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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCTCCGTGTCTTGACCAACTTCCAACAGATTGAATCATTCTCTGCTTTCAATAGCGTCTATAACAATTCGGGCCTTTTTGGAATTTATGCAGTCACTgtaagcttctctcctggagcatcctttttattaaaacctcatgccttttcagggcacgtccgtgtttcacgtcatttagcatagctccggaccctgacgc...

Basic information

species Zea mays
transcript GRMZM2G005036_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G005036_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os05g44916.1 (Oryza sativa), 5'ss of exon 8
ATCTCCGTGTCTTGACCAACTTCCAACAGATTGAATCATTCTCTGCTTTCAATAGCGTCTATAACAATTCGGGCCTTTTTGGAATTTATGCAGTCACTgtaagcttctctcctggagcatcctttttattaaaacctcatgccttt--tcagggcacgtccgtgtttcacgtcatttagcatagctccggaccctgacgc--
||||||||||||||| ||| |    |||||| |||||||||||||||||||  ||  | || |||||||| ||||||||||||||  |||||  |||||||||  |||||  ||||||||      |  ||     ||    || |  ||| |  | |  |  |  |||  ||   | |   |  ||    || |       
ATCTCCGTGTCTTGAACAATTATGGACAGATCGAATCATTCTCTGCTTTCAGCAGTATTTACAACAATTCTGGCCTTTTTGGAATACATGCAACCACTgtaag--tctcttttggagcataaccaatgatatgttttcccttctatattcaagcaatgaaca-gaatcaaatctgcttgtg-aattctttcccttttttttt
















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|40333865|gb|CK367935.1|CK367935
EST:     TCAATAGCGTCTATAACAATTCGGGCCTTTTTGGAATTTATGCAGTCACT                         AGCCCAGACTTTTCATCGAAGGCTGTGGATTTGGCAGCAGGGGAACTCCTG
genomic: TCAATAGCGTCTATAACAATTCGGGCCTTTTTGGAATTTATGCAGTCACTgtaagcttct ... cattcaacagAGCCCAGACTTTTCATCGAAGGCTGTGGATTTGGCAGCAGGGGAACTCCTG
EST: gi|89758987|gb|DY687957.1|DY687957
EST:     TCAATAGCGTCTATAACAATTCGGGCCTTTTTGGAATTTATGCAGTCACT                         AGCCCAGACTTTTCATCGAAGGCTGTGGATTTGGCAGCAGGGGAACTCCTG
genomic: TCAATAGCGTCTATAACAATTCGGGCCTTTTTGGAATTTATGCAGTCACTgtaagcttct ... cattcaacagAGCCCAGACTTTTCATCGAAGGCTGTGGATTTGGCAGCAGGGGAACTCCTG
EST: gi|71438038|gb|DR819088.1|DR819088
EST:     TCAATAGCGTCTATAACAATTCGGGCCTTTTTGGAATTTATGCAGTCACT                         AGCCCAGACTTTTCATCGAAGGCTGTGGATTTGGCAGCAGGGGAACTCCTG
genomic: TCAATAGCGTCTATAACAATTCGGGCCTTTTTGGAATTTATGCAGTCACTgtaagcttct ... cattcaacagAGCCCAGACTTTTCATCGAAGGCTGTGGATTTGGCAGCAGGGGAACTCCTG
EST: gi|32863948|gb|CF003630.1|CF003630
EST:     TCAATAGCGTCTATAACAATTCGGGCCTTTTTGGAATCTATGCAGTCACT                         AGCCCAGACTTTTCATCGAAGGCTGTGGATTTGGCAGCAGGGGAACTCCTG
genomic: TCAATAGCGTCTATAACAATTCGGGCCTTTTTGGAATTTATGCAGTCACTgtaagcttct ... cattcaacagAGCCCAGACTTTTCATCGAAGGCTGTGGATTTGGCAGCAGGGGAACTCCTG
EST: gi|40336960|gb|CK371030.1|CK371030
EST:     TCAATAGCGTCTATAACAATTCGGGCCTTTTTGGAATTTATGCAGTCACT                         AGCCCAGACTTTTCATCGAAGGCTGTGGATTTGGCAGCAGGGGAACTCCTG
genomic: TCAATAGCGTCTATAACAATTCGGGCCTTTTTGGAATTTATGCAGTCACTgtaagcttct ... cattcaacagAGCCCAGACTTTTCATCGAAGGCTGTGGATTTGGCAGCAGGGGAACTCCTG
EST: gi|211246196|gb|FL443898.1|FL443898
EST:     TCAATAGCGTCTATAACAATTCGGGCCTTTTTGGAATTTATGCAGTCACT                         AGCCCAGACTTTTCATCGAAGGCTGTGGATTTGGCAGCAGGGGAACTCCTG
genomic: TCAATAGCGTCTATAACAATTCGGGCCTTTTTGGAATTTATGCAGTCACTgtaagcttct ... cattcaacagAGCCCAGACTTTTCATCGAAGGCTGTGGATTTGGCAGCAGGGGAACTCCTG

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), 46 (downstream exon)
Score: 281

ATCTCCGTGTCTTGACCAACTTCCAACAGATTGAATCATTCTCTGCTTTCAATAGCGTCTATAACAATTCGGGCCTTTTTGGAATTTATGCAGTCACTgtaagcttct ... cattcaacagAGCCCAGACTTTTCATCGAAGGCTGTGGATTTGGCAGCAGGGGAACTCCTGGAGATTGCGACACCTGGAAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 288

ATCTCCGTGTCTTGACCAACTTCCAACAGATTGAATCATTCTCTGCTTTCAATAGCGTCTATAACAATTCGGGCCTTTTTGGAATTTATGCAGTCACTgtaagcttct ... cattcaacagAGCCCAGACTTTTCATCGAAGGCTGTGGATTTGGCAGCAGGGGAACTCCTGGAGATTGCGACACCTGGAAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 258

ATCTCCGTGTCTTGACCAACTTCCAACAGATTGAATCATTCTCTGCTTTCAATAGCGTCTATAACAATTCGGGCCTTTTTGGAATTTATGCAGTCACTgtaagcttct ... cattcaacagAGCCCAGACTTTTCATCGAAGGCTGTGGATTTGGCAGCAGGGGAACTCCTGGAGATTGCGACACCTGGAAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 315

ATCTCCGTGTCTTGACCAACTTCCAACAGATTGAATCATTCTCTGCTTTCAATAGCGTCTATAACAATTCGGGCCTTTTTGGAATTTATGCAGTCACTgtaagcttct ... cattcaacagAGCCCAGACTTTTCATCGAAGGCTGTGGATTTGGCAGCAGGGGAACTCCTGGAGATTGCGACACCTGGAAAAG