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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTAGGACTTGACCAACGGGAACATGATGATCCTACCCCATACTTATTGGCCATATGGACACCAGgcaagctcatttctctttgagtgcatggggtacacatgcaagttcatttttactaatttatgactactttgcag

Basic information

species Zea mays
transcript GRMZM2G131756_T01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G131756_T01 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os05g37350.1 (Oryza sativa), 5'ss of exon 15
CTAGGACTTGACCAACGGGAACATGATGATCCTACCCCATACTTATTGGCCATATGGACACCAGgcaagctcatttctctttgagtgcatg---gggtacacatgcaagttcatttttactaatttatg--actactttgcag
|||| ||| ||||||||||| | ||||||||| |  || ||| | ||||||||||||||||||||||||  ||||| ||||| | |  ||    |        ||   | |  ||||     | | |||   ||||| |||||
CTAGCACTCGACCAACGGGAGCCTGATGATCCAAgtccttacctgttggccatatggacaccaggcaagtgcatttttctttaaatttataactgtccgtgtgtgtgtgctggttttcgtcgagtcatgtggctactgtgcag
















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|32945243|gb|CF050062.1|CF050062
EST:     ACGGGAACATGATGATCCTACCCCATACTTATTGGCCATATGGACACCAG                         AAAAAATAAAGGAAATAACTAAGACACCAAAACTATGCTGTGACCCTCAAA
genomic: ACGGGAACATGATGATCCTACCCCATACTTATTGGCCATATGGACACCAGgcaagctcat ... tactttgcagATGGAATAAAGGAAATAACTAAGACACCAAAACCATGCTGTGACCCTCAAA
EST: gi|211540330|gb|FL320588.1|FL320588
EST:     ACGGGAACATGATGATCCTACCCCATACTTATTGGCCATATGGACACCAG                         ATGGAATAAAGGAAATAACTAAGACACCAAAACCATGCTGTGACCCTCAAA
genomic: ACGGGAACATGATGATCCTACCCCATACTTATTGGCCATATGGACACCAGgcaagctcat ... tactttgcagATGGAATAAAGGAAATAACTAAGACACCAAAACCATGCTGTGACCCTCAAA
EST: gi|60339031|gb|DN206004.1|DN206004
EST:     ACGGGAACATGATGATCCTACCCCATACTTATTGGCCATATGGACACCAG                         ATGGAATAAAGGAAATAACTAAGACACCAAAACCATGCTGTGACCCTCAAA
genomic: ACGGGAACATGATGATCCTACCCCATACTTATTGGCCATATGGACACCAGgcaagctcat ... tactttgcagATGGAATAAAGGAAATAACTAAGACACCAAAACCATGCTGTGACCCTCAAA
EST: gi|5901234|gb|AW042334.1|AW042334
EST:     ACGGGAACATGATGATCCTACCCCATACTTATTGGCCATATGGACACCAG                         ATGGAATAAAGGAAATAACTAAGACACCAAAACCATGCTGTGACCCTCAAA
genomic: ACGGGAACATGATGATCCTACCCCATACTTATTGGCCATATGGACACCAGgcaagctcat ... tactttgcagATGGAATAAAGGAAATAACTAAGACACCAAAACCATGCTGTGACCCTCAAA

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), 48 (downstream exon)
Score: 294

CTAGGACTTGACCAACGGGAACATGATGATCCTACCCCATACTTATTGGCCATATGGACACCAGgcaagctcat ... tactttgcagATGGAATAAAGGAAATAACTAAGACACCAAAACCATGCTGTGACCCTCAAATGGGAGGCGATTTATGCAATAATGAAATGTGCCACAATTGTACTGCAGA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 29

CTAGGACTTGACCAACGGGAACATGATGATCCTACCCCATACTTATTGGCCATATGGACACCAGgcaagctcat ... tactttgcagATGGAATAAAGGAAATAACTAAGACACCAAAACCATGCTGTGACCCTCAAATGGGAGGCGATTTATGCAATAATGAAATGTGCCACAATTGTACTGCAGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 34

CTAGGACTTGACCAACGGGAACATGATGATCCTACCCCATACTTATTGGCCATATGGACACCAGgcaagctcat ... tactttgcagATGGAATAAAGGAAATAACTAAGACACCAAAACCATGCTGTGACCCTCAAATGGGAGGCGATTTATGCAATAATGAAATGTGCCACAATTGTACTGCAGA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 45

CTAGGACTTGACCAACGGGAACATGATGATCCTACCCCATACTTATTGGCCATATGGACACCAGgcaagctcat ... tactttgcagATGGAATAAAGGAAATAACTAAGACACCAAAACCATGCTGTGACCCTCAAATGGGAGGCGATTTATGCAATAATGAAATGTGCCACAATTGTACTGCAGA