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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTTCTACCTCTGGCATGACTCTATGCCTTCTTGCCGTTTCTGTTGTATTTTTTCTCAAGgtatgttcaggtttctttagctaggattcgagtgagaagatgataaaactttattggtaatgtgtgccttatgcagatcctgtacaatatctactgagttttcttctaatccttttttatggttcgttttttccag

Basic information

species Zea mays
transcript GRMZM2G160504_T01
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G160504_T01 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os05g49260.1 (Oryza sativa), 5'ss of exon 13
ATTTCTACCTCTGGCATGACTCTATGCCTTCTTGCCGTTTCTGTTGTATTTTTTCTCAAGgtatgttcaggtttctttagctagg--attcgagtgagaaga------tgataaaactttattggtaatgtgtgcc-ttatgcagatcctgtacaatatctactgagttttc------ttctaatccttttttatggttcgttttttccag
|| |||||  |||| ||||||||| |||||||||| || |||||||||||||||||  |||||  ||||| ||| ||    ||    |||    | | || |      || |  |   |  ||| ||   |      |      ||  || | |  | ||| || ||||  |      ||  |||  |  |  |  | |  ||| || |||
ATCTCTACTGCTGGGATGACTCTAAGCCTTCTTGCAGTATCTGTTGTATTTTTTCTGGAGgtacattcagattttttccagtataccattgtgataaaaaaaatcatatgttgcagtctctttgatagcctacattgtcgcatggactct-tcccctttctcctcagttcactcaatatttcaatattactacaatgattatttgtttcag

upper sequence: GRMZM2G160504_T01 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os05g49270.1 (Oryza sativa), 5'ss of exon 13
ATTTCTACCTCTGGCATGACTCTATGCCTTCTTGCCGTTTCTGTTGTATTTTTTCTCAAGgtatgttcaggtttcttta----------gctaggattcgagtgagaagatg---ataaaactttattggtaatgtgtgccttatgcag---atc------ctgtacaat--atctactgagttttcttctaatccttttttatggttcgttttttccag
|| ||| |  |||| ||||||||| |||| ||||| ||| ||||||||||||| ||||||||| ||||       |  |          |  | | |||   ||      |      || | |  ||   |    | ||  || ||||    |||      || | |  |  ||| ||||| | || |  || |   || || || ||  ||| || |||
ATCTCTTCTGCTGGGATGACTCTAAGCCTCCTTGCAGTTGCTGTTGTATTTTTCCTCAAGgtaagttcctaccagtaaaaaagaaaagggaaaagtttcatctgttgcactatatgcaatattccatatatggcttatgaattttgcaatatatcacaggtctcttctgtcaatccactgaatattttcatattg--ttattgtgatttatttgtttcag
















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|19769428|gb|BQ034149.1|BQ034149
EST:     CTGGCATGACTCTATGCCTTCTTGCCGTTTCTGTTGTATTTTTTCTCAAG                         GATAACATTTCACAGGATTCTAACTCGTACTACATCTTAACAATGATCTCC
genomic: CTGGCATGACTCTATGCCTTCTTGCCGTTTCTGTTGTATTTTTTCTCAAGgtatgttcag ... ttttttccagGATAACATTTCACAGGATTCTAACTCATACTACATCTTAACAATGATCTCC
EST: gi|78120836|gb|DV539220.1|DV539220
EST:     CTGGCATGACTCTATGCCTTCTTGCCGTTTCTGTTGTATTTTTTCTCAAG                         GATAACATTTCACAGGATTCTAACTCATACTACATCTTAACAATGATCTCC
genomic: CTGGCATGACTCTATGCCTTCTTGCCGTTTCTGTTGTATTTTTTCTCAAGgtatgttcag ... ttttttccagGATAACATTTCACAGGATTCTAACTCATACTACATCTTAACAATGATCTCC
EST: gi|19769435|gb|BQ034156.1|BQ034156
EST:     CTGGCATGACTCTATGCCTTCTTGCCGTTTCTGTTGTATTTTTTCTCAAG                         GATAACATTTCACAGGATTCTAACTCGTGCTACATCTTAGCAATGATCTCC
genomic: CTGGCATGACTCTATGCCTTCTTGCCGTTTCTGTTGTATTTTTTCTCAAGgtatgttcag ... ttttttccagGATAACATTTCACAGGATTCTAACTCATACTACATCTTAACAATGATCTCC

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: 44 (upstream exon), 47 (downstream exon)
Score: 13

ATTTCTACCTCTGGCATGACTCTATGCCTTCTTGCCGTTTCTGTTGTATTTTTTCTCAAGgtatgttcag ... ttttttccagGATAACATTTCACAGGATTCTAACTCATACTACATCTTAACAATGATCTCCCTTGTTGGTATTGTG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 51

ATTTCTACCTCTGGCATGACTCTATGCCTTCTTGCCGTTTCTGTTGTATTTTTTCTCAAGgtatgttcag ... ttttttccagGATAACATTTCACAGGATTCTAACTCATACTACATCTTAACAATGATCTCCCTTGTTGGTATTGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 61

ATTTCTACCTCTGGCATGACTCTATGCCTTCTTGCCGTTTCTGTTGTATTTTTTCTCAAGgtatgttcag ... ttttttccagGATAACATTTCACAGGATTCTAACTCATACTACATCTTAACAATGATCTCCCTTGTTGGTATTGTG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 39

ATTTCTACCTCTGGCATGACTCTATGCCTTCTTGCCGTTTCTGTTGTATTTTTTCTCAAGgtatgttcag ... ttttttccagGATAACATTTCACAGGATTCTAACTCATACTACATCTTAACAATGATCTCCCTTGTTGGTATTGTG