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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGGCTAGTTGGTTATGGACTTTCCAGGCTCTTCTATGCTGCTGGGACGGAAGATCTGGCTCTAGATTCACTGTCAAATTCAATGGGCCTATTTTTACAGgtatgtttattggtgtgaatgaatcaactgaaccattttttgcttcctgtgtgaaatggaatttctgttttgagattttgcattactaacaagtacttgtcatcaaattgcag

Basic information

species Zea mays
transcript GRMZM2G108225_T02
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G108225_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os03g59040.1 (Oryza sativa), 5'ss of exon 6
TGGGCTAGTTGGTTATGGACTTTCCAGGCTCTTCTATGCTGCTGGGACGGAAGATCTGGCTCTAGATTCACTGTCAAATTCAATGGGCCTATTTTTACAGgtatgtttattggtgtgaatgaatcaactgaaccattttttgcttcctgtgtgaaatggaatttctgttttgagattttgcattactaacaagtacttgtcatcaaattgcag
 |||||||| || ||||| ||||||||||||||  |||||| |||||||||||||||||||  ||||||||| ||||||||||||||| | ||| | ||||| | ||| ||| | |   |||||||  |        ||    || ||   ||   |       |  | |   || ||  || | |                           
AGGGCTAGTGGGGTATGGGCTTTCCAGGCTCTTTCATGCTGGTGGGACGGAAGATCTGGCTTCAGATTCACTTTCAAATTCAATGGGCTTGTTTCTGCAGgttt-tttgttgattttgttgaatcagttatgtgcacttacagtttctaattgttgttagtaaccaatatctggactt-acactgcag-------------------------
















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|61119737|gb|DN560698.1|DN560698
EST:     AAGATCTGGCTCTAGATTCACTGTCAAATTCAATGGGCCTATTTTTACAA                         AAAACTAACATAATTAGGGACTATTTGGAGGACATAAATGAGATACCAAAG
genomic: AAGATCTGGCTCTAGATTCACTGTCAAATTCAATGGGCCTATTTTTACAGgtatgtttat ... caaattgcagAAAACTAACATAATTAGGGACTATTTGGAGGACATAAATGAGATACCAAAG
EST: gi|148941371|gb|EC886282.2|EC886282
EST:     AAGATCTGGCTCTAGATTCACTGTCAAATTCAATGGGCCTATTTTTACAG                         AAAACTAACATAATTAGGGACTATTTGGAGGACATAAATGAGATACCCAAG
genomic: AAGATCTGGCTCTAGATTCACTGTCAAATTCAATGGGCCTATTTTTACAGgtatgtttat ... caaattgcagAAAACTAACATAATTAGGGACTATTTGGAGGACATAAATGAGATACCAAAG
EST: gi|85152394|gb|DW587719.1|DW587719
EST:     AAGATCTGGCTCTAGATTCACTGTCAAATTCAATGGGCCTATTTTTACAA                         AAAACTAACATAATTAGGGACTATTTGGAGGACATAAATGAGATACCAAAG
genomic: AAGATCTGGCTCTAGATTCACTGTCAAATTCAATGGGCCTATTTTTACAGgtatgtttat ... caaattgcagAAAACTAACATAATTAGGGACTATTTGGAGGACATAAATGAGATACCAAAG
EST: gi|148954555|gb|EC899993.2|EC899993
EST:     AAGATCTGGCTCTAGATTCACTGTCAAATTCAATGGGCCTATTTTTACAG                         AAAACTAACATAATTAGGGACTATTTGGAGGACATAAATGAGATACCAAAG
genomic: AAGATCTGGCTCTAGATTCACTGTCAAATTCAATGGGCCTATTTTTACAGgtatgtttat ... caaattgcagAAAACTAACATAATTAGGGACTATTTGGAGGACATAAATGAGATACCAAAG
EST: gi|149010292|gb|EE042121.2|EE042121
EST:     AAGATCTGGCTCTAGATTCACTGTCAAATTCAATGGGCCTATTTTTACAG                         AAAACTAACATAATTAGGGACTATTTGGAGGACATAAATGAGATACCAAAG
genomic: AAGATCTGGCTCTAGATTCACTGTCAAATTCAATGGGCCTATTTTTACAGgtatgtttat ... caaattgcagAAAACTAACATAATTAGGGACTATTTGGAGGACATAAATGAGATACCAAAG
EST: gi|9953064|gb|BE639647.1|BE639647
EST:     AAGATCTGGCTCTAGATTCATTGTCAAATTCAATGGGTCTATTTTTACAG                         AAAACTAACATAATTAGGGACTATTTGGAGGACATAAATGAGATACCAAAG
genomic: AAGATCTGGCTCTAGATTCACTGTCAAATTCAATGGGCCTATTTTTACAGgtatgtttat ... caaattgcagAAAACTAACATAATTAGGGACTATTTGGAGGACATAAATGAGATACCAAAG
EST: gi|148940819|gb|EC885646.2|EC885646
EST:     AAGATCTGGCTCTAGATTCACTGTCAAATTCAATGGGCCTATTTTTACAG                         AAAACTAACATAATTAGGGACTATTTGGAGGACATAAATGAGATACCAAAG
genomic: AAGATCTGGCTCTAGATTCACTGTCAAATTCAATGGGCCTATTTTTACAGgtatgtttat ... caaattgcagAAAACTAACATAATTAGGGACTATTTGGAGGACATAAATGAGATACCAAAG

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), 49 (downstream exon)
Score: 339

TGGGCTAGTTGGTTATGGACTTTCCAGGCTCTTCTATGCTGCTGGGACGGAAGATCTGGCTCTAGATTCACTGTCAAATTCAATGGGCCTATTTTTACAGgtatgtttat ... caaattgcagAAAACTAACATAATTAGGGACTATTTGGAGGACATAAATGAGATACCAAAGTCCCGCATGTTCTGGCCTCGAGAGATATGGAGTAAATATGCAGATAAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 151

TGGGCTAGTTGGTTATGGACTTTCCAGGCTCTTCTATGCTGCTGGGACGGAAGATCTGGCTCTAGATTCACTGTCAAATTCAATGGGCCTATTTTTACAGgtatgtttat ... caaattgcagAAAACTAACATAATTAGGGACTATTTGGAGGACATAAATGAGATACCAAAGTCCCGCATGTTCTGGCCTCGAGAGATATGGAGTAAATATGCAGATAAAC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 92

TGGGCTAGTTGGTTATGGACTTTCCAGGCTCTTCTATGCTGCTGGGACGGAAGATCTGGCTCTAGATTCACTGTCAAATTCAATGGGCCTATTTTTACAGgtatgtttat ... caaattgcagAAAACTAACATAATTAGGGACTATTTGGAGGACATAAATGAGATACCAAAGTCCCGCATGTTCTGGCCTCGAGAGATATGGAGTAAATATGCAGATAAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 248

TGGGCTAGTTGGTTATGGACTTTCCAGGCTCTTCTATGCTGCTGGGACGGAAGATCTGGCTCTAGATTCACTGTCAAATTCAATGGGCCTATTTTTACAGgtatgtttat ... caaattgcagAAAACTAACATAATTAGGGACTATTTGGAGGACATAAATGAGATACCAAAGTCCCGCATGTTCTGGCCTCGAGAGATATGGAGTAAATATGCAGATAAAC