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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACATGTGGAAAATGGAGACATGTGCATTGTACTTAATGCACAGGATATCAGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGGgttagtacccagcaaaaaatttgttggttacattatttatgagatttttgttaactttctcttgttatgtgtttattcccaaatag

Basic information

species Zea mays
transcript GRMZM2G163473_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G163473_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os05g15370.1 (Oryza sativa), 5'ss of exon 3
CACATGTGGAAAATGGAGACATGTGCATTGTACTTAATGCACAGGATATCAGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGGgttagtacccagcaaaaaatttgttggttacattatttatgagatttttgttaactttctcttgttatgtgtttattcccaaatag
|||||||||||||||||||||||||| |||| ||||||||| | |||||||||||||||||||| |||||||| ||||| || ||||||||||| |||||||| |||     | |   | |  |  |||  ||   || ||   || || || ||  |    | |||||||||| |||  ||||||
CACATGTGGAAAATGGAGACATGTGCGTTGTGCTTAATGCAAAAGATATCAGTGTTACAGGAAGAAAAATGACCGATAAAATCTACTACTGGCACACAGGgtttgtatgtttctagctaatact--gttgaataccttttggttttattatttacaattgtgtcttatgtgttttttc--aaatag

upper sequence: GRMZM2G163473_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os08g06474.1 (Oryza sativa), 5'ss of exon 3
CACATGTGGAAAATGGAGACATGTGCATTGTACTTAATGCACAGGATATCAGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGGgttagtac----ccagcaaaaaatttgttg---gttacattatttatgagatttttgttaactttctcttgttatgt--gtttattcccaaatag
||||||||||||| || ||||||||  | |||||||| ||  | ||||||||||| || |||||||||||||| |||||||||||||||||||| |||||||  |||     | |||||| | |   |     |||  ||   | ||  | ||||   ||||  |  | | |  |||  |||| | ||   | ||
CACATGTGGAAAACGGGGACATGTGTGTCGTACTTAACGCGAAAGATATCAGTGTCACGGGAAGGAAAATGACTGATAAGATTTACTACTGGCACACAGGgtctgtatgtttctagcaaatagtacttgaaatgttgaatacctcatttggtttt-actaacaattgcctatcctgttcgtttttccctcgaaag

upper sequence: GRMZM2G163473_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA19G22420.1 (Glycine max), 5'ss of exon 4
CACATGTGGAAAATGGAGACATGTGCATTGTACTTAATGCACAGGATATCAGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGGgttagtacccagcaaaaaatttgttggttacattatttatgagatttttgttaactttctcttgttatgtgtttattcccaaatag-------------------
|  ||   ||  ||||||||||||||||||| ||||||||| | |||||  |||| || || || ||| | ||||| ||| | ||||||||||||||||||  ||| |   |||       | || | || |  | | |||| || ||  || | | | |   | |   | |  ||   ||||| |                   
CTAATCGTGATGATGGAGACATGTGCATTGTTCTTAATGCAAAAGATATTTGTGTGACTGGGAGAAAACTTACAGACAAGGTCTACTACTGGCATACAGGgcaagtgctttgcatttgtactattagataga--agtgatgaaatattatttgattgttttgggctccttataaat---caaatggtttttttctggttaagatg

upper sequence: GRMZM2G163473_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA19G36450.1 (Glycine max), 5'ss of exon 4
CACATGTGGAAAATGGAGACATGTGCATTGTACTTAATGCACAGGATATCAGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGGgttagtacccagcaaaaaatttgttggttacattatttatgagatt-tttgttaactttct-cttgttatgt--------gtttattcccaaatag----
|  ||   ||  |||| || ||||||||||| ||||||||| | |||||  |||| || || || ||| | ||||| ||| | ||||||||||||||||||  ||| |   |||       | || |||| |     |   | ||| |||  ||  |||   ||| ||||          ||||  | |    ||     
CTAATCGTGATGATGGGGATATGTGCATTGTTCTTAATGCAAAAGATATTTGTGTGACTGGGAGAAAACTTACAGACAAGGTCTACTACTGGCATACAGGgcaagtgctttgcatttgtactattagttagaagggatgaaatattatttaatagttttgagcttcttataaatcaaatggttttcttctggttaaggtg

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|60342857|gb|DN209830.1|DN209830
EST:     AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGG                         GTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
genomic: AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGGgttagtaccc ... tcccaaatagGTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
EST: gi|60343511|gb|DN210484.1|DN210484
EST:     AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGG                         GTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
genomic: AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGGgttagtaccc ... tcccaaatagGTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
EST: gi|60347040|gb|DN214013.1|DN214013
EST:     AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGG                         GTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
genomic: AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGGgttagtaccc ... tcccaaatagGTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
EST: gi|60397634|gb|DN230450.1|DN230450
EST:     AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGG                         GTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
genomic: AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGGgttagtaccc ... tcccaaatagGTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
EST: gi|74241944|gb|DT649858.1|DT649858
EST:     AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGG                         GTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
genomic: AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGGgttagtaccc ... tcccaaatagGTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
EST: gi|74241943|gb|DT649857.1|DT649857
EST:     AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGG                         GTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
genomic: AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGGgttagtaccc ... tcccaaatagGTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
EST: gi|19770416|gb|BQ035137.1|BQ035137
EST:     AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGG                         GTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
genomic: AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGGgttagtaccc ... tcccaaatagGTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
EST: gi|60354692|gb|DN221665.1|DN221665
EST:     AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGG                         GTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
genomic: AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGGgttagtaccc ... tcccaaatagGTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
EST: gi|88752119|gb|DY536260.1|DY536260
EST:     AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGG                         GTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGCCCAGATGGAGAAAGA
genomic: AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGGgttagtaccc ... tcccaaatagGTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
EST: gi|60348718|gb|DN215691.1|DN215691
EST:     AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGG                         GTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
genomic: AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGGgttagtaccc ... tcccaaatagGTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
EST: gi|78112053|gb|DV530449.1|DV530449
EST:     AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGG                         GTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
genomic: AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGGgttagtaccc ... tcccaaatagGTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
EST: gi|211498775|gb|FL140826.1|FL140826
EST:     AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGG                         GTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
genomic: AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGGgttagtaccc ... tcccaaatagGTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
EST: gi|19822368|gb|BQ048392.1|BQ048392
EST:     AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGG                         GTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
genomic: AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGGgttagtaccc ... tcccaaatagGTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
EST: gi|211284263|gb|FL053253.1|FL053253
EST:     AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGG                         GTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
genomic: AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGGgttagtaccc ... tcccaaatagGTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
EST: gi|60349978|gb|DN216951.1|DN216951
EST:     AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGG                         GTATGTTTGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
genomic: AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGGgttagtaccc ... tcccaaatagGTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
EST: gi|211282461|gb|FL053248.1|FL053248
EST:     AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGG                         GTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
genomic: AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGGgttagtaccc ... tcccaaatagGTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
EST: gi|76281753|gb|DV021321.1|DV021321
EST:     AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGG                         GTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
genomic: AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGGgttagtaccc ... tcccaaatagGTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
EST: gi|60357091|gb|DN224064.1|DN224064
EST:     AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGG                         GTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
genomic: AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGGgttagtaccc ... tcccaaatagGTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
EST: gi|60344047|gb|DN211020.1|DN211020
EST:     AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGG                         GTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
genomic: AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGGgttagtaccc ... tcccaaatagGTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
EST: gi|148973081|gb|EE024144.2|EE024144
EST:     AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGG                         GTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
genomic: AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGGgttagtaccc ... tcccaaatagGTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
EST: gi|60395778|gb|DN228648.1|DN228648
EST:     AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGG                         GTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
genomic: AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGGgttagtaccc ... tcccaaatagGTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
EST: gi|60342646|gb|DN209619.1|DN209619
EST:     AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGG                         GTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
genomic: AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGGgttagtaccc ... tcccaaatagGTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
EST: gi|149077053|gb|EE165709.2|EE165709
EST:     AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGG                         GTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
genomic: AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGGgttagtaccc ... tcccaaatagGTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
EST: gi|211468041|gb|FL459168.1|FL459168
EST:     AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGG                         GTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
genomic: AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGGgttagtaccc ... tcccaaatagGTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
EST: gi|37420605|gb|CF647997.1|CF647997
EST:     AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGG                         GTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
genomic: AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGGgttagtaccc ... tcccaaatagGTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
EST: gi|211282457|gb|FL053244.1|FL053244
EST:     AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGG                         GTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
genomic: AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGGgttagtaccc ... tcccaaatagGTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
EST: gi|60342547|gb|DN209520.1|DN209520
EST:     AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGG                         GTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
genomic: AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGGgttagtaccc ... tcccaaatagGTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
EST: gi|78026238|gb|DV494625.1|DV494625
EST:     AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGG                         GTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
genomic: AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGGgttagtaccc ... tcccaaatagGTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
EST: gi|37400998|gb|CF637860.1|CF637860
EST:     AGTGTCACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGG                         GTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA
genomic: AGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGGgttagtaccc ... tcccaaatagGTATGTTGGCCATTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACATGTGGAAAATGGAGACATGTGCATTGTACTTAATGCACAGGATATCAGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGGgttagtacccagcaaaaaatttgttggttacattatttatgagatttttgttaactttctcttgttatgtgtttattcccaaatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA