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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCTGCATGTTCCTTCTATGAGTGAAGAAGAAATAAATTCTCTTCCTGTCTTCAAATATAAAGTCCAGGCACAGCAGGGAAATGCCCCTGCCCGAAAAAGgtaagacgaattatcctttgggtcgatttgttcatatggccataccaagtttgttccagtatctcccatcatcaacaaatgaccaaacatttaattctgaattggagacatggattaatttgtctctatgatgtgtttctaacgaatgtttttcaacag

Basic information

species Zea mays
transcript GRMZM2G492252_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G492252_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os03g16570.3 (Oryza sativa), 5'ss of exon 6
GCCTGCATGTTCCTTCTATGAGTGAAGAAGAAATAAATTCTCTTCCTGTCTTCAAATATAAAGTCCAGGCACAGCAGGGAAATGCCCCTGCCCGAAAAAGgtaagacgaattatcctttgggtcgatttgttcatatggc----------cataccaagtttgttccagtatctcccatcatcaacaaatgaccaaacatttaattctgaattggag-acatggattaatttgtctcta-tgatgtgtttctaacgaatgtttttcaacag
|||  |||| |||||| ||||||||||||||||||||| |||||||||| |||||||| || || |||||||| ||||||| |||| ||  ||||||||||||||| | |||||||||| ||     || || |  ||||          |||   |||| |   | | |  || |||||    | || | ||||| ||| |||||| ||||| |   || | |  |    |||  |||   || |  ||||   || | | |        
GCCCTCATGCTCCTTCGATGAGTGAAGAAGAAATAAATGCTCTTCCTGTATTCAAATACAAGGTTCAGGCACATCAGGGAAGTGCCTCTTTCCGAAAAAGgtaagatgtattatccttttggctacattttttagctggcatagcaaacgcatgataagtcta--caactgccttccatctctgataagtaaccaaccatataattccgaatttgtctactttgtatgggatgtaactaaccatttaattcttttgattctatag------
















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|78074674|gb|DV503108.1|DV503108
EST:     TTCAAATATAAAGTCCAGGCACAGCAGGGAAATGCCCCTGCCCGAAAAAG                         TGATGAGGCATCGCAGCTATCGGTTTCTTCAACTGGCTCCGGCAATGAG
genomic: TTCAAATATAAAGTCCAGGCACAGCAGGGAAATGCCCCTGCCCGAAAAAGgtaagacgaa ... ttttcaacagTGATGAGGCATCGCAGCTATCGGTTTCTTCAACTGGCTCCGGCAATGAG
EST: gi|60359234|gb|DN226207.1|DN226207
EST:     TTCAAATATAAAGTCCAGGCACAGCAGGGAAATGCCCCTGCCCGAAAAAG                         TGATGAGGCATCGCAGCTATCGGTTTCTTCAACTGGCTCCGGCAATGAG
genomic: TTCAAATATAAAGTCCAGGCACAGCAGGGAAATGCCCCTGCCCGAAAAAGgtaagacgaa ... ttttcaacagTGATGAGGCATCGCAGCTATCGGTTTCTTCAACTGGCTCCGGCAATGAG
EST: gi|91052810|gb|EB163228.1|EB163228
EST:     TTCAAATATAAAGTCCAGGCACAGCAGGGAAATGCCCCTGCCCGAAAAAG                         TGATGAGGCATCGCAGCTATCGGTTTCTTCAACTGGCTCCGGCAATGAG
genomic: TTCAAATATAAAGTCCAGGCACAGCAGGGAAATGCCCCTGCCCGAAAAAGgtaagacgaa ... ttttcaacagTGATGAGGCATCGCAGCTATCGGTTTCTTCAACTGGCTCCGGCAATGAG
EST: gi|78123225|gb|DV541609.1|DV541609
EST:     TTCAAATATAAAGTCCAGGCACAGCAGGGAAATGCCCCTGCCCGAAAAAG                         TGATGAGGCATCGCAGCTATCGGTTTCTTCAACTGGCTCCGGCAATGAG
genomic: TTCAAATATAAAGTCCAGGCACAGCAGGGAAATGCCCCTGCCCGAAAAAGgtaagacgaa ... ttttcaacagTGATGAGGCATCGCAGCTATCGGTTTCTTCAACTGGCTCCGGCAATGAG
EST: gi|110517661|gb|EE022248.1|EE022248
EST:     TTCAAATATAAAGTCCAGGCACAGCAGGGAAATGCCCCTGCCCGAAAAAG                         TGATGAGGCATCGCAGCTATCGGTTTCTTCAACTGGCTCCGGCAATGAG
genomic: TTCAAATATAAAGTCCAGGCACAGCAGGGAAATGCCCCTGCCCGAAAAAGgtaagacgaa ... ttttcaacagTGATGAGGCATCGCAGCTATCGGTTTCTTCAACTGGCTCCGGCAATGAG
EST: gi|88758240|gb|DY542381.1|DY542381
EST:     TTCAAATATAAAGTCCAGGCACAGCAGGGAAATGCCCCTGCCCGAAAAAG                         TGATGAGGCATCGCAGCTATCGGTTTTTTCAACTGGCTCCGGCAATGAG
genomic: TTCAAATATAAAGTCCAGGCACAGCAGGGAAATGCCCCTGCCCGAAAAAGgtaagacgaa ... ttttcaacagTGATGAGGCATCGCAGCTATCGGTTTCTTCAACTGGCTCCGGCAATGAG
EST: gi|88754551|gb|DY538692.1|DY538692
EST:     TTCAAATATAAAGTCCAGGCACAGCAGGGAAAGGCCCCTGCCCGAAAAAG                         TGATGAGGCATGGCAGCTATCGGTTTCTTCAACTGGCTCCGGCAATGAG
genomic: TTCAAATATAAAGTCCAGGCACAGCAGGGAAATGCCCCTGCCCGAAAAAGgtaagacgaa ... ttttcaacagTGATGAGGCATCGCAGCTATCGGTTTCTTCAACTGGCTCCGGCAATGAG
EST: gi|16922425|gb|BM075574.1|BM075574
EST:     TTCAAATATAAAGTCCAGGCACAGCAGGGAAATGCCCCTGCCCGAAAAAG                         TGATGAGGCATCGCAGCTATCGGTTTCTTCAACTGGCTCCGGCAATGAT
genomic: TTCAAATATAAAGTCCAGGCACAGCAGGGAAATGCCCCTGCCCGAAAAAGgtaagacgaa ... ttttcaacagTGATGAGGCATCGCAGCTATCGGTTTCTTCAACTGGCTCCGGCAATGAG
EST: gi|71774881|gb|DR972759.1|DR972759
EST:     TTCAAATATAAAGTCCAGGCACAGCAGGGAAATGCCCCTGCCCGAAAAAG                         TGATGAGGCATCGCAGCTATCGGTTTCTTCAACTGGCTCCGGCAATGAG
genomic: TTCAAATATAAAGTCCAGGCACAGCAGGGAAATGCCCCTGCCCGAAAAAGgtaagacgaa ... ttttcaacagTGATGAGGCATCGCAGCTATCGGTTTCTTCAACTGGCTCCGGCAATGAG
EST: gi|60352872|gb|DN219845.1|DN219845
EST:     TTCAAATATAAAGTCCAGGCACAGCAGGGAAATGCCCCTGCCCGAAAAAG                         TGATGAGGCATCGCAGCTATCGGTTTCTTCAACTGGCTCCGGCAATGAG
genomic: TTCAAATATAAAGTCCAGGCACAGCAGGGAAATGCCCCTGCCCGAAAAAGgtaagacgaa ... ttttcaacagTGATGAGGCATCGCAGCTATCGGTTTCTTCAACTGGCTCCGGCAATGAG
EST: gi|86467860|gb|DY234230.1|DY234230
EST:     TTCAAATATAAAGTCCAGGCACAGCAGGGAAATGCCCCTGCCCGAAAAAG                         TGATGAGGCATCGCAGCTATCGGTTTTTTCAACTGGCTCCGGCAATGAG
genomic: TTCAAATATAAAGTCCAGGCACAGCAGGGAAATGCCCCTGCCCGAAAAAGgtaagacgaa ... ttttcaacagTGATGAGGCATCGCAGCTATCGGTTTCTTCAACTGGCTCCGGCAATGAG

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), 48 (downstream exon)
Score: 104

GCCTGCATGTTCCTTCTATGAGTGAAGAAGAAATAAATTCTCTTCCTGTCTTCAAATATAAAGTCCAGGCACAGCAGGGAAATGCCCCTGCCCGAAAAAGgtaagacgaa ... ttttcaacagTGATGAGGCATCGCAGCTATCGGTTTCTTCAACTGGCTCCGGCAATGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 27

GCCTGCATGTTCCTTCTATGAGTGAAGAAGAAATAAATTCTCTTCCTGTCTTCAAATATAAAGTCCAGGCACAGCAGGGAAATGCCCCTGCCCGAAAAAGgtaagacgaa ... ttttcaacagTGATGAGGCATCGCAGCTATCGGTTTCTTCAACTGGCTCCGGCAATGAG


Block sizes: 49 (upstream exon), 38 (downstream exon)
Score: 30

GCCTGCATGTTCCTTCTATGAGTGAAGAAGAAATAAATTCTCTTCCTGTCTTCAAATATAAAGTCCAGGCACAGCAGGGAAATGCCCCTGCCCGAAAAAGgtaagacgaa ... ttttcaacagTGATGAGGCATCGCAGCTATCGGTTTCTTCAACTGGCTCCGGCAATGAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 64

GCCTGCATGTTCCTTCTATGAGTGAAGAAGAAATAAATTCTCTTCCTGTCTTCAAATATAAAGTCCAGGCACAGCAGGGAAATGCCCCTGCCCGAAAAAGgtaagacgaa ... ttttcaacagTGATGAGGCATCGCAGCTATCGGTTTCTTCAACTGGCTCCGGCAATGAG