCCACTTGAGCATCC
EST: gi|60339871|gb|DN206844.1|DN206844
EST:     GTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAG                         GATTTTGTTGACATCAACCTCTGAAGTTTATGGTGATCCACTTGAGCATCC
genomic: GTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAGgtcattgttc ... tgaattgcagGATTTTGTTGACATCAACCTCTGAAGTTTATGGTGATCCACTTGAGCATCC
EST: gi|15100352|gb|BI396143.1|BI396143
EST:     GTTATTGGTACCCTGAACATGCTTGGACTTGCAAAGAGAGTTGGAGCTAG                         GATTTTGTTGACATCAACCTCTGAAGTTTATGGTGATCCACTTGAGCATCC
genomic: GTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAGgtcattgttc ... tgaattgcagGATTTTGTTGACATCAACCTCTGAAGTTTATGGTGATCCACTTGAGCATCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAGgtcattgttcatcatgccattgattcttccagcgcctcatgtgaaaaactcaattacagaatttatttttgaattgcag

- - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT