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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAAGTTAGCCAGCCTGATGGTTCAAAGCAAAGGTATACAGCGAAGCACATTTTGATCGCGACTGGTAGCCGTGCTCAACGTGTCAACATACCTGGAAAGgtttgtaaaattccccacctaccttgtcactaaaacttgcacagtttgattccattaatacttgtttattttctagctgattgatgctgaagatgggtga...

Basic information

species Zea mays
transcript GRMZM5G806449_T03
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G806449_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os02g56850.4 (Oryza sativa), 5'ss of exon 3
TGAAGTTAGCCAGCCTGATGGTTCAAAGCAAAGGTATACAGCGAAGCACATTTTGATCGCGACTGGTAGCCGTGCTCAACGTGTCAACATACCTGGAAAGgtttgtaaaattccccacctacctt---------gtcactaaaacttgcacagt--ttgattccattaatacttgtttattttctagctgattgatgctgaagatgggtga
|||||| |   |||| ||||||||||||||||| |||||||| |||||||| ||||| || ||||||||||| ||||||||||||||||| ||||| |||||    ||||||| |  ||  ||||         ||  || |    ||   |||  || ||  ||||  |||||||||     ||   | ||     |  |          
TGAAGTCACAAAGCCAGATGGTTCAAAGCAAAGATATACAGCAAAGCACATATTGATAGCAACTGGTAGCCGAGCTCAACGTGTCAACATTCCTGGGAAGgta-acaaaattctctgccagcctttgcaaacttgtttcttatgtctggcaagtagttaatagcattgttacttgtttgacaacttctttatattccccaa----------
















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|94477026|gb|EB705984.1|EB705984
EST:     TTTGATCGCGACTGGTAGCCGTGCTCAACGTGGCAACATACCTGGGAAAG                         GATCTGGCTATTACTTCTG
genomic: TTTGATCGCGACTGGTAGCCGTGCTCAACGTGTCAACATACCTGG-AAAGgtttgtaaaa ... cttttttcagGATCTGGCTATTACTTCTG
EST: gi|91056622|gb|EB167040.1|EB167040
EST:     TTTTGATCGCGACTGGTAGCCGTGCTCAACGTGTCAACATACCTGGAAAG                         GATCTGGGTATTACTTCTG
genomic: TTTTGATCGCGACTGGTAGCCGTGCTCAACGTGTCAACATACCTGGAAAGgtttgtaaaa ... cttttttcagGATCTGGCTATTACTTCTG
EST: gi|149099075|gb|EE185096.2|EE185096
EST:     TTTTGATCGCGACTGGTAGCCGTGCTCAACGTGTCAACATACCTGGAAAG                         GATCTGGCTATTACTTCTGATGAGGCCTTGAGCTTGGAGGAGCTTTCAAAG
genomic: TTTTGATCGCGACTGGTAGCCGTGCTCAACGTGTCAACATACCTGGAAAGgtttgtaaaa ... cttttttcagGATCTGGCTATTACTTCTGATGAGGCCTTGAGCTTGGAGGAGCTTCCAAAG
EST: gi|31611942|gb|CD568564.1|CD568564
EST:     TTTTGATCGCGACTGGTAGCCGTGCTCAACGTGTCAACATACCTGGAAAG                         GATCTGGCTATTACTTCTGATGAGGGCTTGAGCTTGGAGGAGCTTCCAAAG
genomic: TTTTGATCGCGACTGGTAGCCGTGCTCAACGTGTCAACATACCTGGAAAGgtttgtaaaa ... cttttttcagGATCTGGCTATTACTTCTGATGAGGCCTTGAGCTTGGAGGAGCTTCCAAAG
EST: gi|148994377|gb|EE034060.2|EE034060
EST:     TTTTGATCGCGACTGGTAGCCGTGCTCAACGTGTCAACATACCTGGAAAG                         GATCTGGCTATTACTTCTGATGAGGCCTTGAGCTTGGAGGAGCTTCCAAAG
genomic: TTTTGATCGCGACTGGTAGCCGTGCTCAACGTGTCAACATACCTGGAAAGgtttgtaaaa ... cttttttcagGATCTGGCTATTACTTCTGATGAGGCCTTGAGCTTGGAGGAGCTTCCAAAG
EST: gi|148943405|gb|EC888464.2|EC888464
EST:     TTTTGATCGCGACTGGTAGCCGTGCTCAACGTGTCAACATACCTGGAAAG                         GATCTGGCTATTACTTCTGATGAGGCCTTGAGCTTGGAGGAGCTTCCAAAG
genomic: TTTTGATCGCGACTGGTAGCCGTGCTCAACGTGTCAACATACCTGGAAAGgtttgtaaaa ... cttttttcagGATCTGGCTATTACTTCTGATGAGGCCTTGAGCTTGGAGGAGCTTCCAAAG
EST: gi|31664370|gb|CD573095.1|CD573095
EST:     TTTTGATCGCGACTGGTAGCCGTGCTCAACGTGTCAACATACCTGGAAAG                         GATCTGGCTATTACTTCTGATGAGGCCTTGAGCTTGGAGGAGCTTCCAAAG
genomic: TTTTGATCGCGACTGGTAGCCGTGCTCAACGTGTCAACATACCTGGAAAGgtttgtaaaa ... cttttttcagGATCTGGCTATTACTTCTGATGAGGCCTTGAGCTTGGAGGAGCTTCCAAAG
EST: gi|67026810|gb|CO455559.1|CO455559
EST:     TTTTGATCGCGACTGGTAGCCGTGCTCAACGTGTCAACATACCTGGAAAG                         GATCTGGCTATTACTTCTGATGAGGCCTTGAGCTTGGAGGAGCTTCCAAAG
genomic: TTTTGATCGCGACTGGTAGCCGTGCTCAACGTGTCAACATACCTGGAAAGgtttgtaaaa ... cttttttcagGATCTGGCTATTACTTCTGATGAGGCCTTGAGCTTGGAGGAGCTTCCAAAG
EST: gi|149014256|gb|EE043820.2|EE043820
EST:     TTTTGATCGCGACTGGTAGCCGTGCTCAACGTGTCAACATACCTGGAAAG                         GATCTGGCTATTACTTCTGATGAGGCCTTGAGCTTGGAGGAGCTTCCAAAG
genomic: TTTTGATCGCGACTGGTAGCCGTGCTCAACGTGTCAACATACCTGGAAAGgtttgtaaaa ... cttttttcagGATCTGGCTATTACTTCTGATGAGGCCTTGAGCTTGGAGGAGCTTCCAAAG
EST: gi|24934176|gb|CA452394.1|CA452394
EST:     TTTTGATCGCGACTGGTAGCCGTGCTCAACGTGTCAACATACCTGGAAAG                         GATCTGGCTATTACTTCTGATGAGGCCTTGAGCTTGGAGGAGCTTCCAAAG
genomic: TTTTGATCGCGACTGGTAGCCGTGCTCAACGTGTCAACATACCTGGAAAGgtttgtaaaa ... cttttttcagGATCTGGCTATTACTTCTGATGAGGCCTTGAGCTTGGAGGAGCTTCCAAAG
EST: gi|24934507|gb|CA452725.1|CA452725
EST:     TTTTGATCGCGACTGGTAGCCGTGCTCAACGTGTCAACATACCTGGAAAG                         GATCTGGCTATTACTTCTGATGAGGCCTTGAGCTTGGAGGAGCTTCCAAAG
genomic: TTTTGATCGCGACTGGTAGCCGTGCTCAACGTGTCAACATACCTGGAAAGgtttgtaaaa ... cttttttcagGATCTGGCTATTACTTCTGATGAGGCCTTGAGCTTGGAGGAGCTTCCAAAG
EST: gi|211426648|gb|FL071976.1|FL071976
EST:     TTTTGATCGCGACTGGTAGCCGBGCTCAACGTGTCMACATACCTGGAAAG                         GATCTGGCTATTACTTCTGATGAGGCCTTGAGCTTGGAGGAGCTTCCAAAG
genomic: TTTTGATCGCGACTGGTAGCCGTGCTCAACGTGTCAACATACCTGGAAAGgtttgtaaaa ... cttttttcagGATCTGGCTATTACTTCTGATGAGGCCTTGAGCTTGGAGGAGCTTCCAAAG
EST: gi|148937231|gb|EC881413.2|EC881413
EST:     TTTTGATCGCGACTGGTAGCCGTGCTCAACGTGTCAACATACCTGGAAAG                         GATCTGGCTATTACTTCTGATGAGGCCTTGAGCTTGGAGGAGCTTCCAAAG
genomic: TTTTGATCGCGACTGGTAGCCGTGCTCAACGTGTCAACATACCTGGAAAGgtttgtaaaa ... cttttttcagGATCTGGCTATTACTTCTGATGAGGCCTTGAGCTTGGAGGAGCTTCCAAAG
EST: gi|149077608|gb|EE166308.2|EE166308
EST:     TTTTGATCGCGACTGGTAGCCGTGCTCAACGTGTCAACATACCTGGAAAG                         GATCTGGCTATTACTTCTGATGAGGCCTTGAGCTTGGAGGAGCTTCCAAAG
genomic: TTTTGATCGCGACTGGTAGCCGTGCTCAACGTGTCAACATACCTGGAAAGgtttgtaaaa ... cttttttcagGATCTGGCTATTACTTCTGATGAGGCCTTGAGCTTGGAGGAGCTTCCAAAG
EST: gi|149074405|gb|EE162793.2|EE162793
EST:     TTTTGATCGCGACTGGTAGCCGTGCTCAACGTGTCAACATACCTGGAAAA                         GATCTGGCTATTACTTCTGAT
genomic: TTTTGATCGCGACTGGTAGCCGTGCTCAACGTGTCAACATACCTGGAAAGgtttgtaaaa ... cttttttcagGATCTGGCTATTACTTCTGAT
EST: gi|76293305|gb|DV032873.1|DV032873
EST:     TTTTGATCGCGACTGGTAGCCGTGCTCAACGTGTCAACATACCTGGAAAG                         GATCTGGCTATTACTTCTGATGAGGCCTTGAGCTTGGAGGAGCTTCCAAAG
genomic: TTTTGATCGCGACTGGTAGCCGTGCTCAACGTGTCAACATACCTGGAAAGgtttgtaaaa ... cttttttcagGATCTGGCTATTACTTCTGATGAGGCCTTGAGCTTGGAGGAGCTTCCAAAG
EST: gi|71311904|gb|DR792431.1|DR792431
EST:     TTTTGATCGCGACTGGTAGCCGTGCTCAACGTGTCAACATACCTGGAAAG                         GATCTGGCTATTACTTCTGATGAGGCCTTGAGCTTGGAGG
genomic: TTTTGATCGCGACTGGTAGCCGTGCTCAACGTGTCAACATACCTGGAAAGgtttgtaaaa ... cttttttcagGATCTGGCTATTACTTCTGATGAGGCCTTGAGCTTGGAGG
EST: gi|149089937|gb|EE179225.2|EE179225
EST:     TTTTGATCGCGACTGGTAGCCGTGCTCAACGTGTCAACATACCTGGAAAG                         GATCTGGCTATTACTTCTGATGAGGCCTTGAGCTTGGAG
genomic: TTTTGATCGCGACTGGTAGCCGTGCTCAACGTGTCAACATACCTGGAAAGgtttgtaaaa ... cttttttcagGATCTGGCTATTACTTCTGATGAGGCCTTGAGCTTGGAG
EST: gi|149108741|gb|EE292941.2|EE292941
EST:     TTTTGATCGCGACTGGTAGCCGTGCTCAACGTGTCAACATACCTGGAAAG                         GATCTGGCTATTACTTCTGATGAGGCCTTGAGCTTGGAGGAGCTTCCAAAG
genomic: TTTTGATCGCGACTGGTAGCCGTGCTCAACGTGTCAACATACCTGGAAAGgtttgtaaaa ... cttttttcagGATCTGGCTATTACTTCTGATGAGGCCTTGAGCTTGGAGGAGCTTCCAAAG
EST: gi|33942527|gb|CF349127.1|CF349127
EST:     TTTTGATCGCGACTGGTAGCCGTGCTCAACGTGTCAACATACCTGGAAAG                         GATCTGGCTATTACTTCTGATGAGGCCTTGAGCTTGGAGGAGCTTCCAAAG
genomic: TTTTGATCGCGACTGGTAGCCGTGCTCAACGTGTCAACATACCTGGAAAGgtttgtaaaa ... cttttttcagGATCTGGCTATTACTTCTGATGAGGCCTTGAGCTTGGAGGAGCTTCCAAAG
EST: gi|47962001|gb|CN844710.1|CN844710
EST:     TTTTGATCGCGACTGGTAGCCGTGCTCAACGTGTCAACATACCTGGAAAG                         GATCTGGCTATTACTTCTGATGAGGCCCTTGAGCTTGGAGGA
genomic: TTTTGATCGCGACTGGTAGCCGTGCTCAACGTGTCAACATACCTGGAAAGgtttgtaaaa ... cttttttcagGATCTGGCTATTACTTCTGATGAGGCC-TTGAGCTTGGAGGA
EST: gi|32938226|gb|CF043045.1|CF043045
EST:     TTTTGATCGCGACTGGTAGCCGTGCTCAACGTGTCAACATACCTGGAAAG                         GATCTGGCTATTACTTCTGATGAGGCCTTGAGCTTGGAGGAGCTTCCAAAG
genomic: TTTTGATCGCGACTGGTAGCCGTGCTCAACGTGTCAACATACCTGGAAAGgtttgtaaaa ... cttttttcagGATCTGGCTATTACTTCTGATGAGGCCTTGAGCTTGGAGGAGCTTCCAAAG
EST: gi|31611973|gb|CD568595.1|CD568595
EST:     TTTTGATCGCGACTGGTAGCCGTGCTCAACGTGTCAACATACCTGGAAAG                         GATCTGGCTATTACTTCTGATGAGGCCTTGAGCTTGGAGGAGCTTCCAAAG
genomic: TTTTGATCGCGACTGGTAGCCGTGCTCAACGTGTCAACATACCTGGAAAGgtttgtaaaa ... cttttttcagGATCTGGCTATTACTTCTGATGAGGCCTTGAGCTTGGAGGAGCTTCCAAAG
EST: gi|76012767|gb|DT939937.1|DT939937
EST:     TTTTGATCGCGACTGGTAGCCGTGCTCAACGTGTCAACATACCTGGAAAG                         GATCTGGCTATTACTTCTGATGAGGCCTTGAGCTTGGAGGAGCTTCCAAAG
genomic: TTTTGATCGCGACTGGTAGCCGTGCTCAACGTGTCAACATACCTGGAAAGgtttgtaaaa ... cttttttcagGATCTGGCTATTACTTCTGATGAGGCCTTGAGCTTGGAGGAGCTTCCAAAG
EST: gi|24934516|gb|CA452734.1|CA452734
EST:     TTTTGATCGCGACTGGTAGCCGTGCTCAACGTGTCAACATACCTGGAAAG                         GATCTGGCTATTACTTCTGATGAGGCCTTGAGCTTGGAGGAGCTTCCAAAG
genomic: TTTTGATCGCGACTGGTAGCCGTGCTCAACGTGTCAACATACCTGGAAAGgtttgtaaaa ... cttttttcagGATCTGGCTATTACTTCTGATGAGGCCTTGAGCTTGGAGGAGCTTCCAAAG

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: 390

TGAAGTTAGCCAGCCTGATGGTTCAAAGCAAAGGTATACAGCGAAGCACATTTTGATCGCGACTGGTAGCCGTGCTCAACGTGTCAACATACCTGGAAAGgtttgtaaaa ... cttttttcagGATCTGGCTATTACTTCTGATGAGGCCTTGAGCTTGGAGGAGCTTCCAAAGCGCGCTGTAATCCTGGGTGGCGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 3032

TGAAGTTAGCCAGCCTGATGGTTCAAAGCAAAGGTATACAGCGAAGCACATTTTGATCGCGACTGGTAGCCGTGCTCAACGTGTCAACATACCTGGAAAGgtttgtaaaa ... cttttttcagGATCTGGCTATTACTTCTGATGAGGCCTTGAGCTTGGAGGAGCTTCCAAAGCGCGCTGTAATCCTGGGTGGCGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 2339

TGAAGTTAGCCAGCCTGATGGTTCAAAGCAAAGGTATACAGCGAAGCACATTTTGATCGCGACTGGTAGCCGTGCTCAACGTGTCAACATACCTGGAAAGgtttgtaaaa ... cttttttcagGATCTGGCTATTACTTCTGATGAGGCCTTGAGCTTGGAGGAGCTTCCAAAGCGCGCTGTAATCCTGGGTGGCGG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 600

TGAAGTTAGCCAGCCTGATGGTTCAAAGCAAAGGTATACAGCGAAGCACATTTTGATCGCGACTGGTAGCCGTGCTCAACGTGTCAACATACCTGGAAAGgtttgtaaaa ... cttttttcagGATCTGGCTATTACTTCTGATGAGGCCTTGAGCTTGGAGGAGCTTCCAAAGCGCGCTGTAATCCTGGGTGGCGG