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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtttgaaactttgaatttaactcataagcgaccggggccttgtattagttgagactacttttgtgttcatgttactaaatgagatcaatctccttttcagAATAAATGTAATGTTGGCTATGCTTTCATCAACATGACCAATGCTCAGCATATCATTCCATTTTATCAG

Basic information

species Zea mays
transcript GRMZM2G459746_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G459746_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os02g31290.1 (Oryza sativa), 3'ss of exon 12
gtagtttgaaactttgaatttaactcataagcgaccggggccttgtattagttgagactacttt-tgtgttcatgttactaaatgagat-caatctccttttcagAATAAATGTAATGTTGGCTATGCTTTCATCAACATGACCAATGCTCAGCATATCATTCCATTTTATCAG
            | |  |||||  |  || || ||     | |  |||| ||| |||     ||   |  ||   ||||| |||| |||     || |||||||||| || || ||||| ||||||||||||||||| ||||||||| ||||||||||||||||||||||||||
--------gtgatctagatttatttagtatgcaactaatacatcatatttgttcagatagtcttgcctaatcgaattactgaatgggatgtgtcctacttttcagAACAAGTGCAATGTAGGCTATGCTTTCATCAATATGACCAATCCTCAGCATATCATTCCATTTTATCAG

upper sequence: GRMZM2G459746_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA08G01040.1 (Glycine max), 3'ss of exon 12
gtagtttgaaactttgaatttaactcataagcgaccggggccttgtattagttgagactacttttgtgttcatgttactaaatgagatcaatctccttttcagAATAAATGTAATGTTGGCTATGCTTTCATCAACATGACCAATGCTCAGCATATCATTCCATTTTATCAG
               | |  ||  || |    ||      | ||   || |   |||      |  |    ||||| |||| |    || |   |  || ||||| |||||||||||||||||||| ||||| |||||||   || ||   || || ||||| ||  |||||
---------------gtaagtatttc-tggttgatttattctttccttttgagaagaaa----tcataaatatgtttctaattttagtctacaacgattgcagAACAAATGTAATGTTGGCTATGCATTCATAAACATGATTGATCCTGGTCAAATTATTCCTTTCCATCAG

upper sequence: GRMZM2G459746_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA04G37810.1 (Glycine max), 3'ss of exon 10
-----------gtagtttgaaactttgaattta-----actcataagcgaccggggccttgtattagttgagactacttttgtgttcatgttactaaatgagatcaatctcctttt-cagAATAAATGTAATGTTGGCTATGCTTTCATCAACATGACCAATGCTCAGCATATCATTCCATTTTATCAG
            |  ||| ||     | |||||     |||    ||      |   |||   |||  |||    |   |  |    ||||| |||| | |  || |       || ||||| |||||||||||||||||||| |||||||| |||| | || ||   || || ||||||||  |  ||
gtatttgccaattgatttcaaggcaagtatttatttggacttgctagttgattgattctttacttaaatgaagtaa---tcataaatatgtttctaagTCAATTCTACAAATGGTTGCAGAACAAATGTAATGTTGGCTATGCATTCATCAATATGATCGATCCTGGACAAATTATTCCATTCCACAAG

upper sequence: GRMZM2G459746_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA06G17250.1 (Glycine max), 3'ss of exon 10
-----------gtagtttgaaactttgaattta-----actcataagcgaccggggccttgtattagttgagactacttttgtgttcatgttactaaatgagatcaatctcctttt-cagAATAAATGTAATGTTGGCTATGCTTTCATCAACATGACCAATGCTCAGCATATCATTCCATTTTATCAG
            |  ||| ||     | |||||     |||    ||   |  |   |||   |||  |||  | |   || |     |||| ||||   |  || |       || ||||| |||||||||||||||||||| |||||||| ||||   || ||   || || ||||||||  | |||
gtatttgccaattgatttcaaggcaagtatttatttggacttgctagttgcttgattctttacttaaatgaagcaa---ttataaatgtgtttctaagGCAATTCTACAAATGGTTGCAGAACAAATGTAATGTTGGCTATGCATTCATCAATATGATTGATCCTGGACAAATTATTCCATTCCACCAG

upper sequence: GRMZM2G459746_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA04G37810.2 (Glycine max), 3'ss of exon 8
gtagtttgaaactttgaatttaactcataagcgaccggggccttgtattagttgagactacttttgtgttcatgttactaaatgagatcaatctcctttt-cagAATAAATGTAATGTTGGCTATGCTTTCATCAACATGACCAATGCTCAGCATATCATTCCATTTTATCAG
        ||   || | ||  |||    ||      |   |||   |||  |||    |   |  |    ||||| |||| | |  || |       || ||||| |||||||||||||||||||| |||||||| |||| | || ||   || || ||||||||  |  ||
------gcaagtatttatttggacttgctagttgattgattctttacttaaatgaagtaa---tcataaatatgtttctaagtcaattctacaaatggttgcagAACAAATGTAATGTTGGCTATGCATTCATCAATATGATCGATCCTGGACAAATTATTCCATTCCACAAG

upper sequence: GRMZM2G459746_T01 (Zea mays), 3'ss of exon 12
lower sequence: EFJ29695 (Selaginella moellendorffii), 3'ss of exon 7
gtagtttgaaactttgaatttaactcataagcgaccggggccttgtattagttgagactacttttgtgttcatgttactaaatgagatcaatctccttttcagAATAAATGTAATGTTGGCTATGCTTTCATCAACATGACCAATGCTCAGCATATCATTCCATTTTATCAG
                                          |  | ||||  |||   |    ||| | | || || | |  |   |   |  ||| | ||||||||||| || ||||||||||| ||||||||||||||| |  |    || ||| | || |||||  ||
-----------------------------------------gtgattttaggcgag--caaaagtgtttccctggtattgaccggctt---ttgcctgtgcagAATAAATGCAACGTTGGCTATGCATTCATCAACATGACCGAGCCAGCTCACATCGTCCCCTTTTACAAG

upper sequence: GRMZM2G459746_T01 (Zea mays), 3'ss of exon 12
lower sequence: EFJ28200 (Selaginella moellendorffii), 3'ss of exon 9
gtagtttgaaactttgaatttaactcataagcgaccggggccttgtattagttgagactacttttgtgttcatgttactaaatgagatcaatctccttttcagAATAAATGTAATGTTGGCTATGCTTTCATCAACATGACCAATGCTCAGCATATCATTCCATTTTATCAG
                                          |  | ||||  |||   |    ||| | | || || | |  |   |   |  ||| | ||||| ||||| || ||||||||||| ||||||||||||||| |  |    || ||| | || |||||  ||
-----------------------------------------gtgattttaggcgag--caaaagtgtttccctggtattgatcggctt---ttgcctgtgcagAACAAATGCAACGTTGGCTATGCATTCATCAACATGACCGAGCCAGCTCACATCGTCCCCTTTTACAAG

upper sequence: GRMZM2G459746_T01 (Zea mays), 3'ss of exon 12
lower sequence: EFJ29693 (Selaginella moellendorffii), 3'ss of exon 9
gtagtttgaaactttgaatttaactcataagcgaccggggccttgtattagttgagactacttttgtgttcatgttactaaatgagatcaatctccttttcagAATAAATGTAATGTTGGCTATGCTTTCATCAACATGACCAATGCTCAGCATATCATTCCATTTTATCAG
                                      |   | |||| |   ||||  |   ||   |||   || || | ||   |   |   | ||||||||||| ||||| || || |||||||||||||||||||      ||  ||||||| | || || |   ||
--------------------------------------gtaatcgtataa--cgagaa-atccttacattc---ttgctgattg---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|30160688|gb|CB924417.1|CB924417
EST:     AAGTCATAAGGGCACTTATGACTTTATTTACTTGCCCAATTGATTTTAAG                         AATAAATGTAATGTTGGCTATGCTTTCATCAACATGACCAATGCTCA
genomic: AAGTCATAAGGGCACTTATGACTTTATTTACTTGCC-AATTGATTTTAAGgtagtttgaa ... tccttttcagAATAAATGTAATGTTGGCTATGCTTTCATCAACATGACCAATGCTCA




















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), 47 (downstream exon)
Score: 44

GTATACCTCCAAGATGCTCTTGGCTGCTATTGATGAAAGTCATAAGGGCACTTATGACTTTATTTACTTGCCAATTGATTTTAAGgtagtttgaa ... tccttttcagAATAAATGTAATGTTGGCTATGCTTTCATCAACATGACCAATGCTCAGCATATCATTCCATTTTATCAG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 54

GTATACCTCCAAGATGCTCTTGGCTGCTATTGATGAAAGTCATAAGGGCACTTATGACTTTATTTACTTGCCAATTGATTTTAAGgtagtttgaa ... tccttttcagAATAAATGTAATGTTGGCTATGCTTTCATCAACATGACCAATGCTCAGCATATCATTCCATTTTATCAG


Block sizes: 43 (upstream exon), 48 (downstream exon)
Score: 27

GTATACCTCCAAGATGCTCTTGGCTGCTATTGATGAAAGTCATAAGGGCACTTATGACTTTATTTACTTGCCAATTGATTTTAAGgtagtttgaa ... tccttttcagAATAAATGTAATGTTGGCTATGCTTTCATCAACATGACCAATGCTCAGCATATCATTCCATTTTATCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 37

GTATACCTCCAAGATGCTCTTGGCTGCTATTGATGAAAGTCATAAGGGCACTTATGACTTTATTTACTTGCCAATTGATTTTAAGgtagtttgaa ... tccttttcagAATAAATGTAATGTTGGCTATGCTTTCATCAACATGACCAATGCTCAGCATATCATTCCATTTTATCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagttgagactacttttgtgttcatgttactaaatgagatcaatctccttttcagAATAAATGTAATGTTGGCTATGCTTTCATCAACATGACCAATGCTCAGCATATCATTCCATTTTATCAG
                           tactaaa  putative branch site (score: 37)
                                       tcaatctccttttc  putative PPT
                          ttactaaat  TA-rich tract