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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGACGAAGTTTCGGATCCCACGAGGATGAAGATAAGAGTTCTGGTAACCCTCAGTCTGGGAAAGCTTTGTATGACTTCACAGCAGGCGGTGATGATGAGgtacgcgggtagtaatcctttttgttgtttgtcttataaattcctgaagtgatacttccatgttcagagtttgatggaatgttggttctgaaatcttttt...

Basic information

species Zea mays
transcript GRMZM2G012319_T01
intron # 23
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G012319_T01 (Zea mays), 5'ss of exon 23
lower sequence: LOC_Os03g15900.2 (Oryza sativa), 5'ss of exon 21
AGGACGAAGTTTCGGATCCCACGAGGATGAAGATAAGAGTTCTGGTAACCCTCAGTCTGGGAAAGCTTTGTATGACTTCACAGCAGGCGGTGATGATGAGgtacgcgggtagtaatcctttttgttgtttgtcttataaattcctgaagt--gatacttccatgttcagagtttgatgg--aatgttggttctgaaatcttttt
 || || ||||| |||||||| ||||| ||||| | |||||| || |||||||| |||||||||||  ||||||||||||||||||| || |||||||||||| |  ||  | |||  | || ||||  | |    |||  ||||||  |   || ||||| || |||||| ||||| |  | |    ||| |||||  |    
TGGTCGGAGTTTTGGATCCCATGAGGACGAAGACAGGAGTTCAGGGAACCCTCAATCTGGGAAAGCACTGTATGACTTCACAGCAGGTGGCGATGATGAGgtatggaggctgaaattgtcttggttggctataacgtaacatcctgagcttcaatgcttccttgatcagagcttgataggcattagctgttgtgaaacat----

upper sequence: GRMZM2G012319_T01 (Zea mays), 5'ss of exon 23
lower sequence: AT2G07360.1 (Arabidopsis thaliana), 5'ss of exon 25
AGGACGAAGTTTCGGATCCCACGAGGATGAAGATAAGAGTTCTGGTAACCCTCAGTCTGGGAAAGCTTTGTATGACTTCACAGCAGGCGGTGATGATGAGgtacgcgggtagtaatcctttttgttgtttgtcttataaattcctgaagtgatacttccatgttcagagtttgatggaatgttggttctgaaatcttttt
    |||||||  | |||  | || || |||  || ||  |||  |    |    | ||| | |||  | ||||||||||||||||| || |||||||||||| ||  |   |  || ||| |    || || || || |    ||||   |||      | | || |  || |   |    ||| | ||          
TTCTCGAAGTTATGAATCAGATGATGAAGAACCTAGGAAATCTACTGGTACAAGATTTGGAACAGCGCTCTATGACTTCACAGCAGGAGGAGATGATGAGgtaagcttgcttttgtcttttattcatttagttttgtatacggttgaaa-aatatgatattatgcaaacgttaaaacacgtatgggtatgttgcag----
















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|60352427|gb|DN219400.1|DN219400
EST:     CTTCACAGCAGGCGGTGATGATGAG                         CTGAGTTTAAACTCTGGAGAAGAAGTGGAGATTGAATACGAGGTCGATGGT
genomic: CTTCACAGCAGGCGGTGATGATGAGgtacgcgggt ... gttttttcagCTGAGTTTAAACTCTGGAGAAGAAGTGGAGATTGAATACGAGGTCGATGGT
EST: gi|211048296|gb|FL052136.1|FL052136
EST:     CTCAGTCTGGGAAAGCTTTGTATGACTTCACAGCAGGCGGTGATGATGAG                         CTGAGTTTAAACTCTGGAGAAGAAGTGGAGATTGAATACGAGGTCGATGGT
genomic: CTCAGTCTGGGAAAGCTTTGTATGACTTCACAGCAGGCGGTGATGATGAGgtacgcgggt ... gttttttcagCTGAGTTTAAACTCTGGAGAAGAAGTGGAGATTGAATACGAGGTCGATGGT
EST: gi|74238553|gb|DT646467.1|DT646467
EST:     CTCAGTCTGGGAAAGCTTTGTATGACTTCACAGCAGGCGGTGATGATGAG                         CTGAGTTTAAACTCTGGAGAAGAAGTGGAGATTGAATA
genomic: CTCAGTCTGGGAAAGCTTTGTATGACTTCACAGCAGGCGGTGATGATGAGgtacgcgggt ... gttttttcagCTGAGTTTAAACTCTGGAGAAGAAGTGGAGATTGAATA
EST: gi|60356301|gb|DN223274.1|DN223274
EST:     CTCAGTCTGGGAAAGCTTTGTATGACTTCACAGCAGGCGGTGATGATGAG                         CTGAGTTTAAACTCTGGAGAAGAAGTGGAGATTGAATACGAGGTCGATGGT
genomic: CTCAGTCTGGGAAAGCTTTGTATGACTTCACAGCAGGCGGTGATGATGAGgtacgcgggt ... gttttttcagCTGAGTTTAAACTCTGGAGAAGAAGTGGAGATTGAATACGAGGTCGATGGT
EST: gi|22546271|gb|BU098582.1|BU098582
EST:     CTCAGTCTGGGAAAGCTTTGTATGACTTCACAGCAGGCGGTGATGATGAG                         CTGAGTTTAAACTCTGGAGAAGAAGTGGAGATTGAATACGAGGTCGATGGT
genomic: CTCAGTCTGGGAAAGCTTTGTATGACTTCACAGCAGGCGGTGATGATGAGgtacgcgggt ... gttttttcagCTGAGTTTAAACTCTGGAGAAGAAGTGGAGATTGAATACGAGGTCGATGGT
EST: gi|26558707|gb|CA830942.1|CA830942
EST:     CTCAGTCTGGGAAAGCTTTGTATGACTTCACAGCAGGCGGTGATGATGAG                         CTGAGTTTAAACTCTGGAGAAGAAGTGGAGATTGAATACGAGGTCGATGGT
genomic: CTCAGTCTGGGAAAGCTTTGTATGACTTCACAGCAGGCGGTGATGATGAGgtacgcgggt ... gttttttcagCTGAGTTTAAACTCTGGAGAAGAAGTGGAGATTGAATACGAGGTCGATGGT
EST: gi|76909470|gb|DV163396.1|DV163396
EST:     CTCAGTCTGGGAAAGCTTTGTATGACTTCACAGCAGGCGGTGATGATGAG                         CTGAGTTTAAACTCTGGAGAAGAAGTGGAGATTGAATACGAGGTCGATGGT
genomic: CTCAGTCTGGGAAAGCTTTGTATGACTTCACAGCAGGCGGTGATGATGAGgtacgcgggt ... gttttttcagCTGAGTTTAAACTCTGGAGAAGAAGTGGAGATTGAATACGAGGTCGATGGT
EST: gi|87156397|gb|DY401186.1|DY401186
EST:     CTCAGTCTGGGAAAGCTTTGTATGACTTCACAGCAGGCGGTGATGATGAG                         CTGAGTTTAAACTCTGGAGAAGAAGTGGAGATTGAATACGAGGTCGATGGT
genomic: CTCAGTCTGGGAAAGCTTTGTATGACTTCACAGCAGGCGGTGATGATGAGgtacgcgggt ... gttttttcagCTGAGTTTAAACTCTGGAGAAGAAGTGGAGATTGAATACGAGGTCGATGGT
EST: gi|60337974|gb|DN204947.1|DN204947
EST:     CTCAGTCTGGGAAAGCTTTGTATGACTTCACAGCAGGCGGTGATGATGAG                         CTGAGTTTAAACTCTGGAGAAGAAGTGGAGATTGAATACGAGGTCGATGGT
genomic: CTCAGTCTGGGAAAGCTTTGTATGACTTCACAGCAGGCGGTGATGATGAGgtacgcgggt ... gttttttcagCTGAGTTTAAACTCTGGAGAAGAAGTGGAGATTGAATACGAGGTCGATGGT
EST: gi|60398288|gb|DN231104.1|DN231104
EST:     CTCAGTCTGGGAAAGCTTTGTATGACTTCACAGCAGGCGGTGATGATGAG                         CTGAGTTTAAACTCTGGAGAAGAAGTGGAGATTGAATACGAGGTCGATGGT
genomic: CTCAGTCTGGGAAAGCTTTGTATGACTTCACAGCAGGCGGTGATGATGAGgtacgcgggt ... gttttttcagCTGAGTTTAAACTCTGGAGAAGAAGTGGAGATTGAATACGAGGTCGATGGT

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: 47 (upstream exon), 49 (downstream exon)
Score: 208

AGGACGAAGTTTCGGATCCCACGAGGATGAAGATAAGAGTTCTGGTAACCCTCAGTCTGGGAAAGCTTTGTATGACTTCACAGCAGGCGGTGATGATGAGgtacgcgggt ... gttttttcagCTGAGTTTAAACTCTGGAGAAGAAGTGGAGATTGAATACGAGGTCGATGGTTGGTATTAT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 199

AGGACGAAGTTTCGGATCCCACGAGGATGAAGATAAGAGTTCTGGTAACCCTCAGTCTGGGAAAGCTTTGTATGACTTCACAGCAGGCGGTGATGATGAGgtacgcgggt ... gttttttcagCTGAGTTTAAACTCTGGAGAAGAAGTGGAGATTGAATACGAGGTCGATGGTTGGTATTAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 296

AGGACGAAGTTTCGGATCCCACGAGGATGAAGATAAGAGTTCTGGTAACCCTCAGTCTGGGAAAGCTTTGTATGACTTCACAGCAGGCGGTGATGATGAGgtacgcgggt ... gttttttcagCTGAGTTTAAACTCTGGAGAAGAAGTGGAGATTGAATACGAGGTCGATGGTTGGTATTAT


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 117

AGGACGAAGTTTCGGATCCCACGAGGATGAAGATAAGAGTTCTGGTAACCCTCAGTCTGGGAAAGCTTTGTATGACTTCACAGCAGGCGGTGATGATGAGgtacgcgggt ... gttttttcagCTGAGTTTAAACTCTGGAGAAGAAGTGGAGATTGAATACGAGGTCGATGGTTGGTATTAT