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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGAAGATCTAAATGGTTGTGCTTTTGTGTATGGCTCATTAAGTTTTGTTGACAAAGTTTCATGTGGAATAGCTCTCTATGTTCTCGAGTCCTATCAAGgtaatgactgtcagctatcttagtactggcacatcatcataagcaaaattaaccttgtaatcttccggtaaaaagttttgatgagattgggatctgacatgcatggcag

Basic information

species Zea mays
transcript GRMZM2G121458_T01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G121458_T01 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os07g39010.2 (Oryza sativa), 5'ss of exon 12
GGAGAAGATCTAAATGGTTGTGCTTTTGTGTATGGCTCATTAAGTTTTGTTGACAAAGTTTCATGTGGAATAGCTCTCTATGTTCTCGAGTCCTATCAAGgtaatgactgtca--gctatcttagtactggcacatcatcataagcaaaattaaccttgtaatcttccggtaaaaagttttgatgagattgggatctgacatgcatggcag
|| |||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||| ||| ||||||| ||| |||| |||||||||||||||||||||||| |    |||| | | ||||  ||||||     |  ||| ||    | ||| | || | |||     |  ||| ||| |||  |  |    ||||||||||
GGTGAAGATCTAAATGGTTGTGCTTTTGTGTATGGCTCATTAAGTTTTGTTGACAAAGTGTCATGCGGACTAGCTCTGTATATTCTTGAGTCCTATCAAGgtaatgactgttactattatcatggcactgatacatca-----aaaaaatttgggatggtacttttacagta-----tgctga-gagtttgaaactt----tgcatggcag

upper sequence: GRMZM2G121458_T01 (Zea mays), 5'ss of exon 12
lower sequence: Vv13s0156g00080.t01 (Vitis vinifera), 5'ss of exon 13
GGAGAAGATCTAAATGGTTGTGCTTTTGTGTATGGCTCATTAAGTTTTGTTGACAAAGTTTCATGTGGAATAGCTCTCTATGTTCTCGAGTCCTATCAAGgtaa--tgact-gtcagctatctt--agtactggcacatcatcataagcaaaattaaccttgtaatcttccggtaaaaagttttgatgagattgggatctgacatgcatggcag
|| ||||||||  |||| ||||| ||||| ||||||||||| |||||  | |||||| ||||||||||  ||||  | |  ||||| ||||| |||  | ||||   ||   |  ||  ||| |  | | ||     ||||   | | || | |  ||||   || |  ||  |  || | ||  |  | ||  | ||    |||         
GGTGAAGATCTCCATGGCTGTGCATTTGTTTATGGCTCATTGAGTTTCTTGGACAAAATTTCATGTGGGCTAGCCTTGTTCGTTCTTGAGTCATATGGAAgtaagtcgataagctagtcatccttcaatgctttt-tatcagtgtcaccagactagaccta--aagcagcccttgcaaggctt--actacatgagtatgacccat---------
















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|88746971|gb|DY531112.1|DY531112
EST:     TGACAAAGTTTCATGTGGAATAGCTCTCTATGTTCTCGAGTCCTATCAAG                         GAAGTACAAAGATCAGATCAAATTTAGGAACAACATCTGGCTATTCAGTTA
genomic: TGACAAAGTTTCATGTGGAATAGCTCTCTATGTTCTCGAGTCCTATCAAGgtaatgactg ... tgcatggcagGAAGTACAAAGATCAGATCAAATTTAGGAACAACATCTGGCTATTCAGTTA
EST: gi|16378537|gb|BI992477.1|BI992477
EST:     TGACAAAGTTTCATGTGGAATAGCTCTCTATGTTCTCGAGTCCTATCAAG                         GAAGTACAAAGATCAGATCAAATTTAGGAACAACATCTGGCTATTCAGTTA
genomic: TGACAAAGTTTCATGTGGAATAGCTCTCTATGTTCTCGAGTCCTATCAAGgtaatgactg ... tgcatggcagGAAGTACAAAGATCAGATCAAATTTAGGAACAACATCTGGCTATTCAGTTA
EST: gi|74246372|gb|DT654286.1|DT654286
EST:     TGACAAAGTTTCATGTGGAATAGCTCTCTATGTTCTCGAGTCCTATCAAG                         GAAGTACAAAGATCAGATCAAATTTAGGAACAACATCTGGCTATTCAGTTA
genomic: TGACAAAGTTTCATGTGGAATAGCTCTCTATGTTCTCGAGTCCTATCAAGgtaatgactg ... tgcatggcagGAAGTACAAAGATCAGATCAAATTTAGGAACAACATCTGGCTATTCAGTTA
EST: gi|13249761|gb|BG360666.1|BG360666
EST:     TGACAAAGTTTCATGTGGAATAGCTCTCTATGTTCTCGAGTCCTATCAAG                         GAAGTACAAAGATCAGATCAAATTTAGGAACAACATCTGGCTATTCAGTTA
genomic: TGACAAAGTTTCATGTGGAATAGCTCTCTATGTTCTCGAGTCCTATCAAGgtaatgactg ... tgcatggcagGAAGTACAAAGATCAGATCAAATTTAGGAACAACATCTGGCTATTCAGTTA

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: 33 (upstream exon), 41 (downstream exon)
Score: 15

GGAGAAGATCTAAATGGTTGTGCTTTTGTGTATGGCTCATTAAGTTTTGTTGACAAAGTTTCATGTGGAATAGCTCTCTATGTTCTCGAGTCCTATCAAGgtaatgactg ... tgcatggcagGAAGTACAAAGATCAGATCAAATTTAGGAACAACATCTGGCTATTCAGTTACAAGACTTGGCTTGGGCTTAGTTCCAGCTGCTTGTTCGCTGCTTTCAGC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 113

GGAGAAGATCTAAATGGTTGTGCTTTTGTGTATGGCTCATTAAGTTTTGTTGACAAAGTTTCATGTGGAATAGCTCTCTATGTTCTCGAGTCCTATCAAGgtaatgactg ... tgcatggcagGAAGTACAAAGATCAGATCAAATTTAGGAACAACATCTGGCTATTCAGTTACAAGACTTGGCTTGGGCTTAGTTCCAGCTGCTTGTTCGCTGCTTTCAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 52

GGAGAAGATCTAAATGGTTGTGCTTTTGTGTATGGCTCATTAAGTTTTGTTGACAAAGTTTCATGTGGAATAGCTCTCTATGTTCTCGAGTCCTATCAAGgtaatgactg ... tgcatggcagGAAGTACAAAGATCAGATCAAATTTAGGAACAACATCTGGCTATTCAGTTACAAGACTTGGCTTGGGCTTAGTTCCAGCTGCTTGTTCGCTGCTTTCAGC


Block sizes: 47 (upstream exon), 41 (downstream exon)
Score: 21

GGAGAAGATCTAAATGGTTGTGCTTTTGTGTATGGCTCATTAAGTTTTGTTGACAAAGTTTCATGTGGAATAGCTCTCTATGTTCTCGAGTCCTATCAAGgtaatgactg ... tgcatggcagGAAGTACAAAGATCAGATCAAATTTAGGAACAACATCTGGCTATTCAGTTACAAGACTTGGCTTGGGCTTAGTTCCAGCTGCTTGTTCGCTGCTTTCAGC