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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgctgtatgccagtaccatgtgctattcttgtttcctttcaaaaattaatggtagattgaagttatgtcagggttcctattttttatgtaattcttgtagTTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGATCAACAGGATCAAGTGGTGCCAGACAGCCAACAATGCTCTCTCCCTTTTGTCTACAAATGATA

Basic information

species Zea mays
transcript GRMZM2G165418_T04
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os06g36770.1 (Oryza sativa), 3'ss of exon 3
-tgctgtatgccagtaccatgtgctattcttgtt---tcctttcaaaaattaatggtagattgaagtt-atgtcagggttcctattttttatgtaattcttgtagTTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGATCAACAGGATCAAGTGGTGCCAGACAGCCAACAATGCTCTCTCCCTTTTGTCTACAAATGATA
 ||  | ||  || ||   ||   |  |||||||   | ||| |   ||||| | | | || |||  | |  ||   |||    ||||| ||| || | || |||||||| |||||||||||||||||||||||||| |||||||||| ||||| |||||||||||||||||| ||| | ||||||||| |||||||||||||||
atgaagcattacattattgtgctatgctcttgttttgttcttgcttgaattacttgcatatggaaactcacatctatgtt----tttttgatg-aactgttctagTTTGATTACCTCAAAAGTTTGGAAATAGAGGAGAAGATCAACAAGATCAGGTGGTGCCAGACAGCCAATAATTCACTCTCCCTTCTGTCTACAAATGATA

upper sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA08G20830.4 (Glycine max), 3'ss of exon 3
tgctgtatgccagtaccatgtgcta-ttcttgtttcctttcaaaaattaatggtagattgaagttatgtcagggttcctattttttatgtaattcttgtagTTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGATCAACAGGATCAAGTGGTGCCAGACAGCCAACAATGCTCTCTCCCTTTTGTCTACAAATGATA
        |  | |  ||    ||  ||  || | |||      || |  | || ||    |   |||| |   ||  |    | |   |  || ||  |||||||||| || || |||||||||||||| || || || ||||  ||||| |||||||| ||||||||   |||| | | |||| | || ||||||||||
--------gtaattttcagtcactggttaatgctgcct-----gaaatgcttgtggagcagaa--atgttaacatttatgacatgtg-attgttgtttcagTTTGACTATCTTAAGAGTTTGGAAATAGAAGAGAAAATTAACAAAATCAAATGGTGCCAAACAGCCAATGGTGCTTTGTTCCTTCTATCCACAAATGATA

upper sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 3
-------tgctgtatgccagtaccatgtgctattcttgtttcctttcaaaaattaatggtagattgaagttatgtcagggttcctattttttatgtaattcttgt--agTTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGATCAACAGGATCAAGTGGTGCCAGACAGCCAACAATGCTCTCTCCCTTTTGTCTACAAATGATA
       |    |  |  | | |    ||   ||  | |   |   |      | |        |||| |  | | |  | | | |  ||   | |  |   ||   |||||||||| || || || |||||||||||||| || ||||| | |||||  |||||||||||||| ||   ||| || |  ||| | ||||| |||||||
gtatttctttcatcagttactcctgcctgaagtttgtttgcaccaccctttgctcactaggctctgaaatgttttaattgatgccacattgcttattctctgtgctcagTTTGACTATCTGAAGAGCTTGGAAATAGAGGAGAAAATCAATAAGATCAGATGGTGCCAGACAGCAAATGGTGCCCTGTTTCTTCTATCTACGAATGATA

upper sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 4
lower sequence: PP1S100_124V6.1 (Physcomitrella patens), 3'ss of exon 3
tgctgtatgccagtaccatgtgctattcttgtttcctttcaaaaattaatggtagattgaagttatgtcagggttcctattttttatgtaattctt---gtagTTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGATCAACAGGATCAAGTGGTGCCAGACAGCCAACAATGCTCTCTCCCTTTTGTCTACAAATGATA
   ||| |     |||  | ||    |  |           | | ||  ||||  ||   | ||     |    | || || |  ||||| ||  |   | |||| || ||||| || ||||||||||||||||| ||||||||||  || |  |||||||||||  ||||   ||| |  |  ||  | ||||||||||| |
---tgtgtagggatactgtttgacggtaatccagttgcattacacttgttggtcaatcctattttacgaacacgtgcttttctgaatgtattttgttatgcagTTCGATTACCTGAAGAGTTTGGAAATAGAGGAGAAGATCAACAAAATAAGATGGTGCCAGACCACCAATGCTGCCCAGTTTCTACTTTCTACAAATGACA

upper sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 4
lower sequence: EFJ09063 (Selaginella moellendorffii), 3'ss of exon 3
tgctgtatgccagtaccatgtgctattcttgtttcctttcaaaaattaatggtagattgaagttatgtcagggttcctattttttatgtaattcttgtagTTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGATCAACAGGATCAAGTGGTGCCAGACAGCCAACAATGCTCTCTCCCTTTTGTCTACAAATGATA
                             ||       || |   || |  |    |||| | ||  |         || ||||  | |   |     |||||||||||||||| ||  |||| |||||||||||||||||||  ||||  ||||| || || || |||   ||||  |   |||| || || ||||| |
----------------------------gtgcgcttgctctatcgttga-agcgtgttgatgctacat---------tacttttgttttggcttccccagTTTGACTACCTCAAGAGCCTGGAGATAGAGGAAAAGATCAACAAAATCAGATGGTGTCACACGGCTAACGGCGCTCGTTTTGTTTTATCCACTAATGACA

upper sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 4
lower sequence: EFJ08844 (Selaginella moellendorffii), 3'ss of exon 3
tgctgtatgccagtaccatgtgctattcttgtttcctttcaaaaattaatggtagattgaagttatgtcagggttcctattttttatgtaattcttgtagTTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGATCAACAGGATCAAGTGGTGCCAGACAGCCAACAATGCTCTCTCCCTTTTGTCTACAAATGATA
                             ||       || |   || |  |    |||| | ||  | |         |||||| | |   |     |||||||||||||||| ||  |||| |||||||||||||||||||  ||||  ||||| || || || |||   ||||  |   |||| || || ||||| |
----------------------------gtgcgcttgctctatcgttga-agcgtgttgatgctacatta-------ctttttttttttggcttccccagTTTGACTACCTCAAGAGCCTGGAGATAGAGGAAAAGATCAACAAAATCAGATGGTGTCACACGGCTAACGGCGCTCGTTTTGTTTTATCCACTAATGACA

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|19057502|gb|BM736169.1|BM736169
EST:     GACACCCAGAGTTCCGCTACAAAACTGAATTTCAGAGTCATGAACCTGAG                         TTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGGTCAACAGGATCAAG
genomic: GACACCCAGAGTTCCGCTACAAAACTGAATTTCAGAGTCATGAACCTGAGgttaataagc ... attcttgtagTTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGATCAACAGGATCAAG
EST: gi|31352864|gb|CD437221.1|CD437221
EST:     GACACCCAGAGTTCCGCTACAAAACTGAATTTCAGAGTCATGAACCTGAG                         TTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGATCAACAGGATCAAG
genomic: GACACCCAGAGTTCCGCTACAAAACTGAATTTCAGAGTCATGAACCTGAGgttaataagc ... attcttgtagTTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGATCAACAGGATCAAG
EST: gi|149084056|gb|EE173454.2|EE173454
EST:     GACACCCAGAGTTCCGCTACAAAACTGAATTTCAGAGTCATGAACCTGAG                         TTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGATCAACAGGATCAAG
genomic: GACACCCAGAGTTCCGCTACAAAACTGAATTTCAGAGTCATGAACCTGAGgttaataagc ... attcttgtagTTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGATCAACAGGATCAAG
EST: gi|19822590|gb|BQ048614.1|BQ048614
EST:     GACACCCAGAGTTCCGCTACAAAACTGAATTTCAGAGTCATGAACCTGAG                         TTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGGTCAACAGGATCAAG
genomic: GACACCCAGAGTTCCGCTACAAAACTGAATTTCAGAGTCATGAACCTGAGgttaataagc ... attcttgtagTTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGATCAACAGGATCAAG
EST: gi|18649538|gb|BM498357.1|BM498357
EST:     GCTACAAAACTGAATTTCAGAGTCATGAACCTGAG                         TTGGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGGTCAACAGGATCAAG
genomic: GCTACAAAACTGAATTTCAGAGTCATGAACCTGAGgttaataagc ... attcttgtagTTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGATCAACAGGATCAAG
EST: gi|71419454|gb|DR804774.1|DR804774
EST:     GACACCCAGAGTTCCGCTACAAAACTGAATTTCAGAGTCATGAACCTGAG                         TTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGATCAACAGGATCAAG
genomic: GACACCCAGAGTTCCGCTACAAAACTGAATTTCAGAGTCATGAACCTGAGgttaataagc ... attcttgtagTTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGATCAACAGGATCAAG
EST: gi|149051574|gb|EE155673.2|EE155673
EST:     GACACCCAGAGTTCCGCTACAAAACTGAATTTCAGAGTCATGAACCTGAG                         TTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGATCAACAGGATCAAG
genomic: GACACCCAGAGTTCCGCTACAAAACTGAATTTCAGAGTCATGAACCTGAGgttaataagc ... attcttgtagTTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGATCAACAGGATCAAG
EST: gi|211384020|gb|FL015615.1|FL015615
EST:     GACACCCAGAGTTCCGCTACAAAACTGAATTTCAGAGTCATGAACCTGAG                         TTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGATCAACAGGATCAAG
genomic: GACACCCAGAGTTCCGCTACAAAACTGAATTTCAGAGTCATGAACCTGAGgttaataagc ... attcttgtagTTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGATCAACAGGATCAAG
EST: gi|211386656|gb|FL015629.1|FL015629
EST:     GACACCCAGAGTTCCGCTACAAAACTGAATTTCAGAGTCATGAACCTGAG                         TTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGATCAACAGGATCAAG
genomic: GACACCCAGAGTTCCGCTACAAAACTGAATTTCAGAGTCATGAACCTGAGgttaataagc ... attcttgtagTTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGATCAACAGGATCAAG
EST: gi|78112474|gb|DV530868.1|DV530868
EST:     GACACCCAGAGTTCCGCTACAAAACTGAATTTCAGAGTCATGAACCTGAG                         TTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGATCAACAGGATCAAG
genomic: GACACCCAGAGTTCCGCTACAAAACTGAATTTCAGAGTCATGAACCTGAGgttaataagc ... attcttgtagTTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGATCAACAGGATCAAG
EST: gi|19057676|gb|BM736343.1|BM736343
EST:     GACACCCAGAGTTCCGCTACAAAACTGAATTTCAGAGTCATGAACCTGAG                         TTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGGTCAACAGGATCAAG
genomic: GACACCCAGAGTTCCGCTACAAAACTGAATTTCAGAGTCATGAACCTGAGgttaataagc ... attcttgtagTTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGATCAACAGGATCAAG
EST: gi|19436843|gb|BM953253.1|BM953253
EST:     GACACCCAGAGTTCCGCTACAAAACTGAATTTCAGAGTCATGAACCTGAG                         TTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGGTCAACAGGATCAAG
genomic: GACACCCAGAGTTCCGCTACAAAACTGAATTTCAGAGTCATGAACCTGAGgttaataagc ... attcttgtagTTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGATCAACAGGATCAAG
EST: gi|211384023|gb|FL015618.1|FL015618
EST:     GACACCCAGAGTTCCGCTACAAAACTGAATTTCAGAGTCATGAACCTGAG                         TTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGATCAACAGGATCAAG
genomic: GACACCCAGAGTTCCGCTACAAAACTGAATTTCAGAGTCATGAACCTGAGgttaataagc ... attcttgtagTTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGATCAACAGGATCAAG
EST: gi|148945029|gb|EC890213.2|EC890213
EST:     GACACCCAGAGTTCCGCTACAAAACTGAATTTCAGAGTCATGAACCTGAG                         TTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGATCAACAGGATCAAG
genomic: GACACCCAGAGTTCCGCTACAAAACTGAATTTCAGAGTCATGAACCTGAGgttaataagc ... attcttgtagTTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGATCAACAGGATCAAG
EST: gi|211386650|gb|FL015623.1|FL015623
EST:     GACACCCAGAGTTCCGCTACAAAACTGAATTTCAGAGTCATGAACCTGAG                         TTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGATCAACAGGATCAAG
genomic: GACACCCAGAGTTCCGCTACAAAACTGAATTTCAGAGTCATGAACCTGAGgttaataagc ... attcttgtagTTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGATCAACAGGATCAAG
EST: gi|211384019|gb|FL015614.1|FL015614
EST:     GACACCCAGAGTTCCGCTACAAAACTGAATTTCAGAGTCATGAACCTGAG                         TTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGATCAACAGGATCAAG
genomic: GACACCCAGAGTTCCGCTACAAAACTGAATTTCAGAGTCATGAACCTGAGgttaataagc ... attcttgtagTTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGATCAACAGGATCAAG
EST: gi|9732635|gb|BE511387.1|BE511387
EST:     GACACCCAGAGTTCCGCTACAAAACTGAATTTCAGAGTCATGAACCTGAG                         TTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGATCAACAGGATCAAG
genomic: GACACCCAGAGTTCCGCTACAAAACTGAATTTCAGAGTCATGAACCTGAGgttaataagc ... attcttgtagTTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGATCAACAGGATCAAG
EST: gi|50332602|gb|CO527728.1|CO527728
EST:     GACACCCAGAGTTCCGCTACAAAACTGAATTTCAGAGTCATGAACCTGAG                         TTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGATCAACAGGATCAAG
genomic: GACACCCAGAGTTCCGCTACAAAACTGAATTTCAGAGTCATGAACCTGAGgttaataagc ... attcttgtagTTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGATCAACAGGATCAAG
EST: gi|19822589|gb|BQ048613.1|BQ048613
EST:     GACACCCAGAGTTCCGCTACAAAACTGAATTTCAGAGTCATGAACCTGAG                         TTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGGTCAACAGGATCAAG
genomic: GACACCCAGAGTTCCGCTACAAAACTGAATTTCAGAGTCATGAACCTGAGgttaataagc ... attcttgtagTTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGATCAACAGGATCAAG
EST: gi|211386648|gb|FL015621.1|FL015621
EST:     ACACCCAGAGTTCCGCTACAAAACTGAATTTCAGAGTCATGAACCNTGAG                         TTTGACTACCTCAAAAAGTT-GGAAATAGAGGAAAAGATCAACAGGGATC
genomic: ACACCCAGAGTTCCGCTACAAAACTGAATTTCAGAGTCATGAACC-TGAGgttaataagc ... attcttgtagTTTGACTACCTCAAAA-GTTTGGAAATAGAGGAAAAGATCAACAGG-ATC
EST: gi|149076328|gb|EE164942.2|EE164942
EST:     GACACCCAGAGTTCCGCTACAAAACTGAATTTCAGAGTCATGAACCTGAG                         TTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGATCAACAGGATCAAG
genomic: GACACCCAGAGTTCCGCTACAAAACTGAATTTCAGAGTCATGAACCTGAGgttaataagc ... attcttgtagTTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGATCAACAGGATCAAG
EST: gi|211386655|gb|FL015628.1|FL015628
EST:     CACCCAGAGTTCCGCTACAAAACTGAATTTCAGAGTCATGAAACCTGAG
genomic: CACCCAGAGTTCCGCTACAAAACTGAATTTCAGAGTCATGAA-CCTGAG
EST: gi|211384022|gb|FL015617.1|FL015617
EST:     GACACCCAGAGTTCCGCTACAAAACTGAATTTCAGAGTCATGAACCTGAG                         TTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGATCAACAGGATCAAG
genomic: GACACCCAGAGTTCCGCTACAAAACTGAATTTCAGAGTCATGAACCTGAGgttaataagc ... attcttgtagTTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGATCAACAGGATCAAG

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: 48 (upstream exon), 49 (downstream exon)
Score: 88

AATGCCAGCCAGAGAGAACTGGAGAGACAAGATGTTCCAGTTACTAGACACCCAGAGTTCCGCTACAAAACTGAATTTCAGAGTCATGAACCTGAGgttaataagc ... attcttgtagTTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGATCAACAGGATCAAGTGGTGCCAGACAGCCAACAATGCTCTCTCCCTTTTGTCTACAAATGATA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 80

AATGCCAGCCAGAGAGAACTGGAGAGACAAGATGTTCCAGTTACTAGACACCCAGAGTTCCGCTACAAAACTGAATTTCAGAGTCATGAACCTGAGgttaataagc ... attcttgtagTTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGATCAACAGGATCAAGTGGTGCCAGACAGCCAACAATGCTCTCTCCCTTTTGTCTACAAATGATA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 113

AATGCCAGCCAGAGAGAACTGGAGAGACAAGATGTTCCAGTTACTAGACACCCAGAGTTCCGCTACAAAACTGAATTTCAGAGTCATGAACCTGAGgttaataagc ... attcttgtagTTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGATCAACAGGATCAAGTGGTGCCAGACAGCCAACAATGCTCTCTCCCTTTTGTCTACAAATGATA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 89

AATGCCAGCCAGAGAGAACTGGAGAGACAAGATGTTCCAGTTACTAGACACCCAGAGTTCCGCTACAAAACTGAATTTCAGAGTCATGAACCTGAGgttaataagc ... attcttgtagTTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGATCAACAGGATCAAGTGGTGCCAGACAGCCAACAATGCTCTCTCCCTTTTGTCTACAAATGATA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaatggtagattgaagttatgtcagggttcctattttttatgtaattcttgtagTTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGATCAACAGGATCAAGTGGTGCCAGACAGCCAACAATGCTCTCTCCCTTTTGTCTACAAATGATA
 aattaat  putative branch site (score: 89)
                                              ttcttgt  putative PPT
                                tattttttatgtaatt  TA-rich tract