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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgttctcctttcctctcccctcgctctgcctccctctaaccgatttaagtggttgctgattggttggttgactgattgatctggtttgtttcgtgtgttcacagGGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATG

Basic information

species Zea mays
transcript GRMZM5G818887_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G818887_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os10g41110.1 (Oryza sativa), 3'ss of exon 1
----gtgcgttctcctttcctctcccctcgctctgcctccctctaaccgatttaagtggttgctgattggttggttgactgattgatctggtttgtttcgtgtgttcacagGGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATG
    |    |||||| || ||| |||  | || |         || ||||||   |||| |   | | ||  |  |||  |||     ||| | ||||| ||||    |||||| ||||||||||| |||||||||||||||||||||||  || | ||||| |||||||||||| | || |
gtaggcctcttctccgttgctccccctcctctgtagggtttggtacccgattgctgtgggtttgggtggggcgtctgatcgatctcggtgggt-gtttcctgtg----cagGGAGGCGGGCGATCCGAGCAAGAGGAAGCCGTATCTCCCTCCCGACAAGCAATTCCTCGTCACCAGGAACG

upper sequence: GRMZM5G818887_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g10290.2 (Oryza sativa), 3'ss of exon 1
gtgcgttctcctttcctctcccctcgctctgcctccctctaaccgatttaagtggttgctgattggttggttgactgattgatctggtttgtttcgtgtgttcacagGGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATG
          || ||  |||||||| |  |||  |||   ||  | |     ||| |   | || |   |  | || || ||||          | |||||    ||||| ||||||||||| |||||||||||||||||||||||  |  | ||||| || ||||||||| | || |
------gtagctctctcctcccctc-cgttgctccccctcaattgctgggtttgggtttgggtttgggtggcgtctcatcgatcc--------ccctgtgt----agGGAGGCGGGCGATCCGAGCAAGAGGAAGCCGTATCTCCCACCTGACAAGCAATTTCTCGTCACCAGGAACG
















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|211324982|gb|FL012751.1|FL012751
EST:     TTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTG                         GGAAGCGGGCGATCCA
genomic: TTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTGgtgcgttctc ... gtgttcacagGGAAGCGGGCGATCCA
EST: gi|148960724|gb|EE011368.2|EE011368
EST:     TTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTG                         GGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCA
genomic: TTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTGgtgcgttctc ... gtgttcacagGGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCA
EST: gi|211324984|gb|FL012753.1|FL012753
EST:     TTCAT-CTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTG                         GGAAGCGGGCGATCCAAGCAAGANGAAGCCGTATCTCCCCGCCAA
genomic: TTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTGgtgcgttctc ... gtgttcacagGGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAA
EST: gi|78091451|gb|DV519825.1|DV519825
EST:     TTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTG                         GGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCA
genomic: TTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTGgtgcgttctc ... gtgttcacagGGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCA
EST: gi|149045355|gb|EE047779.2|EE047779
EST:     TTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTG                         GGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCA
genomic: TTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTGgtgcgttctc ... gtgttcacagGGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCA
EST: gi|76013821|gb|DT940991.1|DT940991
EST:     TTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTG                         GGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCA
genomic: TTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTGgtgcgttctc ... gtgttcacagGGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCA
EST: gi|71313249|gb|DR793148.1|DR793148
EST:     TTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTG                         GGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCA
genomic: TTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTGgtgcgttctc ... gtgttcacagGGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCA
EST: gi|87156323|gb|DY401112.1|DY401112
EST:     TTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTG                         GGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCA
genomic: TTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTGgtgcgttctc ... gtgttcacagGGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCA
EST: gi|211324976|gb|FL012745.1|FL012745
EST:     TTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTG                         GGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCA
genomic: TTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTGgtgcgttctc ... gtgttcacagGGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCA
EST: gi|78113031|gb|DV531425.1|DV531425
EST:     TTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTG                         GGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCA
genomic: TTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTGgtgcgttctc ... gtgttcacagGGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCA
EST: gi|76016277|gb|DT943447.1|DT943447
EST:     TTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTG                         GGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCA
genomic: TTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTGgtgcgttctc ... gtgttcacagGGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCA

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: 174

CGCGCACCGTCTCCGCGTTCCTCGAGAAGGGCGTCCTCTCCGTCCCCGAGTTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTGgtgcgttctc ... gtgttcacagGGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 345

CGCGCACCGTCTCCGCGTTCCTCGAGAAGGGCGTCCTCTCCGTCCCCGAGTTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTGgtgcgttctc ... gtgttcacagGGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 242

CGCGCACCGTCTCCGCGTTCCTCGAGAAGGGCGTCCTCTCCGTCCCCGAGTTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTGgtgcgttctc ... gtgttcacagGGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 233

CGCGCACCGTCTCCGCGTTCCTCGAGAAGGGCGTCCTCTCCGTCCCCGAGTTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTGgtgcgttctc ... gtgttcacagGGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggttgctgattggttggttgactgattgatctggtttgtttcgtgtgttcacagGGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATG
                                   tttgttt  TA-rich tract