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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTGCTATATGCTTGGCGCGAAGTTTCAAGATAATCAACGAATCGTTGACGTCCCTTGACCTGGGTTTCAATGAGATTCGAgtaagcgaacacacagcgcatcctatcagttattggcattcggatatatatatctcgtattctcaaattatttatatttctgacag

Basic information

species Zea mays
transcript GRMZM2G110289_T01
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G110289_T01 (Zea mays), 5'ss of exon 15
lower sequence: LOC_Os06g13050.1 (Oryza sativa), 5'ss of exon 16
GGTGCTATATGCTTGGCGCGAAGTTTCAAGATAATCAACGAATCGTTGACGTCCCTTGACCTGGGTTTCAATGAGATTCGAgtaagcgaacacacagcgca--------------tcctatcagttattggcattcggatatatatatctcgtattctcaa-attatttatatttctgacag
|||||||| |||||||| |||||||||||||| ||||| ||||| ||||| || ||||||||||| || ||||||||| |||||||  |||||  |  |||              |  |||    ||||||       ||  | || ||    ||  |||| |   |||||  | || ||||
GGTGCTATCTGCTTGGCTCGAAGTTTCAAGATCATCAATGAATCTTTGACTTCACTTGACCTGGGCTTTAATGAGATTAGAgtaagtaaacactaaatgcagtgtctttttctttttgtattttctattggtgggtctatgcagatctccaccatgttcaataccctttatgctcctaacag
















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|60354010|gb|DN220983.1|DN220983
EST:     TAATCAACGAATCGTTGACGTCCCTTGACCTGGGTTTCAATGAGATTCGA                         GACGACGGAGCATTCGCATTGGCACAGGCGCTCAAGGCTAACGAGGATCTG
genomic: TAATCAACGAATCGTTGACGTCCCTTGACCTGGGTTTCAATGAGATTCGAgtaagcgaac ... tttctgacagGACGACGGAGCATTCGCATTGGCACAGGCGCTCAAGGCTAACGAGGATCTG
EST: gi|113847821|gb|DW962252.1|DW962252
EST:     TAATCAACGAATCGTTGACGTCCCTTGACCTGGGTTTCAATGAGATTCGA                         GACGACGGAGCATTCGC
genomic: TAATCAACGAATCGTTGACGTCCCTTGACCTGGGTTTCAATGAGATTCGAgtaagcgaac ... tttctgacagGACGACGGAGCATTCGC
EST: gi|67010636|gb|CO439385.1|CO439385
EST:     TAATCAACGAATCGTTGACGTCCCTTGACCTGNGTTTCAATGAGATTCGA                         GACGACGGAGCATTCGCATTGGCACAGGCGCTCAATGCTAACGATGATCTG
genomic: TAATCAACGAATCGTTGACGTCCCTTGACCTGGGTTTCAATGAGATTCGAgtaagcgaac ... tttctgacagGACGACGGAGCATTCGCATTGGCACAGGCGCTCAAGGCTAACGAGGATCTG
EST: gi|60346680|gb|DN213653.1|DN213653
EST:     TAATCAACGAATCGTTGACGTCCCTTGACCTGGGTTTCAATGAGATTCGA                         GACGACGGAGCATTCGCATTGGCACATGCGCTCAAGGCTAACGAGGATCTG
genomic: TAATCAACGAATCGTTGACGTCCCTTGACCTGGGTTTCAATGAGATTCGAgtaagcgaac ... tttctgacagGACGACGGAGCATTCGCATTGGCACAGGCGCTCAAGGCTAACGAGGATCTG
EST: gi|71763770|gb|DR961707.1|DR961707
EST:     TAATCAACGAATCGTTGACGTCCCTTGACCTGGGTTTCAATGAGATTCGA                         GACGACGGAGCATTCGCATTGGCACAGGCGCTCAAGGCTAACGAGGATCTG
genomic: TAATCAACGAATCGTTGACGTCCCTTGACCTGGGTTTCAATGAGATTCGAgtaagcgaac ... tttctgacagGACGACGGAGCATTCGCATTGGCACAGGCGCTCAAGGCTAACGAGGATCTG
EST: gi|60355903|gb|DN222876.1|DN222876
EST:     TAATCAACGAATCGTTGACGTCCCTTGACCTGGGTTTCAATGAGATTCGA                         GACGACGGAGCATTCGCATTGGCACAGGCGCTCAAGGCTAACGAGGATCTG
genomic: TAATCAACGAATCGTTGACGTCCCTTGACCTGGGTTTCAATGAGATTCGAgtaagcgaac ... tttctgacagGACGACGGAGCATTCGCATTGGCACAGGCGCTCAAGGCTAACGAGGATCTG
EST: gi|32937038|gb|CF041857.1|CF041857
EST:     TAATCAACGAATCGTTGACGTCCCTTGACCTGGGTTTCAATGAGATTCGA                         GACGACGGAGCATTCGCATTGGCACAGGTGCTCAAGGCTAACGAGGATCTG
genomic: TAATCAACGAATCGTTGACGTCCCTTGACCTGGGTTTCAATGAGATTCGAgtaagcgaac ... tttctgacagGACGACGGAGCATTCGCATTGGCACAGGCGCTCAAGGCTAACGAGGATCTG
EST: gi|60341143|gb|DN208116.1|DN208116
EST:     TAATCAACGAATCGTTGACGTCCCTTGACCTGGGTTTCAATGAGATTCGA                         GACGACGGAGCATTCGCATTGGCACAGGCGCTCAAGGCTAACGAGGATCTG
genomic: TAATCAACGAATCGTTGACGTCCCTTGACCTGGGTTTCAATGAGATTCGAgtaagcgaac ... tttctgacagGACGACGGAGCATTCGCATTGGCACAGGCGCTCAAGGCTAACGAGGATCTG

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: 135

GGTGCTATATGCTTGGCGCGAAGTTTCAAGATAATCAACGAATCGTTGACGTCCCTTGACCTGGGTTTCAATGAGATTCGAgtaagcgaac ... tttctgacagGACGACGGAGCATTCGCATTGGCACAGGCGCTCAAGGCTAACGAGGATCTGGCGGTCACGTCATTAAATCTCGCAAACAACTTCTTCACGAAATTCGGAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 160

GGTGCTATATGCTTGGCGCGAAGTTTCAAGATAATCAACGAATCGTTGACGTCCCTTGACCTGGGTTTCAATGAGATTCGAgtaagcgaac ... tttctgacagGACGACGGAGCATTCGCATTGGCACAGGCGCTCAAGGCTAACGAGGATCTGGCGGTCACGTCATTAAATCTCGCAAACAACTTCTTCACGAAATTCGGAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 115

GGTGCTATATGCTTGGCGCGAAGTTTCAAGATAATCAACGAATCGTTGACGTCCCTTGACCTGGGTTTCAATGAGATTCGAgtaagcgaac ... tttctgacagGACGACGGAGCATTCGCATTGGCACAGGCGCTCAAGGCTAACGAGGATCTGGCGGTCACGTCATTAAATCTCGCAAACAACTTCTTCACGAAATTCGGAC


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 87

GGTGCTATATGCTTGGCGCGAAGTTTCAAGATAATCAACGAATCGTTGACGTCCCTTGACCTGGGTTTCAATGAGATTCGAgtaagcgaac ... tttctgacagGACGACGGAGCATTCGCATTGGCACAGGCGCTCAAGGCTAACGAGGATCTGGCGGTCACGTCATTAAATCTCGCAAACAACTTCTTCACGAAATTCGGAC