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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagattgaatttaactcataaccttgtattagttgagactacttgtctgctcatgttactaaatgagatcaatctccttttcagAATAAATGTAATGTCGGCTATGCTTTCATCAACATGACCAATCCTCAGCATATCATTCCGTTTTATCAG

Basic information

species Zea mays
transcript GRMZM5G814700_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G814700_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g31290.1 (Oryza sativa), 3'ss of exon 12
-----------gtagattgaatttaactcataaccttgtattagttgagacta-cttgtctgctcatgttactaaatgagat-caatctccttttcagAATAAATGTAATGTCGGCTATGCTTTCATCAACATGACCAATCCTCAGCATATCATTCCGTTTTATCAG
            ||  | | ||  |||| ||| | |  |||| ||| |||    |||| ||  ||   ||||| |||| |||     || |||||||||| || || ||||| ||||||||||||||||| |||||||||||||||||||||||||| |||||||||
gtgatctagatttatttagtatgcaactaata-catcatatttgttcagatagtcttgcctaatcgaattactgaatgggatgtgtcctacttttcagAACAAGTGCAATGTAGGCTATGCTTTCATCAATATGACCAATCCTCAGCATATCATTCCATTTTATCAG

upper sequence: GRMZM5G814700_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT5G07290.1 (Arabidopsis thaliana), 3'ss of exon 11
-----------------------gtagattgaatttaactcataaccttgtattagttgagactacttgtctgctcatgttactaaatgagatcaatctcctttt-cagAATAAATGTAATGTCGGCTATGCTTTCATCAACATGACCAATCCTCAGCATATCATTCCGTTTTATCAG
                        |  ||  |||  |    |   |    |  ||| | ||  || || ||| |    | || |||||||        ||  ||| ||||||||||| |||||||| ||||||||||||||| | | | | ||| |  ||||  ||||||||||| ||
gtatgcaggcctcttacctgttttttcatctaatggagtctaatgcagccttatagcttagggtattt-tctacat-cgata-taaatgaaccttccttctatttgcagAATAAATGCAATGTCGGATATGCTTTCATCAACCTTATCGAACCTGAAAATATTGTTCCGTTTTATAAG

upper sequence: GRMZM5G814700_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ29695 (Selaginella moellendorffii), 3'ss of exon 7
gtagattgaatttaactcataaccttgtattagttgagactacttgtctgctcatgttactaaatgagatcaatctccttttcagAATAAATGTAATGTCGGCTATGCTTTCATCAACATGACCAATCCTCAGCATATCATTCCGTTTTATCAG
                        |  | ||||  |||   |  ||| | |   || || | |  |    |  |  ||| | ||||||||||| || || |||||||| ||||||||||||||| | ||    || ||| | || |||||  ||
-----------------------gtgattttaggcgagcaaaagtgtttccc--tggtattgaccgg---cttttgcctgtgcagAATAAATGCAACGTTGGCTATGCATTCATCAACATGACCGAGCCAGCTCACATCGTCCCCTTTTACAAG

upper sequence: GRMZM5G814700_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ29693 (Selaginella moellendorffii), 3'ss of exon 9
gtagattgaatttaactcataaccttgtattagttgagactacttgtctgctcatgttactaaatgagatcaatctccttttcagAATAAATGTAATGTCGGCTATGCTTTCATCAACATGACCAATCCTCAGCATATCATTCCGTTTTATCAG
                   ||| | | ||         | | |||   | ||     | || | ||   |   |   | ||||||||||| ||||| || || |||||||||||||||||||     |||  ||||||| | || || |   ||
------------------gtaatcgtataacga---gaaatccttacattct-----tgctgattg---ttggttctcctttcagAATAAGTGTAACGTGGGGTATGCTTTCATCAACATGATTGCACCTGTGCATATCGTCCCTTTCTTCAAG

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|22542340|gb|BU092793.1|BU092793
EST:     AAAGTCATAAGGGCACTTATGATTTTATTTACTTGCCAATTGATTTTAAG                         AATAAATGTAATGTCGGCTATGCTTTCATCAACATGACCAATCCTCAGCAT
genomic: AAAGTCATAAGGGCACTTATGATTTTATTTACTTGCCAATTGATTTTAAGgtagattgaa ... tccttttcagAATAAATGTAATGTCGGCTATGCTTTCATCAACATGACCAATCCTCAGCAT
EST: gi|91877858|gb|EB407815.1|EB407815
EST:     AAAGTCATAAGGGCACTTATGATTTTATTTACTTGCCAATTGATTTTAAG                         AATAAATGTAATGTCGGCTATGCTTTTC-TCAACATG
genomic: AAAGTCATAAGGGCACTTATGATTTTATTTACTTGCCAATTGATTTTAAGgtagattgaa ... tccttttcagAATAAATGTAATGTCGGCTATGCTTT-CATCAACATG
EST: gi|67013397|gb|CO442146.1|CO442146
EST:     ATTGATTTTAAG                         AATAAATGTAATGTCGGCTATGCTTTCATCAACATGACCAATCCTCAGCAT
genomic: ATTGATTTTAAGgtagattgaa ... tccttttcagAATAAATGTAATGTCGGCTATGCTTTCATCAACATGACCAATCCTCAGCAT
EST: gi|26558461|gb|CA830696.1|CA830696
EST:     AAAGTCATAAGGGCACTTATGATTTTATTTACTTGCCAATTGATTTTAAG                         AATAAATGTAATGTCGGCTATGCTTTCATCAACATGACCAATCCTCAGCAT
genomic: AAAGTCATAAGGGCACTTATGATTTTATTTACTTGCCAATTGATTTTAAGgtagattgaa ... tccttttcagAATAAATGTAATGTCGGCTATGCTTTCATCAACATGACCAATCCTCAGCAT
EST: gi|211008041|gb|FL362435.1|FL362435
EST:     AAAGTCATAAGGGCACTTATGATTTTATTTACTTGCCAATTGATTTTAAG                         AATAAATGTAATGTCGGCTATGCTTTCATCAACATGACCAATCCTCAGCAT
genomic: AAAGTCATAAGGGCACTTATGATTTTATTTACTTGCCAATTGATTTTAAGgtagattgaa ... tccttttcagAATAAATGTAATGTCGGCTATGCTTTCATCAACATGACCAATCCTCAGCAT
EST: gi|71307207|gb|DR789770.1|DR789770
EST:     AAAGTCATAAGGGCACTTATGATTTTATTTACTTGCCAATTGATTTTAAG                         AATAAATGTAATGTCGGCTATGCTTTCATCAACATGACCAATCCTCAGCAT
genomic: AAAGTCATAAGGGCACTTATGATTTTATTTACTTGCCAATTGATTTTAAGgtagattgaa ... tccttttcagAATAAATGTAATGTCGGCTATGCTTTCATCAACATGACCAATCCTCAGCAT
EST: gi|33093066|gb|CF053060.1|CF053060
EST:     AAAGTCATAAGGGCACTTATGATTTTATTTACTTGCCAATTGATTTTAAG                         AATAAATGTAATGTCGGCTATGCTTTCATCAACATGACCAATCCTCAGCAT
genomic: AAAGTCATAAGGGCACTTATGATTTTATTTACTTGCCAATTGATTTTAAGgtagattgaa ... tccttttcagAATAAATGTAATGTCGGCTATGCTTTCATCAACATGACCAATCCTCAGCAT
EST: gi|32867814|gb|CF007496.1|CF007496
EST:     AAAGTCATAAGGGCACTTATGATTTTATTTACTTGCCAATTGATTTTAAG                         AATAAATGTAATGTCGGCTATGCTTTCATCAACATGACCAATCCTCAGCAT
genomic: AAAGTCATAAGGGCACTTATGATTTTATTTACTTGCCAATTGATTTTAAGgtagattgaa ... tccttttcagAATAAATGTAATGTCGGCTATGCTTTCATCAACATGACCAATCCTCAGCAT
EST: gi|71772002|gb|DR969939.1|DR969939
EST:     AAAGTCATAAGGGCACTTATGATTTTATTTACTTGCCAATTGATTTTTAG                         AATAAATGTAATGTCGGCTATGCTTTCATCAACATGACCAATCCTCAGCAT
genomic: AAAGTCATAAGGGCACTTATGATTTTATTTACTTGCCAATTGATTTTAAGgtagattgaa ... tccttttcagAATAAATGTAATGTCGGCTATGCTTTCATCAACATGACCAATCCTCAGCAT

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: 45 (upstream exon), 49 (downstream exon)
Score: 326

GTATACCTCCAAGATGCTCTTGGCTGCTATTGATGAAAGTCATAAGGGCACTTATGATTTTATTTACTTGCCAATTGATTTTAAGgtagattgaa ... tccttttcagAATAAATGTAATGTCGGCTATGCTTTCATCAACATGACCAATCCTCAGCATATCATTCCGTTTTATCAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 172

GTATACCTCCAAGATGCTCTTGGCTGCTATTGATGAAAGTCATAAGGGCACTTATGATTTTATTTACTTGCCAATTGATTTTAAGgtagattgaa ... tccttttcagAATAAATGTAATGTCGGCTATGCTTTCATCAACATGACCAATCCTCAGCATATCATTCCGTTTTATCAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 163

GTATACCTCCAAGATGCTCTTGGCTGCTATTGATGAAAGTCATAAGGGCACTTATGATTTTATTTACTTGCCAATTGATTTTAAGgtagattgaa ... tccttttcagAATAAATGTAATGTCGGCTATGCTTTCATCAACATGACCAATCCTCAGCATATCATTCCGTTTTATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 382

GTATACCTCCAAGATGCTCTTGGCTGCTATTGATGAAAGTCATAAGGGCACTTATGATTTTATTTACTTGCCAATTGATTTTAAGgtagattgaa ... tccttttcagAATAAATGTAATGTCGGCTATGCTTTCATCAACATGACCAATCCTCAGCATATCATTCCGTTTTATCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagttgagactacttgtctgctcatgttactaaatgagatcaatctccttttcagAATAAATGTAATGTCGGCTATGCTTTCATCAACATGACCAATCCTCAGCATATCATTCCGTTTTATCAG
                           tactaaa  putative branch site (score: 382)
                                       tcaatctccttttc  putative PPT
                          ttactaaat  TA-rich tract