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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACTACCTCAGGACGGTGGTTCCGTCACAACTCTTGGCAGAGCGCGGCTCCAATCTTGTCGTCATCAACCCAGgttcggccctgcagaaaccctagcactcccatgtccttggtccagttttttttctgggttctaatgcgccatttctcgcaatttttgaaacctaagttaa...

Basic information

species Zea mays
transcript GRMZM2G101250_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G101250_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os04g09860.1 (Oryza sativa), 5'ss of exon 2
GACTACCTCAGGACGGTGGTTCCGTCACAACTCTTGGCAGAGCGCGGCTCCAATCTTGTCGTCATCAACCCAGgttcggccctgcagaaaccctagcactcccatgtc--cttggtc--cagttttttttctgggttctaatgcgccatttctcgcaatttttgaaacctaagttaa
|| ||||||| |||||||||||| ||||| ||  |||| ||||||||| |||| || |||||||||||||||||| || |||| | ||||||||||| | |  || ||    |||||  |   |  | || ||||| ||| | ||      |  |   || |||| |   | |    
GATTACCTCAAGACGGTGGTTCCATCACAGCTGATGGCCGAGCGCGGCGCCAACCTCGTCGTCATCAACCCAGgtgcgcccctccggaaaccctagc-ccctgatatcaatctggtcatcccctcctcttttgggtgctatttcgtatggccaagtccttcttgagattcatgc---
















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|211065118|gb|FL021085.1|FL021085
EST:     GTCACAACTCTTGGCAGAGCGCGGCTCCAATCTTGTCGTCATCAACCCAG                         GATCGGGAAATGTGCGAATGGGGTTTGCTAGTCAGGATGTGCCATTCAATA
genomic: GTCACAACTCTTGGCAGAGCGCGGCTCCAATCTTGTCGTCATCAACCCAGgttcggccct ... tcttttatagGATCGGGAAATGTGCGAATGGGGTTTGCTAGTCAGGATGTGCCATTCAATA
EST: gi|211065127|gb|FL021094.1|FL021094
EST:     GTCACAACTCTTGGCAGAGCGCGGCTCCAATCTTGTCGTCATCAACCCAG                         GATCGGGAAATGTGCGAATGGGGTTTGCTAGTCAGGATGTGCCATTCAATA
genomic: GTCACAACTCTTGGCAGAGCGCGGCTCCAATCTTGTCGTCATCAACCCAGgttcggccct ... tcttttatagGATCGGGAAATGTGCGAATGGGGTTTGCTAGTCAGGATGTGCCATTCAATA
EST: gi|211065129|gb|FL021096.1|FL021096
EST:     GTCACAACTCTTGGCAGAGCGCGGCTCCNATCTTGTCGTCATCAACCCAG                         GATCGGGAAATGTGCGAATGGGGTTTGCTAGTCAGGATGTGCCATTCAATA
genomic: GTCACAACTCTTGGCAGAGCGCGGCTCCAATCTTGTCGTCATCAACCCAGgttcggccct ... tcttttatagGATCGGGAAATGTGCGAATGGGGTTTGCTAGTCAGGATGTGCCATTCAATA
EST: gi|211065122|gb|FL021089.1|FL021089
EST:     GTCACAACTCTTGGCAGAGCGCGGCTCCAATCTTGTCGTCATCAACCCAG                         GATCGGGAAATGTGCGAATGGGGTTTGCTAGTCAGGATGTGCCATTCAATA
genomic: GTCACAACTCTTGGCAGAGCGCGGCTCCAATCTTGTCGTCATCAACCCAGgttcggccct ... tcttttatagGATCGGGAAATGTGCGAATGGGGTTTGCTAGTCAGGATGTGCCATTCAATA
EST: gi|211067851|gb|FL021097.1|FL021097
EST:     GTCACAACTCTTGGCAGAGCGCGGCTCCAATCTTGTCGTCATCAACCCAG                         GATCGGGAAATGTGCGAATGGGGTTTGCTAGTCAGGATGTGCCATTCAATA
genomic: GTCACAACTCTTGGCAGAGCGCGGCTCCAATCTTGTCGTCATCAACCCAGgttcggccct ... tcttttatagGATCGGGAAATGTGCGAATGGGGTTTGCTAGTCAGGATGTGCCATTCAATA
EST: gi|211065128|gb|FL021095.1|FL021095
EST:     GTCACAACTCTTGGCAGAGCGCGGCTCCAATCTTGTCGTCATCAACCCAG                         GATCGGGAAATGTGCGAATGGGGTTTGCTAGTCAGGATGTGCCATTCAATA
genomic: GTCACAACTCTTGGCAGAGCGCGGCTCCAATCTTGTCGTCATCAACCCAGgttcggccct ... tcttttatagGATCGGGAAATGTGCGAATGGGGTTTGCTAGTCAGGATGTGCCATTCAATA
EST: gi|211065119|gb|FL021086.1|FL021086
EST:     GTCACAACTCTTGGCAGAGCGCGGCTCCAATCTTGTCGTCATCAACCCAG                         GATCGGGAAATGTGCGAATGGGGTTTGCTAGTCAGGATGTGCCATTCAATA
genomic: GTCACAACTCTTGGCAGAGCGCGGCTCCAATCTTGTCGTCATCAACCCAGgttcggccct ... tcttttatagGATCGGGAAATGTGCGAATGGGGTTTGCTAGTCAGGATGTGCCATTCAATA
EST: gi|91056341|gb|EB166759.1|EB166759
EST:     GTCACAACTCTTGGCAGAGCGCGGCTCCAATCTTGTCGTCATCAACCCAG                         GATCGGGAAATGTGCGAATGGGGTTTGCTAGTCAGGATGTGCCATTCAATA
genomic: GTCACAACTCTTGGCAGAGCGCGGCTCCAATCTTGTCGTCATCAACCCAGgttcggccct ... tcttttatagGATCGGGAAATGTGCGAATGGGGTTTGCTAGTCAGGATGTGCCATTCAATA
EST: gi|211065125|gb|FL021092.1|FL021092
EST:     GTCACAACTCTTGGCAGAGCGCGGCTCCAATCTTGTCGTCATCAACCCAG                         GATCGGGAAATGTGCGAATGGGGTTTGCTAGTCAGGATGTGCCATTCAATA
genomic: GTCACAACTCTTGGCAGAGCGCGGCTCCAATCTTGTCGTCATCAACCCAGgttcggccct ... tcttttatagGATCGGGAAATGTGCGAATGGGGTTTGCTAGTCAGGATGTGCCATTCAATA
EST: gi|148934269|gb|EC878292.2|EC878292
EST:     GTCACAACTCTTGGCAGAGCGCGGCTCCAATCTTGTCGTCATCAACCCAG                         GATCGGGAAATGTGCGAATGGGGTTTGCTAGTCAGGATGTGCCATTCAATA
genomic: GTCACAACTCTTGGCAGAGCGCGGCTCCAATCTTGTCGTCATCAACCCAGgttcggccct ... tcttttatagGATCGGGAAATGTGCGAATGGGGTTTGCTAGTCAGGATGTGCCATTCAATA

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 1 RNA-Seqlibrary.


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 2

GACTACCTCAGGACGGTGGTTCCGTCACAACTCTTGGCAGAGCGCGGCTCCAATCTTGTCGTCATCAACCCAGgttcggccct ... tcttttatagGATCGGGAAATGTGCGAATGGGGTTTGCTAGTCAGGATGTGCCATTCAATATACCACATTGCATTGCCCGACACATCAATCCACAAGAGGGCGAAGAACC




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