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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCATTCCTACATGTTTCTGCAGGGAGGAGTGGCTTGCCGTGCTCCCACGTGCGCTTGTTGCAGCGTTCGTCAAGACTGATAAAGATTTTCAGGCAGTGGgtaagtaagtccctgttattgtccagcttagtatatttgacaatactgatgtcacgtttcatagaatcacgtagtccttaaacaggcatatattgcttag...

Basic information

species Zea mays
transcript GRMZM2G135444_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G135444_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os09g28560.1 (Oryza sativa), 5'ss of exon 2
GCCATTCCTACATGTTTCTGCAGGGAGGAGTGGCTTGCCGTGCTCCCACGTGCGCTTGTTGCAGCGTTCGTCAAGACTGATAAAGATTTTCAGGCAGTGGgtaagtaagtccctgttattgtccagcttagtatatttgacaatactgatgtcacgtttcatagaatcacgtagtccttaaacaggcatatattgcttag----
||||||||| || ||||  ||||||| ||||||||||| ||||| || ||||||||||| ||||| || |||||||| || |||||||| |||||||| ||||| | || ||   ||  |||| ||||||  | |||   ||||| | | |      ||     || || | |  | ||  |       ||| | | |      
GCCATTCCTTCAGGTTTGAGCAGGGATGAGTGGCTTGCAGTGCTTCCTCGTGCGCTTGTCGCAGCATTTGTCAAGACAGACAAAGATTTCCAGGCAGTAGgtaaatcaggcca-attcctgtcaagcttacgacatt---caatatttaagcagtactttgataaaacaggcaaacgttgtaatctttcataatccatcactat
















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|148946428|gb|EC891737.2|EC891737
EST:     TGCGCTTGTTGCAGCGTTCGTCAAGACTGATAAAGATTTTCAGGCAGTGG                         ATGAAACTTCTGGCACAACTGTGACATTTGTGATAATAGACGAGTGGGTTG
genomic: TGCGCTTGTTGCAGCGTTCGTCAAGACTGATAAAGATTTTCAGGCAGTGGgtaagtaagt ... actttttcagATGAAACTTCTGGCACAACTGTGACATTTGTGATAATAGACGAGTGGGTTG
EST: gi|149095947|gb|EE181613.2|EE181613
EST:     TGCGCTTGTTGCAGCGTTCGTCAAGACTGATAAAGATTTTCAGGCAGTGG                         ATGAAACTTCTGGCACAACTGTGACATTTGTGATAATAGACGAGTGGGTTG
genomic: TGCGCTTGTTGCAGCGTTCGTCAAGACTGATAAAGATTTTCAGGCAGTGGgtaagtaagt ... actttttcagATGAAACTTCTGGCACAACTGTGACATTTGTGATAATAGACGAGTGGGTTG
EST: gi|148940139|gb|EC884892.2|EC884892
EST:     TGCGCTTGTTGCAGCGTTCGTCAAGACTGATAAAGATTTTCAGGCAGTGG                         ATGAAACTTCTGGCACAACTGTGACATTTGTGATAATAGACGAGTGGGTTG
genomic: TGCGCTTGTTGCAGCGTTCGTCAAGACTGATAAAGATTTTCAGGCAGTGGgtaagtaagt ... actttttcagATGAAACTTCTGGCACAACTGTGACATTTGTGATAATAGACGAGTGGGTTG
EST: gi|149101338|gb|EE187455.2|EE187455
EST:     TGCGCTTGTTGCAGCGTTCGTCAAGACTGATAAAGATTTTCAGGCAGTGG                         ATGAAACTTCTGGCACAACTGTGACATTTGTGATAATAGACGAGTGGGTTG
genomic: TGCGCTTGTTGCAGCGTTCGTCAAGACTGATAAAGATTTTCAGGCAGTGGgtaagtaagt ... actttttcagATGAAACTTCTGGCACAACTGTGACATTTGTGATAATAGACGAGTGGGTTG
EST: gi|149096893|gb|EE182691.2|EE182691
EST:     TGCGCTTGTTGCAGCGTTCGTCAAGACTGATAAAGATTTTCAGGCAGTGG                         ATGAAACTTCTGGCACAACTGTGACATTTGTGATAATAGACGAGTGGGTTG
genomic: TGCGCTTGTTGCAGCGTTCGTCAAGACTGATAAAGATTTTCAGGCAGTGGgtaagtaagt ... actttttcagATGAAACTTCTGGCACAACTGTGACATTTGTGATAATAGACGAGTGGGTTG
EST: gi|211393741|gb|FL095552.1|FL095552
EST:     TGCGCTTGTTGCAGCGTTCGTCAAGACTGATAAAGATTTTYAGGCAGTGG                         ATGAAACTTCTGGCACAACTGTGACATTTGTGATAATAGACGA
genomic: TGCGCTTGTTGCAGCGTTCGTCAAGACTGATAAAGATTTTCAGGCAGTGGgtaagtaagt ... actttttcagATGAAACTTCTGGCACAACTGTGACATTTGTGATAATAGACGA
EST: gi|211391125|gb|FL095548.1|FL095548
EST:     TGCGCTTGTTGCAGCGTTCGTCAAGACTGATAAAGATTTTCAGGCAGTGG                         ATGAAACTTCTGGCACAACTGTGACATTTGTGATAATAGACGAGTGGGTTG
genomic: TGCGCTTGTTGCAGCGTTCGTCAAGACTGATAAAGATTTTCAGGCAGTGGgtaagtaagt ... actttttcagATGAAACTTCTGGCACAACTGTGACATTTGTGATAATAGACGAGTGGGTTG
EST: gi|211393739|gb|FL095550.1|FL095550
EST:     TGCGCTTGTTGCAGCGTTCGTCAAGACTGATAAAGATTTTCAGGCAGTGG                         ATGAAACTTCTGGCACAACTGTGACATTTGTGATAATAGACGAGTGG
genomic: TGCGCTTGTTGCAGCGTTCGTCAAGACTGATAAAGATTTTCAGGCAGTGGgtaagtaagt ... actttttcagATGAAACTTCTGGCACAACTGTGACATTTGTGATAATAGACGAGTGG
EST: gi|149083526|gb|EE172858.2|EE172858
EST:     TGCGCTTGTTGCAGCGTTCGTCAAGACTGATAAAGATTTTCAGGCAGTGG                         ATGAAACTTCTGGCACAACTGTGACATTTGTGATAATAGACGAGTGGGTTG
genomic: TGCGCTTGTTGCAGCGTTCGTCAAGACTGATAAAGATTTTCAGGCAGTGGgtaagtaagt ... actttttcagATGAAACTTCTGGCACAACTGTGACATTTGTGATAATAGACGAGTGGGTTG
EST: gi|211391126|gb|FL095549.1|FL095549
EST:     TGCGCTTGTTGCAGCGTTCGTCAAGACTGATAAAGATTTTCAGGCAGTGG                         ATTGAAACTTCTGGCACAACTGTGACATTTGTGA
genomic: TGCGCTTGTTGCAGCGTTCGTCAAGACTGATAAAGATTTTCAGGCAGTGGgtaagtaagt ... actttttcagAT-GAAACTTCTGGCACAACTGTGACATTTGTGA
EST: gi|211393742|gb|FL095553.1|FL095553
EST:     TGCGCTTGTTGCAGCGTTCGTCAAGACTGATAAAGATTTTCAGGCAGTGG                         ATGAAACTTCTGGCACAACTGTGACATTTGTGATAATAGACGAGTGGGTTG
genomic: TGCGCTTGTTGCAGCGTTCGTCAAGACTGATAAAGATTTTCAGGCAGTGGgtaagtaagt ... actttttcagATGAAACTTCTGGCACAACTGTGACATTTGTGATAATAGACGAGTGGGTTG

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), 48 (downstream exon)
Score: 161

GCCATTCCTACATGTTTCTGCAGGGAGGAGTGGCTTGCCGTGCTCCCACGTGCGCTTGTTGCAGCGTTCGTCAAGACTGATAAAGATTTTCAGGCAGTGGgtaagtaagt ... actttttcagATGAAACTTCTGGCACAACTGTGACATTTGTGATAATAGACGAGTGGGTTGTGACTGTAGCATCTGTCGGTGATTCACGTTGCATACTAGAATCTGCCGA




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