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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattgtcggttctacaagcttgtgaattgtcttctatagaagcataaaatctgatcacccctaaaatgattttgtatggcagGTCCTCGGTACGCCAACAAGGGAAGAAATTAAATGCATGAACCCAAATTACACAGAGTTTAAGTTCCCACAAATCAAAGCACACCCATGGCACAAG

Basic information

species Zea mays
transcript GRMZM2G024151_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G024151_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g14860.1 (Oryza sativa), 3'ss of exon 9
gtaattgtcggttcta----caagcttgtgaattgtcttctatagaagcataaaatctgatcacccctaaaatgattttgtatggcagGTCCTCGGTACGCCAACAAGGGAAGAAATTAAATGCATGAACCCAAATTACACAGAGTTTAAGTTCCCACAAATCAAAGCACACCCATGGCACAAG
|| | || |  ||||       || | |      |  || |   || |   | ||  |  | ||    ||| ||||     || ||||||||| || || || |||||||| ||||||||||||||||| ||||| || || ||||| ||||| ||||| || |||||||||||||||||||||
gttagtgccaattctggtgtttagttggccttgcgagttgttcggaggtgcagaagtttgtaacattaaaactgatcacacatcgcagGTCCTTGGAACACCTACAAGGGAGGAAATTAAATGCATGAATCCAAACTATACCGAGTTCAAGTTTCCACAGATTAAAGCACACCCATGGCACAAG

upper sequence: GRMZM2G024151_T01 (Zea mays), 3'ss of exon 8
lower sequence: PP1S60_100V6.1 (Physcomitrella patens), 3'ss of exon 8
-----------------------------------------gtaattgtcggttctacaagcttgtgaattgtcttctatagaagcataaaatctgatcacccctaaaatgattttgtatggcagGTCCTCGGTACGCCAACAAGGGAAGAAATTAAATGCATGAACCCAAATTACACAGAGTTTAAGTTCCCACAAATCAAAGCACACCCATGGCACAAG
                                         ||| |||   | |      |  |||     |  |  |||       |  | | |         | |    |  || | ||||||||  | || || || ||  | || || || || |||||||| || || ||||| ||||| ||||| || |||||||| || |||||||||||||| 
gtagggcacaggcgatgcacggtgttgtgttgaagggtggcgtacttgcttgctggttgtgactgttgcgggagtgttatgatgctgtggagtgta--tgttattgaggaaaagttttgtggcagGTGTTGGGGACACCGACTCGTGAGGAGATCAAGTGCATGAATCCGAACTACACGGAGTTCAAGTTTCCGCAAATCAAGGCTCACCCATGGCACAAA

upper sequence: GRMZM2G024151_T01 (Zea mays), 3'ss of exon 8
lower sequence: PP1S306_62V6.1 (Physcomitrella patens), 3'ss of exon 7
----------------------------------------------gtaattgtcggttctacaagcttgtgaattgtcttctata-gaagcataaaatctgatcacccctaaaatgattttgtatggcagGTCCTCGGTACGCCAACAAGGGAAGAAATTAAATGCATGAACCCAAATTACACAGAGTTTAAGTTCCCACAAATCAAAGCACACCCATGGCACAAG
                                                  ||| |||||      |    ||   | |||| |    |  | ||   |      |       | | | ||  || ||||||||  | || || || ||  | || || || || |||||||| || || ||||||||||| ||||| ||||||||||| || ||||| |||||||| 
gtgggacacacgtggtacacgttgtttgtgtggaagggtcgccttctgggttggcggtttggtttgtagctgtggtatcttgttcgtgttggatgtgagtatggcgttgaccagacgtttccgtgtggcagGTTTTGGGGACACCGACTCGTGAGGAGATCAAGTGCATGAATCCGAACTACACAGAGTTCAAGTTTCCACAAATCAAGGCGCACCCGTGGCACAAA

upper sequence: GRMZM2G024151_T01 (Zea mays), 3'ss of exon 8
lower sequence: EFJ07216 (Selaginella moellendorffii), 3'ss of exon 9
gtaattgtcggttctacaagcttgtgaattgtcttctatagaagcataaaatctgatcacccctaaaatgattttgtatggcagGTCCTCGGTACGCCAACAAGGGAAGAAATTAAATGCATGAACCCAAATTACACAGAGTTTAAGTTCCCACAAATCAAAGCACACCCATGGCACAAG
      ||  |   | ||  ||||    || | |||| |       |   |   | ||   |  ||   || ||  | | ||||||| | ||||| || ||  | || ||||| ||||||||||| ||||| ||||| |||||||||||||| || || ||||| || || |||||||||
------gtacgca-tgcattcttgctcttttttttctgttttttt-tgcgagtcgctcttgctcaa---gacttgcttttgcagGTCTTAGGTACTCCTACTCGCGAGGAAATCAAATGCATGAATCCAAACTACACGGAGTTTAAGTTCCCTCAGATTAAAGCGCATCCCTGGCACAAG

upper sequence: GRMZM2G024151_T01 (Zea mays), 3'ss of exon 8
lower sequence: EFJ07923 (Selaginella moellendorffii), 3'ss of exon 9
gtaattgtcggttctacaagcttgtgaattgtcttctatagaagcataaaatctgatcacccctaaaatgattttgtatggcagGTCCTCGGTACGCCAACAAGGGAAGAAATTAAATGCATGAACCCAAATTACACAGAGTTTAAGTTCCCACAAATCAAAGCACACCCATGGCACAAG
            |   || || |      | |||| | |       |   |   | ||   |  ||   || ||  | | ||||||| | ||||| || ||  |||| ||||| ||||||||||| ||||| ||||| |||||||||||||| || || ||||| || || |||||||||
-----------gtacgcatgcattcttgctctcttttttctt--tttgcgagtcgctcttgctcaa---gacttgcttttgcagGTCTTAGGTACTCCTACTCGGGAGGAAATCAAATGCATGAATCCAAACTACACGGAGTTTAAGTTCCCTCAGATTAAAGCGCATCCCTGGCACAAG

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|60337200|gb|DN204173.1|DN204173
EST:     CTTTGTTTCCGGGTGAAAGTGGTGTGGACCAACTTGTTGAAATCATCAAG                         GTCCTCGGTACGCCAACAAGGGAAGAAATTAAATGCATGAACCCAAATTAC
genomic: CTTTGTTTCCGGGTGAAAGTGGTGTGGACCAACTTGTTGAAATCATCAAGgtaattgtcg ... tgtatggcagGTCCTCGGTACGCCAACAAGGGAAGAAATTAAATGCATGAACCCAAATTAC
EST: gi|60349350|gb|DN216323.1|DN216323
EST:     CTTTGTTTCCGGGTGAAAGTGGTGTGGACCAACTTGTTGAAATCATCAAG                         GTCCTCGGTACGCCAACAAGGGAAGAAATTAAATGCATGAACCCAAATTAC
genomic: CTTTGTTTCCGGGTGAAAGTGGTGTGGACCAACTTGTTGAAATCATCAAGgtaattgtcg ... tgtatggcagGTCCTCGGTACGCCAACAAGGGAAGAAATTAAATGCATGAACCCAAATTAC
EST: gi|60340745|gb|DN207718.1|DN207718
EST:     CTTTGTTTCCGGGTGAAAGTGGTGTGGACCAACTTGTTGAAATCATCAAG                         GTCCTCGGTACGCCAACAAGGGAAGAAATTAAATGCATGAACCCAAATTAC
genomic: CTTTGTTTCCGGGTGAAAGTGGTGTGGACCAACTTGTTGAAATCATCAAGgtaattgtcg ... tgtatggcagGTCCTCGGTACGCCAACAAGGGAAGAAATTAAATGCATGAACCCAAATTAC
EST: gi|60344051|gb|DN211024.1|DN211024
EST:     TGTGGACCAACTT-TTGAAATCATCAAG                         GTCCTCGGTACGCCAACAAGGGAAGAAATTAAATGCATGAACCCAAATTAC
genomic: TGTGGACCAACTTGTTGAAATCATCAAGgtaattgtcg ... tgtatggcagGTCCTCGGTACGCCAACAAGGGAAGAAATTAAATGCATGAACCCAAATTAC
EST: gi|61117968|gb|DN558929.1|DN558929
EST:     CTTTGTTTCCGGGTGAAAGTGGTGTGGACCAACTTGTCGAAATCATCAAG                         GTCCTCGGTACGCCAACAAGGGAAGAAATTAAATGCATGAACCCAAATTAC
genomic: CTTTGTTTCCGGGTGAAAGTGGTGTGGACCAACTTGTTGAAATCATCAAGgtaattgtcg ... tgtatggcagGTCCTCGGTACGCCAACAAGGGAAGAAATTAAATGCATGAACCCAAATTAC
EST: gi|211161694|gb|FL418712.1|FL418712
EST:     CTTTGTTTCCGGGTGAAAGTGGTGTGGACCAACTTGTCGAAATCATCAAG                         GTCCTCGGTACGCCAACAAGGGAAGAAATTAAATGCATGAACCCAAATTAC
genomic: CTTTGTTTCCGGGTGAAAGTGGTGTGGACCAACTTGTTGAAATCATCAAGgtaattgtcg ... tgtatggcagGTCCTCGGTACGCCAACAAGGGAAGAAATTAAATGCATGAACCCAAATTAC
EST: gi|61117965|gb|DN558926.1|DN558926
EST:     CTTTGTTTCCGGGTGAAAGTGGTGTGGACCAACTTGTCGAAATCATCAAG                         GTCCTCGGTACGCCAACAAGGGAAGAAATTAAATGCATGAACCCAAATTAC
genomic: CTTTGTTTCCGGGTGAAAGTGGTGTGGACCAACTTGTTGAAATCATCAAGgtaattgtcg ... tgtatggcagGTCCTCGGTACGCCAACAAGGGAAGAAATTAAATGCATGAACCCAAATTAC
EST: gi|60395743|gb|DN228613.1|DN228613
EST:     CTTTGTTTCCGGGTGAAAGTGGTGTGGACCAACTTGTTGAAATCATCAAG                         GTCCTCGGTACGCCAACAAGGGAAGAAATTAAATGCATGAACCCAAATTAC
genomic: CTTTGTTTCCGGGTGAAAGTGGTGTGGACCAACTTGTTGAAATCATCAAGgtaattgtcg ... tgtatggcagGTCCTCGGTACGCCAACAAGGGAAGAAATTAAATGCATGAACCCAAATTAC
EST: gi|60338887|gb|DN205860.1|DN205860
EST:     CTTTGTTTCCGGGTGAAAGTGGTGTGGACCAACTTGTTGAAATCATCAAG                         GTCCTCGGTACGCCAACAAGGGAAGAAATTAAATGCATGAACCCAAATTAC
genomic: CTTTGTTTCCGGGTGAAAGTGGTGTGGACCAACTTGTTGAAATCATCAAGgtaattgtcg ... tgtatggcagGTCCTCGGTACGCCAACAAGGGAAGAAATTAAATGCATGAACCCAAATTAC
EST: gi|4967195|gb|AI691889.1|AI691889
EST:     ACTTGTTGAAATCATCAAG                         GTCCTCGGTACGCCANCAAGGGAAGAAATTAAATGCATGAACCCAAATTAC
genomic: ACTTGTTGAAATCATCAAGgtaattgtcg ... tgtatggcagGTCCTCGGTACGCCAACAAGGGAAGAAATTAAATGCATGAACCCAAATTAC
EST: gi|61117966|gb|DN558927.1|DN558927
EST:     CTTTGTTTCCGGGTGAAAGTGGTGTGGACCAACTTGTCGAAATCATCAAG                         GTCCTCGGTACGCCAACAAGGGAAGAAATTAAATGCATGAACCCAAATTAC
genomic: CTTTGTTTCCGGGTGAAAGTGGTGTGGACCAACTTGTTGAAATCATCAAGgtaattgtcg ... tgtatggcagGTCCTCGGTACGCCAACAAGGGAAGAAATTAAATGCATGAACCCAAATTAC
EST: gi|60394497|gb|DN227367.1|DN227367
EST:     CTTTGTTTCCGGGTGAAAGTGGTGTGGACCAACTTGTTGAAATCATCAAG                         GTCCTCGGTACGCCAACAAGGGAAGAAATTAAATGCATGAACCCAAATTAC
genomic: CTTTGTTTCCGGGTGAAAGTGGTGTGGACCAACTTGTTGAAATCATCAAGgtaattgtcg ... tgtatggcagGTCCTCGGTACGCCAACAAGGGAAGAAATTAAATGCATGAACCCAAATTAC
EST: gi|33097248|gb|CF057208.1|CF057208
EST:     CTTTGTTTCCGGGTGAAAGTGGTGTGGACCAACTTGTTGAAATCATCAAG                         GTCCTCGGTACGCCAACAAGGGAAGAAATTAAATGCATGAACCCAAATTAC
genomic: CTTTGTTTCCGGGTGAAAGTGGTGTGGACCAACTTGTTGAAATCATCAAGgtaattgtcg ... tgtatggcagGTCCTCGGTACGCCAACAAGGGAAGAAATTAAATGCATGAACCCAAATTAC
EST: gi|60349962|gb|DN216935.1|DN216935
EST:     CTTTGTTTCCGGGTGAAAGTGGTGTGGACCAACTTGTTGAAATCATCAAA                         GTCCTCGGTACG
genomic: CTTTGTTTCCGGGTGAAAGTGGTGTGGACCAACTTGTTGAAATCATCAAGgtaattgtcg ... tgtatggcagGTCCTCGGTACG
EST: gi|60346367|gb|DN213340.1|DN213340
EST:     CTTTGTTTCCGGGTGAAAGTGGTGTGGACCAACTTGTTGAAATCATCAAG                         GTCCTCGGTACGCCAACAAGGGAAGAAATTAAATGCATGAACCCAAATTAC
genomic: CTTTGTTTCCGGGTGAAAGTGGTGTGGACCAACTTGTTGAAATCATCAAGgtaattgtcg ... tgtatggcagGTCCTCGGTACGCCAACAAGGGAAGAAATTAAATGCATGAACCCAAATTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtcttctatagaagcataaaatctgatcacccctaaaatgattttgtatggcagGTCCTCGGTACGCCAACAAGGGAAGAAATTAAATGCATGAACCCAAATTACACAGAGTTTAAGTTCCCACAAATCAAAGCACACCCATGGCACAAG
                               ccctaaa  putative branch site (score: 3)
                                  taaaatgattttgtat  TA-rich tract