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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTTCCGAACATGAAATTCAATGTTGCTAAAGTCCTGCAATCACTTGTACCAATCCTTGACCAATCTgtaagttgtagtcatcaactctgttgctgcgatcctatttttatcaatatttggctttttgcctaccccaattgaatgcgtatttgcag

Basic information

species Zea mays
transcript GRMZM2G102858_T01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G102858_T01 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os09g07510.1 (Oryza sativa), 5'ss of exon 12
GGTTCCGAACATGAAATTCAATGTTGCTAAAGTCCTGCAATCACTTGTACCAATCCTTGACCAATCTgtaagttgtagt-----catcaactctgttgctgcgatcctatttttatca-atattt---ggctttttgcctaccccaattgaatgcgta-tttgcag
 || || ||||| |||||||||||||| || || |||||  ||||| |||| |||||||| |||||||| ||||| |||       |   ||   || ||    || || |  |||   | ||||   || | || |  ||    |  ||||| | || |||| ||
AGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACCGATCCTTGATCAATCTgtgagttgcagtattttttttgccttgattcctttcttcgtaatgctataggacatttacaggttattggggtatatta--tgaatacttactttgtag

upper sequence: GRMZM2G102858_T01 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os09g07510.3 (Oryza sativa), 5'ss of exon 12
GGTTCCGAACATGAAATTCAATGTTGCTAAAGTCCTGCAATCACTTGTACCAATCCTTGACCAATCTgtaagttgtagt-----catcaactctgttgctgcgatcctatttttatca-atattt---ggctttttgcctaccccaattgaatgcgta-tttgcag------------
 || || ||||| |||||||||||||| || || |||||  ||||| |||| |||||||| |||||||| ||||| |||       |   ||   || ||    || || |  |||   | ||||   || | || |  ||    |  ||||| | || |||| ||            
AGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACCGATCCTTGATCAATCTgtgagttgcagtattttttttgccttgattcctttcttcgtaatgctataggacatttacaggttattggggtatatta--tgaatacttactttgtaggttgtggagaag
















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|60354743|gb|DN221716.1|DN221716
EST:     TCAATGTTGCTAAAGTCCTGCAATCACTTGTACCAATCCTTGACCAATCT                         GTTGTGGAGAAGACAGTGAAACCATGCCTAGTTGAGCTCAGTGAGGACCCA
genomic: TCAATGTTGCTAAAGTCCTGCAATCACTTGTACCAATCCTTGACCAATCTgtaagttgta ... gtatttgcagGTTGTGGAGAAGACAGTGAAACCATGCCTAGTTGAGCTCAGTGAGGACCCA
EST: gi|166443326|gb|EG172666.1|EG172666
EST:     TCAATGTCGCTAAAGTCCTGCAATCACTTGTACCAATCCTTGATCAATCT                         GTTGTGGAGAAGACAGTG
genomic: TCAATGTTGCTAAAGTCCTGCAATCACTTGTACCAATCCTTGACCAATCTgtaagttgta ... gtatttgcagGTTGTGGAGAAGACAGTG
EST: gi|60356763|gb|DN223736.1|DN223736
EST:     TCAATGTTGCTAAAGTCCTGCAATCACTTGTACCAATCCTTGACCAATCT                         GTTGTGGAGAAGACAGTGAAACCATGCCTAGTTGAGCTCAGTGAGGACCCA
genomic: TCAATGTTGCTAAAGTCCTGCAATCACTTGTACCAATCCTTGACCAATCTgtaagttgta ... gtatttgcagGTTGTGGAGAAGACAGTGAAACCATGCCTAGTTGAGCTCAGTGAGGACCCA
EST: gi|149079804|gb|EE168801.2|EE168801
EST:     TCAATGTTGCTAAAGTCCTGCAATCACTTGTACCAATCCTTGACCAATCT                         GTTGTGGAGAAGACAGTGAAACCATGCCTAGTTGAGCTCAGTGAGGACCCA
genomic: TCAATGTTGCTAAAGTCCTGCAATCACTTGTACCAATCCTTGACCAATCTgtaagttgta ... gtatttgcagGTTGTGGAGAAGACAGTGAAACCATGCCTAGTTGAGCTCAGTGAGGACCCA
EST: gi|4681251|gb|AI629921.1|AI629921
EST:     TCAATGTTGCTAAAGTCCTGCAATCACTTGTACCAATCCTTGACCAATCT                         GTTGTGGAGAAGACAGTGAAACCATGCCTAGTTGAGCTCAGTGAGGACCCA
genomic: TCAATGTTGCTAAAGTCCTGCAATCACTTGTACCAATCCTTGACCAATCTgtaagttgta ... gtatttgcagGTTGTGGAGAAGACAGTGAAACCATGCCTAGTTGAGCTCAGTGAGGACCCA
EST: gi|18661338|gb|BM501361.1|BM501361
EST:     TCAATGTCGCTAAAGTCCTGCAATCACTTGTACCAATCCTTGATCAATCT                         GTTGTGGAGAAGACAGTGAAACCATGCTTAGTTGAGCTCAGTGAGGACCCA
genomic: TCAATGTTGCTAAAGTCCTGCAATCACTTGTACCAATCCTTGACCAATCTgtaagttgta ... gtatttgcagGTTGTGGAGAAGACAGTGAAACCATGCCTAGTTGAGCTCAGTGAGGACCCA
EST: gi|50336585|gb|CO531711.1|CO531711
EST:     TCAATGTTGCTAAAGTCCTGCAATCACTTGTACCAATCCTTGACCAATCT                         GTTGTGGAGAAGACAGTGAAACCATGCCTAGTTGAGCTCAGTGAGGACCCA
genomic: TCAATGTTGCTAAAGTCCTGCAATCACTTGTACCAATCCTTGACCAATCTgtaagttgta ... gtatttgcagGTTGTGGAGAAGACAGTGAAACCATGCCTAGTTGAGCTCAGTGAGGACCCA
EST: gi|7227754|gb|AW566395.1|AW566395
EST:     TCAATGTCGCTAAAGTCCTGCAATCACTTGTACCAATCCTTGATCAATCT                         GTTGTGGAGAAGACAGTGAAACCATGCTTAGTTGAGCTCAGTGAGGACCCA
genomic: TCAATGTTGCTAAAGTCCTGCAATCACTTGTACCAATCCTTGACCAATCTgtaagttgta ... gtatttgcagGTTGTGGAGAAGACAGTGAAACCATGCCTAGTTGAGCTCAGTGAGGACCCA
EST: gi|60399443|gb|DN232255.1|DN232255
EST:     TCAATGTTGCTAAAGTCCTGCAATCACTTGTACCAATCCTTGACCAATCT                         GTTGTGGAGAAGACAGTGAAACCATGCCTAGTTGAGCTCAGTGAGGACCCA
genomic: TCAATGTTGCTAAAGTCCTGCAATCACTTGTACCAATCCTTGACCAATCTgtaagttgta ... gtatttgcagGTTGTGGAGAAGACAGTGAAACCATGCCTAGTTGAGCTCAGTGAGGACCCA
EST: gi|50336586|gb|CO531712.1|CO531712
EST:     TCAATGTTGCTAAAGTCCTGCAATCACTTGTACCAATCCTTGACCAATCT                         GTTGTGGAGAAGACAGTGAAACCATGCCTAGTTGAGCTCAGTGAGGACCCA
genomic: TCAATGTTGCTAAAGTCCTGCAATCACTTGTACCAATCCTTGACCAATCTgtaagttgta ... gtatttgcagGTTGTGGAGAAGACAGTGAAACCATGCCTAGTTGAGCTCAGTGAGGACCCA
EST: gi|40303113|gb|CK347500.1|CK347500
EST:     TCAATGTCGCTAAAGTCCTGCAATCACTTGTACCAATCCTTGATCAATCT                         GTTGTGGAGAAGACAGTGAAACCATGCTTAGTTGAGCTCAGTGAGGACCCA
genomic: TCAATGTTGCTAAAGTCCTGCAATCACTTGTACCAATCCTTGACCAATCTgtaagttgta ... gtatttgcagGTTGTGGAGAAGACAGTGAAACCATGCCTAGTTGAGCTCAGTGAGGACCCA
EST: gi|116814772|gb|EC857388.1|EC857388
EST:     TCAATGTTGCTAAAGT-CTGCAATCACTTGTACCAATCCTTGATCAATCT                         GTTGTGGAGAAGACAGTGAAACCATGCCTAGTTGAGCTCAGTGAGGACCCA
genomic: TCAATGTTGCTAAAGTCCTGCAATCACTTGTACCAATCCTTGACCAATCTgtaagttgta ... gtatttgcagGTTGTGGAGAAGACAGTGAAACCATGCCTAGTTGAGCTCAGTGAGGACCCA

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: 48 (upstream exon), 48 (downstream exon)
Score: 202

GGTTCCGAACATGAAATTCAATGTTGCTAAAGTCCTGCAATCACTTGTACCAATCCTTGACCAATCTgtaagttgta ... gtatttgcagGTTGTGGAGAAGACAGTGAAACCATGCCTAGTTGAGCTCAGTGAGGACCCAGATGTAGATGTAAGATACTACGCACACCAAGCCCTTCGGGCGTGTGACC


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 114

GGTTCCGAACATGAAATTCAATGTTGCTAAAGTCCTGCAATCACTTGTACCAATCCTTGACCAATCTgtaagttgta ... gtatttgcagGTTGTGGAGAAGACAGTGAAACCATGCCTAGTTGAGCTCAGTGAGGACCCAGATGTAGATGTAAGATACTACGCACACCAAGCCCTTCGGGCGTGTGACC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 167

GGTTCCGAACATGAAATTCAATGTTGCTAAAGTCCTGCAATCACTTGTACCAATCCTTGACCAATCTgtaagttgta ... gtatttgcagGTTGTGGAGAAGACAGTGAAACCATGCCTAGTTGAGCTCAGTGAGGACCCAGATGTAGATGTAAGATACTACGCACACCAAGCCCTTCGGGCGTGTGACC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 112

GGTTCCGAACATGAAATTCAATGTTGCTAAAGTCCTGCAATCACTTGTACCAATCCTTGACCAATCTgtaagttgta ... gtatttgcagGTTGTGGAGAAGACAGTGAAACCATGCCTAGTTGAGCTCAGTGAGGACCCAGATGTAGATGTAAGATACTACGCACACCAAGCCCTTCGGGCGTGTGACC