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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATTGTCTTCCAGgttagttgcaacaactcctgacttagatatgttttattatgcagctatctgtggtattgctatcccggactagcagttttcatgttttaggtctttcatagcttgtgtgccaaggtcctttttgtaatcagatgcatctcctaatttgcaatgccatttgacctgttcatag

Basic information

species Zea mays
transcript GRMZM5G835235_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G835235_T04 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g14860.1 (Oryza sativa), 5'ss of exon 4
ACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATTGTCTTCCAGgttagttgcaacaactcctgacttagatatgttttat---------------tatgcagctatctgtggtattgctatcccggactagcagttttcatgttttaggtctttcatagcttgtgtgc--caaggtcctttttgtaa------tcagatg-----catctcctaatttgcaatgccatttgacctgttcatag
||||| ||||||||||||||||| |||||||| |||||||| ||||||||||||||||||||||||||||||| ||   |  ||  |||| ||| |                || | ||||| || |   ||   || | |  |||||||    |  | || || ||     || | |  |   |   ||  | || ||  |||        | |||     ||| ||   | | |  ||  |||||   |  ||   ||
ACAGTTAGCTACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAGgttagttgcaacatctttgggttttcatatatttcaccaatcaccaggaagctaagtagctaact-taacatcattaactct-actagcaccactttttttgtatgtagcaaattgttgatacacgataaccttctcttgttaagatgtcctaaatgttcttcatgtctgtaatagtgatatcattttgaccattttcag

upper sequence: GRMZM5G835235_T04 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g14860.4 (Oryza sativa), 5'ss of exon 4
ACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATTGTCTTCCAGgttagttgcaacaactcctgacttagatatgttttat---------------tatgcagctatctgtggtattgctatcccggactagcagttttcatgttttaggtctttcatagcttgtgtgccaaggtccttt-ttgtaa-------tcagatg-----catctcctaatttgcaatgccatttgacctgttcatag
    | ||||||||||||||||| |||||||| |||||||| ||||||||||||||||||||||||||||||| ||   |  ||  |||| ||| |                || | ||||| || |   ||   || | |  |||||||    |  | || || ||     || | |  |   | |    | | | |||| |         | |||     ||| ||   | | |  ||  |||||   |  ||   ||
----TTAGCTACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAGgttagttgcaacatctttgggttttcatatatttcaccaatcaccaggaagctaagtagctaact-taacatcattaactct-actagcaccactttttttgtatgtagcaaattgttgatacacgataaccttctcttgttaagatgtcctaaatgttcttcatgtctgtaatagtgatatcattttgaccattttcag
















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|67039601|gb|CO465856.1|CO465856
EST:     ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATTGTCTTCCAG                         GCCAAGTGTTTGGAAACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAA
genomic: ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATTGTCTTCCAGgttagttgca ... ctgttcatagGCCAAGTGTTTGGAAACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAA
EST: gi|22819758|gb|BU499848.1|BU499848
EST:     ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATTGTCTTCCAG                         GCCAAGTGTTTGGAAACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAA
genomic: ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATTGTCTTCCAGgttagttgca ... ctgttcatagGCCAAGTGTTTGGAAACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAA
EST: gi|211304795|gb|FL143344.1|FL143344
EST:     ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATTGTCTTCCAG                         GCCAAGTGTTTGGAAACGGGTGAGACTGTTGCCATAAAGAA
genomic: ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATTGTCTTCCAGgttagttgca ... ctgttcatagGCCAAGTGTTTGGAAACGGGTGAGACTGTTGCCATAAAGAA
EST: gi|87156577|gb|DY401366.1|DY401366
EST:     ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATTGTCTTCCAG                         GCCAAGTGTTTGGAAACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAA
genomic: ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATTGTCTTCCAGgttagttgca ... ctgttcatagGCCAAGTGTTTGGAAACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAA
EST: gi|211304794|gb|FL143343.1|FL143343
EST:     ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATTGTCTTCCAG                         GCCAAGTGTTTGGAAACGGGTGAGACTGTTGCCATAAAGAAGGTTCTT
genomic: ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATTGTCTTCCAGgttagttgca ... ctgttcatagGCCAAGTGTTTGGAAACGGGTGAGACTGTTGCCATAAAGAAGGTTCTT
EST: gi|24773942|gb|CA409196.1|CA409196
EST:     ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATTGTCTTCCAG                         GCCAAGTGTTTGGAAACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAA
genomic: ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATTGTCTTCCAGgttagttgca ... ctgttcatagGCCAAGTGTTTGGAAACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAA
EST: gi|26559736|gb|CA831971.1|CA831971
EST:     ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATTGTCTTCCAG                         GCCAAGTGTTTGGAAACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAA
genomic: ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATTGTCTTCCAGgttagttgca ... ctgttcatagGCCAAGTGTTTGGAAACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAA
EST: gi|32865540|gb|CF005222.1|CF005222
EST:     ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATTGTCTTCCAG                         GCCAAGTGTTTGGAAACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTC
genomic: ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATTGTCTTCCAGgttagttgca ... ctgttcatagGCCAAGTGTTTGGAAACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTC
EST: gi|32931957|gb|CF036769.1|CF036769
EST:     ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATTGTCTTCCAG                         GCCAAGTGTTTGGAAACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAA
genomic: ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATTGTCTTCCAGgttagttgca ... ctgttcatagGCCAAGTGTTTGGAAACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAA
EST: gi|32933926|gb|CF038738.1|CF038738
EST:     ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATTGTCTTCCAG                         GCCAAGTGTTTGGAAACGGGTGAGACTGTTGCCACAAAGAAGGTTCTTCAA
genomic: ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATTGTCTTCCAGgttagttgca ... ctgttcatagGCCAAGTGTTTGGAAACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 179

ACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATTGTCTTCCAGgttagttgca ... ctgttcatagGCCAAGTGTTTGGAAACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAAGACAAGCGTTACAAGAACCGCGAACTGCAGACCATGCGCCTCCTTGACC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 87

ACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATTGTCTTCCAGgttagttgca ... ctgttcatagGCCAAGTGTTTGGAAACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAAGACAAGCGTTACAAGAACCGCGAACTGCAGACCATGCGCCTCCTTGACC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 140

ACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATTGTCTTCCAGgttagttgca ... ctgttcatagGCCAAGTGTTTGGAAACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAAGACAAGCGTTACAAGAACCGCGAACTGCAGACCATGCGCCTCCTTGACC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 77

ACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATTGTCTTCCAGgttagttgca ... ctgttcatagGCCAAGTGTTTGGAAACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAAGACAAGCGTTACAAGAACCGCGAACTGCAGACCATGCGCCTCCTTGACC