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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGCGCGGCGTCGTTGGCCGTGCGGTTCGCCAACAACGGCCACCCGACCCTCGTCGTCTCCACCGACCCTGCGCACTCGCTCAGCGATTCCTTCGCACAGgtcgctcatcccgttgaatgcctctgcttttgagacatgcttgattctctagaataacttgttactgtattacttaactgcttcattttgctacctcggcgtttcag

Basic information

species Zea mays
transcript GRMZM2G105539_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G105539_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os02g51100.1 (Oryza sativa), 5'ss of exon 1
CTGCGCGGCGTCGTTGGCCGTGCGGTTCGCCAACAACGGCCACCCGACCCTCGTCGTCTCCACCGACCCTGCGCACTCGCTCAGCGATTCCTTCGCACAGgtcgctcatcccgttgaatgcctctgcttttgagacatgcttgattctctagaataacttgttactgtattacttaactgcttcattttgctacctcggcgtttcag
||||||||||||| |||||||||| |||||||||||||| ||||| ||||||||||||||||||||||| |||||||| |||||||| |||||||| ||||||||    ||||| ||   |||  ||| |         || | |||       |  |||||    ||| | | || ||        || || |||   | ||| ||
CTGCGCGGCGTCGCTGGCCGTGCGCTTCGCCAACAACGGGCACCCCACCCTCGTCGTCTCCACCGACCCCGCGCACTCCCTCAGCGACTCCTTCGCGCAGgtcgcctcccccgtcgagcacct--gctgt---------ctcggttc---gaggtttcttgtgtgcgtactgcgtagctaacatcacttcctgcctactcattttag
















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|148958813|gb|EC905077.2|EC905077
EST:     TCGTCGTCTCCACCGACCCTGCGCACTCGCTCAGCGATTCCTTCGCACAG                         GATTTGAGTGGCGGGACGCTCGTGCAGGTCGAGGGCCCTGATTCACCTCTG
genomic: TCGTCGTCTCCACCGACCCTGCGCACTCGCTCAGCGATTCCTTCGCACAGgtcgctcatc ... ggcgtttcagGATTTGAGTGGCGGGACGCTCGTGCAGGTCGAGGGCCCTGATTCACCTCTG
EST: gi|211515140|gb|FL351614.1|FL351614
EST:     TCGTCGTCTCCACCGANCCTGCGCACTCGCTCAGCGATTCCTTCGCACAG                         GATTTGAGTGGCGGGAC
genomic: TCGTCGTCTCCACCGACCCTGCGCACTCGCTCAGCGATTCCTTCGCACAGgtcgctcatc ... ggcgtttcagGATTTGAGTGGCGGGAC
EST: gi|211378591|gb|FL355184.1|FL355184
EST:     TCGTCGTCTCCACCGACCCTGCGCACTCGCTCAGCGATTCCTTCGCACAG                         GATTTGAGTGGCGGGACGCTCGTGCAGGTCG
genomic: TCGTCGTCTCCACCGACCCTGCGCACTCGCTCAGCGATTCCTTCGCACAGgtcgctcatc ... ggcgtttcagGATTTGAGTGGCGGGACGCTCGTGCAGGTCG
EST: gi|148962847|gb|EE013769.2|EE013769
EST:     TCGTCGTCTCCACCGACCCTGCGCACTCGCTCAGCGATTCCTTCGCACAG                         GATTTGAGTGGCGGGACGCTCGTGCAGGTCGAGGGCCCTGATTCACCTCTG
genomic: TCGTCGTCTCCACCGACCCTGCGCACTCGCTCAGCGATTCCTTCGCACAGgtcgctcatc ... ggcgtttcagGATTTGAGTGGCGGGACGCTCGTGCAGGTCGAGGGCCCTGATTCACCTCTG
EST: gi|211263383|gb|FL364886.1|FL364886
EST:     TCGTCGTCTCCACCGACCCTGCGCACTCGCTCAGCGATTCCTTCGCACAG                         GATTTGAGTGGCGGGA
genomic: TCGTCGTCTCCACCGACCCTGCGCACTCGCTCAGCGATTCCTTCGCACAGgtcgctcatc ... ggcgtttcagGATTTGAGTGGCGGGA
EST: gi|211308753|gb|FL367414.1|FL367414
EST:     TCGTCGTCTCCACYGACCCTGCGCACTCGCTCAGCGATTCCTTCGCACAG                         GATTTGAGTGGCGGGACGCTCGTGCAGGTCGAGGGCCCTGATTCA
genomic: TCGTCGTCTCCACCGACCCTGCGCACTCGCTCAGCGATTCCTTCGCACAGgtcgctcatc ... ggcgtttcagGATTTGAGTGGCGGGACGCTCGTGCAGGTCGAGGGCCCTGATTCA

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: 46 (upstream exon), 46 (downstream exon)
Score: 74

CTGCGCGGCGTCGTTGGCCGTGCGGTTCGCCAACAACGGCCACCCGACCCTCGTCGTCTCCACCGACCCTGCGCACTCGCTCAGCGATTCCTTCGCACAGgtcgctcatc ... ggcgtttcagGATTTGAGTGGCGGGACGCTCGTGCAGGTCGAGGGCCCTGATTCACCTCTGTTTGCGCTTGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 156

CTGCGCGGCGTCGTTGGCCGTGCGGTTCGCCAACAACGGCCACCCGACCCTCGTCGTCTCCACCGACCCTGCGCACTCGCTCAGCGATTCCTTCGCACAGgtcgctcatc ... ggcgtttcagGATTTGAGTGGCGGGACGCTCGTGCAGGTCGAGGGCCCTGATTCACCTCTGTTTGCGCTTGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 90

CTGCGCGGCGTCGTTGGCCGTGCGGTTCGCCAACAACGGCCACCCGACCCTCGTCGTCTCCACCGACCCTGCGCACTCGCTCAGCGATTCCTTCGCACAGgtcgctcatc ... ggcgtttcagGATTTGAGTGGCGGGACGCTCGTGCAGGTCGAGGGCCCTGATTCACCTCTGTTTGCGCTTGAG


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 65

CTGCGCGGCGTCGTTGGCCGTGCGGTTCGCCAACAACGGCCACCCGACCCTCGTCGTCTCCACCGACCCTGCGCACTCGCTCAGCGATTCCTTCGCACAGgtcgctcatc ... ggcgtttcagGATTTGAGTGGCGGGACGCTCGTGCAGGTCGAGGGCCCTGATTCACCTCTGTTTGCGCTTGAG