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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtacagcacggacactccgccgctttggatttatcgcgcggcctcttcctatttgctccggctctggaattcgtgtaccttacctcgttgctgtgcgcagGAGAGCAAGCAGTGGGGGAAGACGCCCCAGGAGGCGGTGGGCGCAGGCGGCGGTCGCCAAGTGGATCTAGATGAAGAGGATGACCTGGAGGAGTTCCGGC

Basic information

species Zea mays
transcript GRMZM2G075551_T02
intron # 1
splice site 3'
intron type U2

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|211437406|gb|FL427297.1|FL427297
EST:     CAGGGGAACCCTCATCCCCCTGTCGTCTCCCTTATTGGGGGCCAGACATG                         GAGAGCAAGCAATGGGGGAAGACGCCCCAGGAGGTGGTGGGCGCAGGCGGC
genomic: CAGGGGAACCCTCATCCCCCTGTCGTCTCCCTTATTGGGGGCCAGACATGgtcagtacag ... ctgtgcgcagGAGAGCAAGCAGTGGGGGAAGACGCCCCAGGAGGCGGTGGGCGCAGGCGGC
EST: gi|211069021|gb|FL413437.1|FL413437
EST:     CAGGGGAACCCTCATCCCCCTGTCGTCTCCCTTATTGGGGGCCAGACATG                         GAGAGCAAGCAATGGGGGAAGACGCCCCAGGAGGTGGTGGGCGCAGGCGGC
genomic: CAGGGGAACCCTCATCCCCCTGTCGTCTCCCTTATTGGGGGCCAGACATGgtcagtacag ... ctgtgcgcagGAGAGCAAGCAGTGGGGGAAGACGCCCCAGGAGGCGGTGGGCGCAGGCGGC
EST: gi|71433465|gb|DR814515.1|DR814515
EST:     CAGGGGAACCCTCATCCCCCTGTCGTCTCCCTTATTGGGGGCCAGACATG                         GAGAGCAAGCAGTGGGGGAAGACGCCCCAGGAGGCGGTGGGCGCAGGCGGC
genomic: CAGGGGAACCCTCATCCCCCTGTCGTCTCCCTTATTGGGGGCCAGACATGgtcagtacag ... ctgtgcgcagGAGAGCAAGCAGTGGGGGAAGACGCCCCAGGAGGCGGTGGGCGCAGGCGGC
EST: gi|211431309|gb|FL387541.1|FL387541
EST:     CAGGGGAACCCTCATCCCCCTGTCGTCTCCCTTATTGGGGGCCAGACATG                         GAGAGCAAGCAATGGGGGAAGACGCCCCAGGAGGTGGTGGGCGCAGGCGGC
genomic: CAGGGGAACCCTCATCCCCCTGTCGTCTCCCTTATTGGGGGCCAGACATGgtcagtacag ... ctgtgcgcagGAGAGCAAGCAGTGGGGGAAGACGCCCCAGGAGGCGGTGGGCGCAGGCGGC
EST: gi|74234698|gb|DT642612.1|DT642612
EST:     CAGGGGAACCCTCATCCCCCTGTCGTCTCCCTTATTGGGGGCCAGACATG                         GAGAGCAAGCAGTGGGGGAAGACGCCCCAGGAGGCGGTGGGCGCAGGCGGC
genomic: CAGGGGAACCCTCATCCCCCTGTCGTCTCCCTTATTGGGGGCCAGACATGgtcagtacag ... ctgtgcgcagGAGAGCAAGCAGTGGGGGAAGACGCCCCAGGAGGCGGTGGGCGCAGGCGGC
EST: gi|211426224|gb|FL393456.1|FL393456
EST:     CAGGGGAACCCTCATCCCCCTGTCGTCTCCCTTATTGGGGGCCAGACATG                         GAGAGCAAGCAATGGGGGAAGACGCCCCAGGAGGTGGTGGGCGCAGGCGGC
genomic: CAGGGGAACCCTCATCCCCCTGTCGTCTCCCTTATTGGGGGCCAGACATGgtcagtacag ... ctgtgcgcagGAGAGCAAGCAGTGGGGGAAGACGCCCCAGGAGGCGGTGGGCGCAGGCGGC
EST: gi|74244524|gb|DT652438.1|DT652438
EST:     CAGGGGAACCCTCATCCCCCTGTCGTCTCCCTTATTGGGGGCCAGACATG                         GAGAGCAAGCAGTGGGGGAAGACGCCCCAGGAGGCGGTGGGCGCAGGCGGC
genomic: CAGGGGAACCCTCATCCCCCTGTCGTCTCCCTTATTGGGGGCCAGACATGgtcagtacag ... ctgtgcgcagGAGAGCAAGCAGTGGGGGAAGACGCCCCAGGAGGCGGTGGGCGCAGGCGGC
EST: gi|76932418|gb|DV173042.1|DV173042
EST:     CAGGGGAACCCTCATCCCCCTGTCGTCTCCCTTATTGGGGGCCAGACATG                         GAGAGCAAGCAGTGGGGGAAGACGCCCCAGGAGGCGGTGGGCGCAGGCGGC
genomic: CAGGGGAACCCTCATCCCCCTGTCGTCTCCCTTATTGGGGGCCAGACATGgtcagtacag ... ctgtgcgcagGAGAGCAAGCAGTGGGGGAAGACGCCCCAGGAGGCGGTGGGCGCAGGCGGC
EST: gi|211013868|gb|FL375768.1|FL375768
EST:     CAGGGGAACCCTCATCCCCCTGTCGTCTCCCTTATTGGGGGCCAGACATG                         GAGAGCAAGCAATGGGGGAAGACGCCCCAGGAGGTGGTGGGCGCAGGCGGC
genomic: CAGGGGAACCCTCATCCCCCTGTCGTCTCCCTTATTGGGGGCCAGACATGgtcagtacag ... ctgtgcgcagGAGAGCAAGCAGTGGGGGAAGACGCCCCAGGAGGCGGTGGGCGCAGGCGGC
EST: gi|91879045|gb|EB409002.1|EB409002
EST:     CAGGGGAACCCTCATCCCCCTGTCGTCTCCCTTATTGGGGGCCAGACATG                         GAGAGCAAGCAGTGGGGGAAGACGCCCCAGGAGGCGGTGGGCGCAGGCGGC
genomic: CAGGGGAACCCTCATCCCCCTGTCGTCTCCCTTATTGGGGGCCAGACATGgtcagtacag ... ctgtgcgcagGAGAGCAAGCAGTGGGGGAAGACGCCCCAGGAGGCGGTGGGCGCAGGCGGC
EST: gi|211410899|gb|FL400127.1|FL400127
EST:     AGGGGGAAACCTCATCCCCCTGTCGTCTCCCTTATTGGGGGCCAGACATG                         GAGAGCAAGCAGTGGGGGAAGACGCCCCAGGAGGCGGTGGGCGCAGGCGGC
genomic: A-GGGGAACCCTCATCCCCCTGTCGTCTCCCTTATTGGGGGCCAGACATGgtcagtacag ... ctgtgcgcagGAGAGCAAGCAGTGGGGGAAGACGCCCCAGGAGGCGGTGGGCGCAGGCGGC
EST: gi|89761563|gb|DY689524.1|DY689524
EST:     CAGGGGAACCCTCATCCCCCTGTCGTCTCCCTTATTGGGGGCCAGACATG                         GAGAGCAAGCAGTGGGGGAAGACGCCCCAGGAGGCGGTGGGCGCAGGCGGC
genomic: CAGGGGAACCCTCATCCCCCTGTCGTCTCCCTTATTGGGGGCCAGACATGgtcagtacag ... ctgtgcgcagGAGAGCAAGCAGTGGGGGAAGACGCCCCAGGAGGCGGTGGGCGCAGGCGGC
EST: gi|211212015|gb|FL385212.1|FL385212
EST:     CAGGGGAACCCTCATCCCCCTGTCGTCTCCCTTATTGGGGGCCAGACATG                         GAGAGCAAGCAATGGGGGAAGACGCCCCAGGAGGTGGTGGGCGCAGGCGGC
genomic: CAGGGGAACCCTCATCCCCCTGTCGTCTCCCTTATTGGGGGCCAGACATGgtcagtacag ... ctgtgcgcagGAGAGCAAGCAGTGGGGGAAGACGCCCCAGGAGGCGGTGGGCGCAGGCGGC
EST: gi|71422270|gb|DR805672.1|DR805672
EST:     CAGGGGAACCCTCATCCCCCTGTCGTCTCCCTTATTGGGGGCCAGACATG                         GAGAGCAAGCAGTGGGGGAAGACGCCCCAGGAGGCGGTGGGCGCAGGCGGC
genomic: CAGGGGAACCCTCATCCCCCTGTCGTCTCCCTTATTGGGGGCCAGACATGgtcagtacag ... ctgtgcgcagGAGAGCAAGCAGTGGGGGAAGACGCCCCAGGAGGCGGTGGGCGCAGGCGGC
EST: gi|71324316|gb|DR798859.1|DR798859
EST:     CAGGGGAACCCTCATCCCCCTGTCGTCTCCCTTATTGGGGGCCAGACATG                         GAGAGCAAGCAGTGGGGGAAGACGCCCCAGGAGGCGGTGGGCGCAGGCGGC
genomic: CAGGGGAACCCTCATCCCCCTGTCGTCTCCCTTATTGGGGGCCAGACATGgtcagtacag ... ctgtgcgcagGAGAGCAAGCAGTGGGGGAAGACGCCCCAGGAGGCGGTGGGCGCAGGCGGC
EST: gi|211141769|gb|FL408611.1|FL408611
EST:     CAGGGGAACCCTCATCCCCCTGTCGTCTCCCTTATTGGGGGCCAGACATG                         GAGAGCAAGCAGTGGGGGAAGACGCCCCAGGAGGCGGTGGGCGCAGGCGGC
genomic: CAGGGGAACCCTCATCCCCCTGTCGTCTCCCTTATTGGGGGCCAGACATGgtcagtacag ... ctgtgcgcagGAGAGCAAGCAGTGGGGGAAGACGCCCCAGGAGGCGGTGGGCGCAGGCGGC
EST: gi|211042325|gb|FL393069.1|FL393069
EST:     CAGGGGAACCCTCATCCCCCTGTCGTCTCCCTTATTGGGGGCCAGACATG                         GAGAGCAAGCAATGGGGGAAGACGCCCCAGGAGGTGGTGGGCGCAGGCGGC
genomic: CAGGGGAACCCTCATCCCCCTGTCGTCTCCCTTATTGGGGGCCAGACATGgtcagtacag ... ctgtgcgcagGAGAGCAAGCAGTGGGGGAAGACGCCCCAGGAGGCGGTGGGCGCAGGCGGC
EST: gi|76283408|gb|DV022976.1|DV022976
EST:     CAGGGGAACCCTCATCCCCCTGTCGTCTCCCTTATTGGGGGCCAGACATG                         GAGAGCAAGCAGTGGGGGAAGACGCCCCAGGAGGCGGTGGGCGCAGGCGGC
genomic: CAGGGGAACCCTCATCCCCCTGTCGTCTCCCTTATTGGGGGCCAGACATGgtcagtacag ... ctgtgcgcagGAGAGCAAGCAGTGGGGGAAGACGCCCCAGGAGGCGGTGGGCGCAGGCGGC
EST: gi|211439991|gb|FL426844.1|FL426844
EST:     CAGGGGAACCCTCATCCCCCTGTCGTCTCCCTTATTGGGGGCCAGACATG                         GAGAGCAAGCAGTGGGGGAAGACGCCCCAGGAGGCGGTGGGCGCAGGCGGC
genomic: CAGGGGAACCCTCATCCCCCTGTCGTCTCCCTTATTGGGGGCCAGACATGgtcagtacag ... ctgtgcgcagGAGAGCAAGCAGTGGGGGAAGACGCCCCAGGAGGCGGTGGGCGCAGGCGGC
EST: gi|93281364|gb|EB673628.1|EB673628
EST:     CAGGGGAACCCTCATCCCCCTGTCGTCTCCCTTATTGGGGGCCAGACATG                         GAGAGCAAGCAGTGGGGGAAGACGCCCCAGGAGGCGGTGGGCGCAGGCGGC
genomic: CAGGGGAACCCTCATCCCCCTGTCGTCTCCCTTATTGGGGGCCAGACATGgtcagtacag ... ctgtgcgcagGAGAGCAAGCAGTGGGGGAAGACGCCCCAGGAGGCGGTGGGCGCAGGCGGC
EST: gi|76290174|gb|DV029742.1|DV029742
EST:     CAGGGGAACCCTCATCCCCCTGTCGTCTCCCTTATTGGGGGCCAGACATG                         GAGAGCAAGCAGTGGGGGAAGACGCCCCAGGAGGCGGTGGGCGCAGGCGGC
genomic: CAGGGGAACCCTCATCCCCCTGTCGTCTCCCTTATTGGGGGCCAGACATGgtcagtacag ... ctgtgcgcagGAGAGCAAGCAGTGGGGGAAGACGCCCCAGGAGGCGGTGGGCGCAGGCGGC
EST: gi|211030009|gb|FL411228.1|FL411228
EST:     CAGGGGAA-CCTCATCCCCCTGTCGTCTCCCTTATTGGGGGCCAGACATG                         GAGAGCAAGCAATGGGGGAAGACGCCCCAGGAGGTGGTGGGCGCAGGCGGC
genomic: CAGGGGAACCCTCATCCCCCTGTCGTCTCCCTTATTGGGGGCCAGACATGgtcagtacag ... ctgtgcgcagGAGAGCAAGCAGTGGGGGAAGACGCCCCAGGAGGCGGTGGGCGCAGGCGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcctatttgctccggctctggaattcgtgtaccttacctcgttgctgtgcgcagGAGAGCAAGCAGTGGGGGAAGACGCCCCAGGAGGCGGTGGGCGCAGGCGGCGGTCGCCAAGTGGATCTAGATGAAGAGGATGACCTGGAGGAGTTCCGGC
                               accttac  putative branch site (score: 3)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtacagcacggacactccgccgctttggatttatcgcgcggcctcttcctatttgctccggctctggaattcgtgtaccttacctcgttgctgtgcgcagGAGAGCAAGCAGTGGGGGAAGACGCCCCAGGAGGCGGTGGGCGCAGGCGGCGGTCGCCAAGTGGATCTAGATGAAGAGGATGACCTGGAGGAGTTCCGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG