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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGCTGGACCAGAGCTAGTGCAAGCATGCCGGAAAGTTCCAGAGGTCAAACCAGGAGTCCGTTGTCCTACTGGAGAAGCTAGGATTACTCCgttagtacttcgtacctatctattcactttgattgtttcataagtcggaatgttcaaacctaaaatttatgtatcctttacacatccctttgcccaatattcgatgtgagcag

Basic information

species Zea mays
transcript GRMZM2G062425_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G062425_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g21830.1 (Oryza sativa), 5'ss of exon 3
---------CTGCTGGACCAGAGCTAGTGCAAGCATGCCGGAAAGTTCCAGAGGTCAAACCAGGAGTCCGTTGTCCTACTGGAGAAGCTAGGATTACTCCgttagtacttcgtacctatctattcactttgattgtttcataagtcggaatgttcaaacctaaaatttatgtatcctttacacatccctttgccca-atattcgatgtgagcag
         |||||||||| || || ||  | |||||||| |||||||||||||||||| | ||||| || || || ||||||||||||||||||||||||||||| | |  | |||   || ||| | ||| || |       || |||||       || ||    |  ||||  |     ||  | || ||   || ||  |||||| |||
TACATCGAACTGCTGGACCTGAACTCGTAGAGGCATGCCGTAAAGTTCCAGAGGTCAAATCTGGAGTTCGCTGCCCCACTGGAGAAGCTAGGATTACTCCgttagtgcctt-tccct---taatcaatctgactgatg---gcatcagaatgccatcttctgaacaccacatatctct-----atatcattacctgtatgttgaatgtgaacag

upper sequence: GRMZM2G062425_T02 (Zea mays), 5'ss of exon 3
lower sequence: AT2G40600.1 (Arabidopsis thaliana), 5'ss of exon 3
---------CTGCTGGACCAGAGCTAGTGCAAGCATGCCGGAAAGTTCCAGAGGTCAAACCAGGAGTCCGTTGTCCTACTGGAGAAGCTAGGATTACTCCgttagtacttcgtacctatctattcactttgattgtttcataagtcggaat-gttcaaacctaaaatttatgtatcctttacacatccctttgcccaatattcgatgtgagcag
         ||||||| ||| | ||       ||||||    | ||||| || ||    || |||||||||||||| ||||||||||| || |||||||||| ||       ||||  | | || |||    |       ||  | |   | |||  ||  |   |||  ||  |  |    | | |  || |    | |    ||  || |||
TACATAGAGCTGCTGGGCCACAACTCAGAGCTGCATGCTATGAGGTTCCTGAAGTTCGTCCTGGAGTCCGTTGTCCAACTGGAGAAGCAAGAATTACTCCgtgaga-----ttaccctttttttaactcgtgtataaatgtagattgaggtagtttgaaattggtattgttgagtgat--ggaaaccagttggattgaaa---aattggaacag
















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|60346456|gb|DN213429.1|DN213429
EST:     GAGGTCAAACCAGGAGTCCGTTGTCCTACTGGAGAAGCTAGGATTACTCC                         TGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATA
genomic: GAGGTCAAACCAGGAGTCCGTTGTCCTACTGGAGAAGCTAGGATTACTCCgttagtactt ... atgtgagcagTGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATA
EST: gi|60350894|gb|DN217867.1|DN217867
EST:     GAGGTCAAACCAGGAGTCCGTTGTCCTACTGGAGAAGCTAGGATTACTCC                         TGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATA
genomic: GAGGTCAAACCAGGAGTCCGTTGTCCTACTGGAGAAGCTAGGATTACTCCgttagtactt ... atgtgagcagTGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATA
EST: gi|60340981|gb|DN207954.1|DN207954
EST:     GTCAAACCAGGAGTTCGTTGTCCTACTGGAGAAGCTAGGATTACTCC                         TGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATA
genomic: GTCAAACCAGGAGTCCGTTGTCCTACTGGAGAAGCTAGGATTACTCCgttagtactt ... atgtgagcagTGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATA
EST: gi|32916032|gb|CF020844.1|CF020844
EST:     GAGGTCAAACCAGGAGTTCGTTGTCCTACTGGAGAAGCTAGGATTACTCC                         TGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATA
genomic: GAGGTCAAACCAGGAGTCCGTTGTCCTACTGGAGAAGCTAGGATTACTCCgttagtactt ... atgtgagcagTGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATA
EST: gi|60400550|gb|DN233357.1|DN233357
EST:     GAGGTCAAACCAGGAGTCCGTTGTCCTACTGGAGAAGCTAGGATTACTCC                         TGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATA
genomic: GAGGTCAAACCAGGAGTCCGTTGTCCTACTGGAGAAGCTAGGATTACTCCgttagtactt ... atgtgagcagTGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATA
EST: gi|211409605|gb|FL451596.1|FL451596
EST:     TCAAACCAGGAGTCCGTTGTCCTACTGGAGAAGCTAGGATTACTCC                         TGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATA
genomic: TCAAACCAGGAGTCCGTTGTCCTACTGGAGAAGCTAGGATTACTCCgttagtactt ... atgtgagcagTGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATA
EST: gi|149058791|gb|EE156812.2|EE156812
EST:     GAGGTCAAACCAGGAGTCCGTTGTCCTACTGGAGAAGCTAGGATTACTCC                         TGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATA
genomic: GAGGTCAAACCAGGAGTCCGTTGTCCTACTGGAGAAGCTAGGATTACTCCgttagtactt ... atgtgagcagTGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATA
EST: gi|30087019|gb|CB885227.1|CB885227
EST:     GTCCGTTGTCCTACTGGAGAAGCTAGGATTACTCC                         TGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATA
genomic: GTCCGTTGTCCTACTGGAGAAGCTAGGATTACTCCgttagtactt ... atgtgagcagTGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATA
EST: gi|4646952|gb|AI622027.1|AI622027
EST:     AGCTAGGATTACTCC                         TGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATA
genomic: AGCTAGGATTACTCCgttagtactt ... atgtgagcagTGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATA
EST: gi|71768330|gb|DR966267.1|DR966267
EST:     CGTTGTCCTACTGGAGAAGCTAGGATTACTCC                         TGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATA
genomic: CGTTGTCCTACTGGAGAAGCTAGGATTACTCCgttagtactt ... atgtgagcagTGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATA
EST: gi|60337208|gb|DN204181.1|DN204181
EST:     GAGGTCAAACCAGGAGTTCGTTGTCCTACTGGAGAAGCTAGGATTACTCC                         TGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATA
genomic: GAGGTCAAACCAGGAGTCCGTTGTCCTACTGGAGAAGCTAGGATTACTCCgttagtactt ... atgtgagcagTGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATA
EST: gi|71760661|gb|DR958598.1|DR958598
EST:     GAGGTCAAACCAGGAGTCCGTTGTCCTACTGGAGAAGCTAGGATTACTCC                         TGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATA
genomic: GAGGTCAAACCAGGAGTCCGTTGTCCTACTGGAGAAGCTAGGATTACTCCgttagtactt ... atgtgagcagTGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATA
EST: gi|91874149|gb|EB404106.1|EB404106
EST:     GAGGTCAAACCAGGAGTCCGTTGTCCTACTGGAGAAGCTAGGATTACTCC                         TGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATA
genomic: GAGGTCAAACCAGGAGTCCGTTGTCCTACTGGAGAAGCTAGGATTACTCCgttagtactt ... atgtgagcagTGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATA
EST: gi|29544033|gb|CB604413.1|CB604413
EST:     GAGGTCAAACCAGGAGTCCGTTGTCCTACTGGAGAAGCTAGGATTACTCC                         TGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATA
genomic: GAGGTCAAACCAGGAGTCCGTTGTCCTACTGGAGAAGCTAGGATTACTCCgttagtactt ... atgtgagcagTGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATA
EST: gi|60347033|gb|DN214006.1|DN214006
EST:     GAGGTCAAACCAGGAGTCCGTTGTCCTACTGGAGAAGCTAGGATTACTCC                         TGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATA
genomic: GAGGTCAAACCAGGAGTCCGTTGTCCTACTGGAGAAGCTAGGATTACTCCgttagtactt ... atgtgagcagTGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATA
EST: gi|12968348|gb|BG265294.1|BG265294
EST:     GAGGTCAAACCAGGAGTTCGTTGTCCTACTGGAGAAGCTAGGATTACTCC                         TGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATA
genomic: GAGGTCAAACCAGGAGTCCGTTGTCCTACTGGAGAAGCTAGGATTACTCCgttagtactt ... atgtgagcagTGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATA
EST: gi|71444605|gb|DR825655.1|DR825655
EST:     GAGGTCAAACCAGGAGTCCGTTGTCCTACTGGAGAAGCTAGGATTACTCC                         TGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATA
genomic: GAGGTCAAACCAGGAGTCCGTTGTCCTACTGGAGAAGCTAGGATTACTCCgttagtactt ... atgtgagcagTGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATA
EST: gi|27576007|gb|CA998701.1|CA998701
EST:     GAGGTCAAACCAGGAGTCCGTTGTCCTACTGGAGAAGCTAGGATTACTCC                         TGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATA
genomic: GAGGTCAAACCAGGAGTCCGTTGTCCTACTGGAGAAGCTAGGATTACTCCgttagtactt ... atgtgagcagTGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATA
EST: gi|20208345|gb|BQ134434.1|BQ134434
EST:     GAGGTCAAACCAGGAGTTCGTTGTCCTACTGGAGAAGCTAGGATTACTCC                         TGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATA
genomic: GAGGTCAAACCAGGAGTCCGTTGTCCTACTGGAGAAGCTAGGATTACTCCgttagtactt ... atgtgagcagTGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATA
EST: gi|211448985|gb|FL452542.1|FL452542
EST:     GAGGTCAAACCAGGAGTCCGTTGTCCTACTGGAGAAGCTAGGATTACTCC                         TGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATA
genomic: GAGGTCAAACCAGGAGTCCGTTGTCCTACTGGAGAAGCTAGGATTACTCCgttagtactt ... atgtgagcagTGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATA
EST: gi|76284272|gb|DV023840.1|DV023840
EST:     GAGGTCAAACCAGGAGTCCGTTGTCCTACTGGAGAAGCTAGGATTACTCC                         TGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATA
genomic: GAGGTCAAACCAGGAGTCCGTTGTCCTACTGGAGAAGCTAGGATTACTCCgttagtactt ... atgtgagcagTGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATA
EST: gi|78073968|gb|DV502402.1|DV502402
EST:     GAGGTCAAACCAGGAGTCCGTTGTCCTACTGGAGAAGCTAGGATTACTCC                         TGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATA
genomic: GAGGTCAAACCAGGAGTCCGTTGTCCTACTGGAGAAGCTAGGATTACTCCgttagtactt ... atgtgagcagTGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATA
EST: gi|50322938|gb|CO518064.1|CO518064
EST:     AGGTCAAACCAGGAGTCCGTTGTCCTACTGGAGAAGCTAGGATTACTCC                         TGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATA
genomic: AGGTCAAACCAGGAGTCCGTTGTCCTACTGGAGAAGCTAGGATTACTCCgttagtactt ... atgtgagcagTGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATA
EST: gi|88752056|gb|DY536197.1|DY536197
EST:     GAGGTCAAACCAGGAGTCCGTTGTCTTACTGGAGAAGCTAGGATTACTCC                         TGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATA
genomic: GAGGTCAAACCAGGAGTCCGTTGTCCTACTGGAGAAGCTAGGATTACTCCgttagtactt ... atgtgagcagTGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATA
EST: gi|78544379|gb|DV621877.1|DV621877
EST:     GAGGTCAAACCAGGAGTTCGTTGTCCTACTGGAGAAGCTAGGATTACTCC                         TGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATA
genomic: GAGGTCAAACCAGGAGTCCGTTGTCCTACTGGAGAAGCTAGGATTACTCCgttagtactt ... atgtgagcagTGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATA
EST: gi|8516517|gb|BE123242.1|BE123242
EST:     TGGAGAAGCTAGGATTACTCC                         TGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATA
genomic: TGGAGAAGCTAGGATTACTCCgttagtactt ... atgtgagcagTGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATA
EST: gi|71775282|gb|DR973160.1|DR973160
EST:     GAGGTCAAACCAGGAGTCCGTTGTCCTACTGGAGAAGCTAGGATTACTCC                         TGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATA
genomic: GAGGTCAAACCAGGAGTCCGTTGTCCTACTGGAGAAGCTAGGATTACTCCgttagtactt ... atgtgagcagTGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATA
EST: gi|32916033|gb|CF020845.1|CF020845
EST:     GAGGTCAAACCAGGAGTTCGTTGTCCTACTGGAGAAGCTAGGATTACTCC                         TGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATA
genomic: GAGGTCAAACCAGGAGTCCGTTGTCCTACTGGAGAAGCTAGGATTACTCCgttagtactt ... atgtgagcagTGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATA
EST: gi|27521916|gb|CA989022.1|CA989022
EST:     GAGGTCAAACCAGGAGTCCGTTGTCCTACTGGAGAAGCTAGGATTACTCC                         TGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACCCTGTTGGCCCTATATA
genomic: GAGGTCAAACCAGGAGTCCGTTGTCCTACTGGAGAAGCTAGGATTACTCCgttagtactt ... atgtgagcagTGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATA
EST: gi|30031764|gb|CB833615.1|CB833615
EST:     TCCGTTGTCCTACTGGAGAAGCTAGGATTACTCC                         TGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATA
genomic: TCCGTTGTCCTACTGGAGAAGCTAGGATTACTCCgttagtactt ... atgtgagcagTGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATA
EST: gi|16927502|gb|BM080571.1|BM080571
EST:     GAGGTCAAACCAGGAGTCCGTTGTCCTACTGGAGAAGCTAGGATTACTCC                         TGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATA
genomic: GAGGTCAAACCAGGAGTCCGTTGTCCTACTGGAGAAGCTAGGATTACTCCgttagtactt ... atgtgagcagTGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATA
EST: gi|78118087|gb|DV536474.1|DV536474
EST:     GAGGTCAAACCAGGAGTCCGTTGTCCTACTGGAGAAGCTAGGATTACTCC                         TGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATA
genomic: GAGGTCAAACCAGGAGTCCGTTGTCCTACTGGAGAAGCTAGGATTACTCCgttagtactt ... atgtgagcagTGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGCTGGACCAGAGCTAGTGCAAGCATGCCGGAAAGTTCCAGAGGTCAAACCAGGAGTCCGTTGTCCTACTGGAGAAGCTAGGATTACTCCgttagtacttcgtacctatctattcactttgattgtttcataagtcggaatgttcaaacctaaaatttatgtatcctttacacatccctttgcccaatattcgatgtgagcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC