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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCAACTTGCAGTGAGTACTCTATGCAGGCGTACAAACGATATGGTGTTGTAAAGGGTTCCATCTTGACTGCTTGGCGCCTTTGCCGTTGTAATCCTCTTGgtatgtagttttttttctctatgtgcttagttatctctgttgtttgacatttttcatatatgtatagatctgtgtcacataacatttaatttgtgggacttagacctctctgatttatatgcag

Basic information

species Zea mays
transcript GRMZM5G819212_T05
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G819212_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g15970.5 (Oryza sativa), 5'ss of exon 3
CCAACTTGCAGTGAGTACTCTATGCAGGCGTACAAACGATATGGTGTTGTAAAGGGTTCCATCTTGACTGCTTGGCGCCTTTGCCGTTGTAATCCTCTTGgtatgtagttttttttctctatgtgcttagttatctctgttgtttgacatttttcatatatgtatagatctgtgtcacataacatttaatttgtgggacttagacctctctgatttatatgcag
|||||||||||||||||||||||||| || |||||| ||| ||||||| ||||||| | |||||||| |||||||| || ||||| ||||||||||||||||||||| |||||| | || | ||||| | | || || | || | || | | ||| ||| || | ||||| | | || | | | || | | |||
CCAACTTGCAGTGAGTACTCTATGCAAGCATACAAAAAATACGGTGTTGCAAAGGGTACAATCTTGACAGCTTGGCGTCTATGCCGCTGTAATCCTCTTGgtatgtaggttttttcgttg--gttcatagttcttttgatttctt--cgacagtcgca---gtctgcacctgcatcatatcatatttatt-----aaattt---cttttacaataaacaaacag

upper sequence: GRMZM5G819212_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os11g47930.1 (Oryza sativa), 5'ss of exon 4
CCAACTTGCAGTGAGTACTCTATGCAGGCGTACAAACGATATGGTGTTGTAAAGGGTTCCATCTTGACTGCTTGGCGCCTTTGCCGTTGTAATCCTCTTGgtatgtagttttttttctctatgtgcttagttatctctgttg-tttgacatttttcatatatgtatagatctgtgtcacataacatttaatttgtgggacttagacctctctgatttatatgcag
||||||||||| ||||||||||||| || |||||| ||| || |||| ||||||| | |||||||| |||||||| || |||| |||||||||||||||||||||| ||||| | || | ||||| | | || ||||||| | | | || | | ||| ||| || | || || ||| | ||| | | | |||
CCAACTTGCAGCCAGTACTCTATGCAAGCATACAAAAAATACGGCGTTGCAAAGGGTACAATCTTGACAGCTTGGCGTCTATGCCATTGTAATCCTCTTGgtatgtaggtttttcgttg---gttcatagttcttttgatttctttgacagt---cgca---gtctgcacctgcatcatatcatatcta-----------ttaaatttctttt-ccaacaaacag

upper sequence: GRMZM5G819212_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv08s0007g00520.t01 (Vitis vinifera), 5'ss of exon 3
CCAACTTGCAGTGAGTACTCTATGCAGGCGTACAAACGATATGGTGTTGTAAAGGGTTCCATCTTGACTGCTTGGCGCCTTTGCCGTTGTAATCCTCTTGgtatgtagttttttttctctatgtgcttagttatc---------tctgt-----tgtttgacatttttcatatatgtat--------agatctgtgtcacataacattta-atttgtgggacttagacctctctgatttatatgcag
|| || || |||||||| || ||| | || || || |||||| ||||||||||| || ||||||| ||||||| || ||||| |||||||| ||||||| | | | | | | ||| || | ||||| | | |||| | || ||||| | | | | | || ||| || ||| | | || | ||| | | |||
CCCACATGTAGTGAGTATTCCATGGAAGCCTATAAGAAATATGGAGTTGTAAAGGGCACCGTCTTGACCACTTGGCGTCTCTGCCGCTGTAATCCCCTTGgtacaatttctactctttttgcaatcttgaataccatacaaaattctgtgctcttttctgacctagttatggtatgttttcggtcttaagagtatatttcacctcatgggcatctgtaaatatgaagccaattatattcttttccag

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|211290851|gb|FL314522.1|FL314522
EST:     AAAGGGTTCCATCTTGACTGCTTGGCGCCTTTGCCGTTGTAATCCTCTTG                         GTGGATATGGGTATGATCCTCCAAAATGGTTTGGCGAGGAAGATGTACCTC
genomic: AAAGGGTTCCATCTTGACTGCTTGGCGCCTTTGCCGTTGTAATCCTCTTGgtatgtagtt ... ttatatgcagGTGGATATGGGTATGATCCTCCAAAATGGTTTGGCGAGGAAGATGTACCTC
EST: gi|33467473|gb|CF244522.1|CF244522
EST:     AAAGGGTTCCATCTTGACTGCTTGGCGCCTTTGCCGTTGTAATCCTCTTG                         GTGGATATGGGTATGATCCTCCAAAATGGTTTGGCGAGGAAGATGTACCTC
genomic: AAAGGGTTCCATCTTGACTGCTTGGCGCCTTTGCCGTTGTAATCCTCTTGgtatgtagtt ... ttatatgcagGTGGATATGGGTATGATCCTCCAAAATGGTTTGGCGAGGAAGATGTACCTC
EST: gi|22521084|gb|BU079895.1|BU079895
EST:     AAAGGGTTCCATCTTGACTGCTTGGCGCCTTTGCCGTTGTAATCCTCTTG                         GTGGATATGGGTATGATCCTCCAAAATGGTTTGGCGAGGAAGATGTACCTC
genomic: AAAGGGTTCCATCTTGACTGCTTGGCGCCTTTGCCGTTGTAATCCTCTTGgtatgtagtt ... ttatatgcagGTGGATATGGGTATGATCCTCCAAAATGGTTTGGCGAGGAAGATGTACCTC
EST: gi|211269504|gb|FL311290.1|FL311290
EST:     AAAGGGTTCCATCTTGACTGCTTGGCGCCTTTGCCGTTGTAATCCTCTTG                         GTGGATATGGGTATGATCCTCCAAAATGGTTTGGCGAG
genomic: AAAGGGTTCCATCTTGACTGCTTGGCGCCTTTGCCGTTGTAATCCTCTTGgtatgtagtt ... ttatatgcagGTGGATATGGGTATGATCCTCCAAAATGGTTTGGCGAG
EST: gi|5296116|gb|AI782991.1|AI782991
EST:     AAAGGGTTCCATCTTGACTGCTTGGCGCCTTTGCCGTTGTAATCCTCTTG                         GTGGATATGGGTATGATCCTCCAAAATGGTTTGGCGAGGAAGATGTACCTC
genomic: AAAGGGTTCCATCTTGACTGCTTGGCGCCTTTGCCGTTGTAATCCTCTTGgtatgtagtt ... ttatatgcagGTGGATATGGGTATGATCCTCCAAAATGGTTTGGCGAGGAAGATGTACCTC
EST: gi|78022966|gb|DV491353.1|DV491353
EST:     AAAGGGTTCCATCTTGACTGCTTGGCGCCTTTGCCGTTGTAATCCTCTTG                         GTGGATATGGGTATGATCCTCCAAAATGGTTTGGCGAGGAAGATGTACCTC
genomic: AAAGGGTTCCATCTTGACTGCTTGGCGCCTTTGCCGTTGTAATCCTCTTGgtatgtagtt ... ttatatgcagGTGGATATGGGTATGATCCTCCAAAATGGTTTGGCGAGGAAGATGTACCTC
EST: gi|211336107|gb|FL367026.1|FL367026
EST:     AAAGGGTTCCATCTTGACTGCTTGGCGCCTTTGCCGTTGTAATCCTCTTG                         GTGGATATGGGTATGATCCTCCAAAATGGTTTGGCGAGGAAGATGTACCT
genomic: AAAGGGTTCCATCTTGACTGCTTGGCGCCTTTGCCGTTGTAATCCTCTTGgtatgtagtt ... ttatatgcagGTGGATATGGGTATGATCCTCCAAAATGGTTTGGCGAGGAAGATGTACCT

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: 47 (upstream exon), 45 (downstream exon)
Score: 20

CCAACTTGCAGTGAGTACTCTATGCAGGCGTACAAACGATATGGTGTTGTAAAGGGTTCCATCTTGACTGCTTGGCGCCTTTGCCGTTGTAATCCTCTTGgtatgtagtt ... ttatatgcagGTGGATATGGGTATGATCCTCCAAAATGGTTTGGCGAGGAAGATGTACCTCTGCAATAGTAATGCCTAGTAATTGAAAGTACAGGCATTGTAATTCTTCA


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 49

CCAACTTGCAGTGAGTACTCTATGCAGGCGTACAAACGATATGGTGTTGTAAAGGGTTCCATCTTGACTGCTTGGCGCCTTTGCCGTTGTAATCCTCTTGgtatgtagtt ... ttatatgcagGTGGATATGGGTATGATCCTCCAAAATGGTTTGGCGAGGAAGATGTACCTCTGCAATAGTAATGCCTAGTAATTGAAAGTACAGGCATTGTAATTCTTCA


Block sizes: 45 (upstream exon), 41 (downstream exon)
Score: 15

CCAACTTGCAGTGAGTACTCTATGCAGGCGTACAAACGATATGGTGTTGTAAAGGGTTCCATCTTGACTGCTTGGCGCCTTTGCCGTTGTAATCCTCTTGgtatgtagtt ... ttatatgcagGTGGATATGGGTATGATCCTCCAAAATGGTTTGGCGAGGAAGATGTACCTCTGCAATAGTAATGCCTAGTAATTGAAAGTACAGGCATTGTAATTCTTCA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 32

CCAACTTGCAGTGAGTACTCTATGCAGGCGTACAAACGATATGGTGTTGTAAAGGGTTCCATCTTGACTGCTTGGCGCCTTTGCCGTTGTAATCCTCTTGgtatgtagtt ... ttatatgcagGTGGATATGGGTATGATCCTCCAAAATGGTTTGGCGAGGAAGATGTACCTCTGCAATAGTAATGCCTAGTAATTGAAAGTACAGGCATTGTAATTCTTCA