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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCGGAAGTTCTTCATATACGTGCAGGACTACGAGGAGGACGACCCCAAGTCCCACGAGGGCCTGGACCTCAACAAGGTCACCACCAGGGAAGTCATCTCgtgagtcgtcgtcgcgcgctctttgatttcatttcacccagctgtgctgcggtttcagttgctagactagaatgtttgttgttgtcttggacgatcgatcgagcag

Basic information

species Zea mays
transcript GRMZM2G084440_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G084440_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os03g16900.1 (Oryza sativa), 5'ss of exon 5
CCCGGAAGTTCTTCATATACGTGCAGGACTACGAGGAGGACGACCCCAAGTCCCACGAGGGCCTGGACCTCAACAAGGTCACCACCAGGGAAGTCATCTCgtgagtcgtc---gtcgcgcgctctttgatttcatttcacccagctgtgctgcggtttcagttgctagactagaatgtttgttgttgtcttggacgatcgatcgagcag
|  |||| |||||||||||||||||||| ||||| ||||| || || ||||| ||||| |||||||| ||  |||||||||| || || ||||||||||||| ||| | |   || ||   || ||      ||    ||  || |||  |  |    || ||  ||  |  |  | | || ||||  ||||   |             
CTAGGAAATTCTTCATATACGTGCAGGATTACGAAGAGGATGATCCAAAGTCACACGAAGGCCTGGATCTGCACAAGGTCACGACGAGAGAAGTCATCTCgtaagttgactaagttgctgactgttaacaaacagaaaaca-agttgtattttgccaccatttcttatgcaggcgt-tatgatgtttgcttgtcag-------------
















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|78119657|gb|DV538041.1|DV538041
EST:     TCCCACGAGGGCCTGGACCTCAACAAGGTCACCACCAGGGAAGTCATCTC                         CAAATACGGATTGGAGGATGATACGGTCGACTTTATCGGGCATGCGCTAGC
genomic: TCCCACGAGGGCCTGGACCTCAACAAGGTCACCACCAGGGAAGTCATCTCgtgagtcgtc ... gatcgagcagCAAATACGGATTGGAGGATGATACGGTCGACTTTATCGGGCATGCGCTAGC
EST: gi|78108949|gb|DV527366.1|DV527366
EST:     TCCCACGAGGGCCTGGACCTCAACAAGGTCACCACCAGGGAAGTCATCTC                         CAAATACGGATTGGAGGATGATACGGTCGACTTTATCGGGCATGCGCTAGC
genomic: TCCCACGAGGGCCTGGACCTCAACAAGGTCACCACCAGGGAAGTCATCTCgtgagtcgtc ... gatcgagcagCAAATACGGATTGGAGGATGATACGGTCGACTTTATCGGGCATGCGCTAGC
EST: gi|211267087|gb|FL311760.1|FL311760
EST:     TCCCACGAGGGCCTGGACCTCAACAAGGTCACCACCAGGGAAGTCATCTC                         CAAATACGGATTGGAGGACGATACGGTCGACTTTATC
genomic: TCCCACGAGGGCCTGGACCTCAACAAGGTCACCACCAGGGAAGTCATCTCgtgagtcgtc ... gatcgagcagCAAATACGGATTGGAGGATGATACGGTCGACTTTATC
EST: gi|6827020|gb|AW330663.1|AW330663
EST:     TCCCACGAGGGCCTGGACCTGAACAAGGTCACCACCAGGGAAGTCATCTC                         CAAATACGGATTGGAGGATGATACGGTGGACTTTATCGGGCATGCGCTAGC
genomic: TCCCACGAGGGCCTGGACCTCAACAAGGTCACCACCAGGGAAGTCATCTCgtgagtcgtc ... gatcgagcagCAAATACGGATTGGAGGATGATACGGTCGACTTTATCGGGCATGCGCTAGC
EST: gi|50324747|gb|CO519873.1|CO519873
EST:     TCCCACGAGGGCCTGGACCTCAACAAGGTCACCACCAGGGAAGTCATCTC                         CAAATACGGATTGGAGGATGATACGGTCGACTTTATCGGGCATGCGCTAGC
genomic: TCCCACGAGGGCCTGGACCTCAACAAGGTCACCACCAGGGAAGTCATCTCgtgagtcgtc ... gatcgagcagCAAATACGGATTGGAGGATGATACGGTCGACTTTATCGGGCATGCGCTAGC
EST: gi|211349904|gb|FL349175.1|FL349175
EST:     TCCCACGAGGGCCTGGACCTCAACAAGGTCACCACNAGGGAAGTCATCTC                         CAAATACGGATTGGAGGACGATACGGTCGACTTTATCGGGCATGCGCTAGC
genomic: TCCCACGAGGGCCTGGACCTCAACAAGGTCACCACCAGGGAAGTCATCTCgtgagtcgtc ... gatcgagcagCAAATACGGATTGGAGGATGATACGGTCGACTTTATCGGGCATGCGCTAGC
EST: gi|78179007|gb|DV549380.1|DV549380
EST:     TCCCACGAGGGCCTGGACCTGAACAAGGTCACCACCAGGGAAGTCATCTC                         CAAATACGGATTGGAGGATGATACGGTGGACTTTATCGGGCATGCGCTAGC
genomic: TCCCACGAGGGCCTGGACCTCAACAAGGTCACCACCAGGGAAGTCATCTCgtgagtcgtc ... gatcgagcagCAAATACGGATTGGAGGATGATACGGTCGACTTTATCGGGCATGCGCTAGC
EST: gi|78093304|gb|DV521678.1|DV521678
EST:     TCCCACGAGGGCCTGGACCTCAACAAGGTCACCACCAGGGAAGTCATCTC                         CAAATACGGATTGGAGGATGATACGGTCGACTTTATCGGGCATGCGCTAGC
genomic: TCCCACGAGGGCCTGGACCTCAACAAGGTCACCACCAGGGAAGTCATCTCgtgagtcgtc ... gatcgagcagCAAATACGGATTGGAGGATGATACGGTCGACTTTATCGGGCATGCGCTAGC

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), 49 (downstream exon)
Score: 236

CCCGGAAGTTCTTCATATACGTGCAGGACTACGAGGAGGACGACCCCAAGTCCCACGAGGGCCTGGACCTCAACAAGGTCACCACCAGGGAAGTCATCTCgtgagtcgtc ... gatcgagcagCAAATACGGATTGGAGGATGATACGGTCGACTTTATCGGGCATGCGCTAGCACTTCACCGGGACGACAGCTACCTTGACGAGCCTGCAATCGACACTGTC




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