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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGATACAGACTACTGGCTCTTATCGGACAACACAGGAGTTAGCATGACGAACATGTGGGAGACAGGACgtatccttctaatagtctgtcacccactattatctttcatactcgcaccaagtttctgatctagtttagcacatgtgaaacctgtaaaccctttaaccaaacaatgcag

Basic information

species Zea mays
transcript GRMZM2G052515_T01
intron # 13
splice site 5'
intron type U12 (go to U12 genes for details)

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|211512270|gb|FL436231.1|FL436231
EST:     CTTATCGGACAACACAGGAGTTAGCATGACGAACATGTGGGAGACAGGAC                         CAGATGAGTGGGATGGGATTGAGAAATTCAACGCGGAGGATTTCTTGGAAG
genomic: CTTATCGGACAACACAGGAGTTAGCATGACGAACATGTGGGAGACAGGACgtatccttct ... aacaatgcagCAGATGAGTGGGATGGGATTGAGAAATTCAACGCGGAGGATTTCTTGGAAG
EST: gi|78111264|gb|DV529661.1|DV529661
EST:     CTTATCGGACAACACAGGAGTTAGCATGACGAACATGTGGGAGACAGGAC                         CAGATGAGTGGGATGGGATTGAGAAATTCAACGCGGAGGATTTCTTGGAAG
genomic: CTTATCGGACAACACAGGAGTTAGCATGACGAACATGTGGGAGACAGGACgtatccttct ... aacaatgcagCAGATGAGTGGGATGGGATTGAGAAATTCAACGCGGAGGATTTCTTGGAAG
EST: gi|32945810|gb|CF050629.1|CF050629
EST:     CTTATCGGACAACACAGGAGTTAGCATGACGAACATGTGGGAGACAGGAC                         CAGATGAGTGGGACGGGATTGAGAAATTCAACGCGGAGGATTTCTTGGAAG
genomic: CTTATCGGACAACACAGGAGTTAGCATGACGAACATGTGGGAGACAGGACgtatccttct ... aacaatgcagCAGATGAGTGGGATGGGATTGAGAAATTCAACGCGGAGGATTTCTTGGAAG
EST: gi|110504398|gb|EE017326.1|EE017326
EST:     CTTATCGGACAACACAGGAGTTAGCATGACGAACATGTGGGAGACAGGAC                         CAGATGAGTGGGATGGGATTGAGAAATTCAACGCGGAGGATTTCTTGGAAG
genomic: CTTATCGGACAACACAGGAGTTAGCATGACGAACATGTGGGAGACAGGACgtatccttct ... aacaatgcagCAGATGAGTGGGATGGGATTGAGAAATTCAACGCGGAGGATTTCTTGGAAG
EST: gi|211359787|gb|FL457494.1|FL457494
EST:     CTTATCGGACAACACAGGAGTTAGCATGACGAACATGTGGGAGACAGGAC                         CAGATGAGTGGGATGGGATTGAGAAATTCAACGCGGAGGATTTCTTGGAAG
genomic: CTTATCGGACAACACAGGAGTTAGCATGACGAACATGTGGGAGACAGGACgtatccttct ... aacaatgcagCAGATGAGTGGGATGGGATTGAGAAATTCAACGCGGAGGATTTCTTGGAAG
EST: gi|50335209|gb|CO530335.1|CO530335
EST:     CTTATCGGACAACACAGGAGTTAGCATGACGAACATGTGGGAGACAGGAC                         CAGATGAGTGGGATGGGATTGAGAAATTCAACGCGGAGGATTTCTTGGAAG
genomic: CTTATCGGACAACACAGGAGTTAGCATGACGAACATGTGGGAGACAGGACgtatccttct ... aacaatgcagCAGATGAGTGGGATGGGATTGAGAAATTCAACGCGGAGGATTTCTTGGAAG
EST: gi|60394836|gb|DN227705.1|DN227705
EST:     CTTATCGGACAACACAGGAGTTAGCATGACGAACATGTGGGAGACAGGAC                         CAGATGAGTGGGATGGGATTGAGAAATTCAACGCGGAGGATTTCTTGGAAG
genomic: CTTATCGGACAACACAGGAGTTAGCATGACGAACATGTGGGAGACAGGACgtatccttct ... aacaatgcagCAGATGAGTGGGATGGGATTGAGAAATTCAACGCGGAGGATTTCTTGGAAG
EST: gi|211512271|gb|FL436232.1|FL436232
EST:     CTTATCGGACAACACAGGAGTTAGCATGACGAACATGTGGGAGACAGGAC                         CAGATGAGTGGGATGGGATTGAGAAATTCAACGCGGAGGATTTCTTGGAAG
genomic: CTTATCGGACAACACAGGAGTTAGCATGACGAACATGTGGGAGACAGGACgtatccttct ... aacaatgcagCAGATGAGTGGGATGGGATTGAGAAATTCAACGCGGAGGATTTCTTGGAAG
EST: gi|31664297|gb|CD573022.1|CD573022
EST:     CTTATCGGACAACACAGGAGTTAGCATGACGAACATGTGGGAGACAGGAC                         CAGATGAGTGGGATGGGATTGAGAAATTCAACGCGGAGGATTTCTTGGAAG
genomic: CTTATCGGACAACACAGGAGTTAGCATGACGAACATGTGGGAGACAGGACgtatccttct ... aacaatgcagCAGATGAGTGGGATGGGATTGAGAAATTCAACGCGGAGGATTTCTTGGAAG
EST: gi|211465343|gb|FL454187.1|FL454187
EST:     CTTATCGGACAACACAGGAGTTAGCATGACGAACATGTGGGAGACAGGAC                         CAGATGAGTGGGATGGGATTGAGAAATTCAACGCGGAGGATTTCTTGGAAG
genomic: CTTATCGGACAACACAGGAGTTAGCATGACGAACATGTGGGAGACAGGACgtatccttct ... aacaatgcagCAGATGAGTGGGATGGGATTGAGAAATTCAACGCGGAGGATTTCTTGGAAG
EST: gi|78543582|gb|DV621080.1|DV621080
EST:     GCATGACGAACATGTGGGAGACAGGAC                         CAGATGAGTGGGATGGGATTGAGAAATTCAACGCGGAGGATTTCTTGGAAG
genomic: GCATGACGAACATGTGGGAGACAGGACgtatccttct ... aacaatgcagCAGATGAGTGGGATGGGATTGAGAAATTCAACGCGGAGGATTTCTTGGAAG
EST: gi|31664296|gb|CD573021.1|CD573021
EST:     ATGACGAACATGTGGGAGACAGGAC                         CAGATGAGTGGGATGGGATTGAGAAATTCAACGCGGAGGATTTCTTGGAAG
genomic: ATGACGAACATGTGGGAGACAGGACgtatccttct ... aacaatgcagCAGATGAGTGGGATGGGATTGAGAAATTCAACGCGGAGGATTTCTTGGAAG
EST: gi|60394828|gb|DN227697.1|DN227697
EST:     CTTATCGGACAACACAGGAGTTAGCATGACGAACATGTGGGAGACAGGAC                         CAGATGAGTGGGATGGGATTGAGAAATTCAACGCGGAGGATTTCTTGGAAG
genomic: CTTATCGGACAACACAGGAGTTAGCATGACGAACATGTGGGAGACAGGACgtatccttct ... aacaatgcagCAGATGAGTGGGATGGGATTGAGAAATTCAACGCGGAGGATTTCTTGGAAG
EST: gi|76284708|gb|DV024276.1|DV024276
EST:     CTTATCGGACAACACAGGAGTTAGCATGACGAACATGTGGGAGACAGGAC                         CAGATGAGTGGGATGGGATTGAGAAATTCAACGCGGAGGATTTCTTGGAAG
genomic: CTTATCGGACAACACAGGAGTTAGCATGACGAACATGTGGGAGACAGGACgtatccttct ... aacaatgcagCAGATGAGTGGGATGGGATTGAGAAATTCAACGCGGAGGATTTCTTGGAAG
EST: gi|149098349|gb|EE184322.2|EE184322
EST:     CTTATCGGACAACACAGGAGTTAGCATGACGAACATGTGGGAGACAGGAC                         CAGATGAGTGGGATGGGATTGAGAAATTCAACGCGGAGGATTTCTTGGAAG
genomic: CTTATCGGACAACACAGGAGTTAGCATGACGAACATGTGGGAGACAGGACgtatccttct ... aacaatgcagCAGATGAGTGGGATGGGATTGAGAAATTCAACGCGGAGGATTTCTTGGAAG

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), 43 (downstream exon)
Score: 56

GCTGATACAGACTACTGGCTCTTATCGGACAACACAGGAGTTAGCATGACGAACATGTGGGAGACAGGACgtatccttct ... aacaatgcagCAGATGAGTGGGATGGGATTGAGAAATTCAACGCGGAGGATTTCTTGGAAGTGGGCACTCCCCAGCAGCAGGATAAACCAGCCGATGTCGTGGATGACGA


Block sizes: 46 (upstream exon), 39 (downstream exon)
Score: 6

GCTGATACAGACTACTGGCTCTTATCGGACAACACAGGAGTTAGCATGACGAACATGTGGGAGACAGGACgtatccttct ... aacaatgcagCAGATGAGTGGGATGGGATTGAGAAATTCAACGCGGAGGATTTCTTGGAAGTGGGCACTCCCCAGCAGCAGGATAAACCAGCCGATGTCGTGGATGACGA


Block sizes: 38 (upstream exon), 37 (downstream exon)
Score: 6

GCTGATACAGACTACTGGCTCTTATCGGACAACACAGGAGTTAGCATGACGAACATGTGGGAGACAGGACgtatccttct ... aacaatgcagCAGATGAGTGGGATGGGATTGAGAAATTCAACGCGGAGGATTTCTTGGAAGTGGGCACTCCCCAGCAGCAGGATAAACCAGCCGATGTCGTGGATGACGA


Block sizes: 42 (upstream exon), 43 (downstream exon)
Score: 5

GCTGATACAGACTACTGGCTCTTATCGGACAACACAGGAGTTAGCATGACGAACATGTGGGAGACAGGACgtatccttct ... aacaatgcagCAGATGAGTGGGATGGGATTGAGAAATTCAACGCGGAGGATTTCTTGGAAGTGGGCACTCCCCAGCAGCAGGATAAACCAGCCGATGTCGTGGATGACGA