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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccaccccggcaaatgcggagaggctgctttgaacctgggacctagtgattcagtgagatagctctttgaaataacgctcattatttcattgcttttgcagTTCATCCTGAATCTTGGAATCCGATGTGGTCTGTTGCAAG

Basic information

species Zea mays
transcript GRMZM2G116919_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G116919_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os06g09330.2 (Oryza sativa), 3'ss of exon 2
-------------------------ccaccccggcaaatgcggagaggctgctttgaacctgggacctagtgattcagtgagatagctctttgaaataacgctcattatttc------att--gcttttgcagTTCATCCTGAATCTTGGAATCCGATGTGGTCTGTTGCAAG
                           ||      | ||||  |  |  |     |      |    |  | | |     |  ||    ||||||| ||    ||| | ||       |||  | ||||||||||||||| |||||||||||||| ||||||||||| |||||
gtaagttaatatgatcatattttttttactttattatatgc--aaggtttatcccgtgatcagattatgattacttttatatttaatgatttgaaacaatttccatcacttttaatttattatgtttttgcagTTCATCCGGAATCTTGGAATCCTATGTGGTCTGTGGCAAG

upper sequence: GRMZM2G116919_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA16G01680.1 (Glycine max), 3'ss of exon 6
ccaccccggcaaatgcggagaggctgctttgaacctgggacctagtgattcagtgagatagctctt-------tgaaataacgctcattatttcattgcttttgcagTTCATCCTGAATCTTGGAATCCGATGTGGTCTGTTGCAAG
        | || | |        |   ||| | |    | | | |  |    |||| || | | |       |  ||||   ||      ||   | |||||||||||||||| |||  ||||||||| |||||||||||  ||||
--------gtaagttctc---ttttctgttgtagcacaaaacaattagtatcatgagttaacccatattacaatttaatatttctgcacgatttgctacttttgcagTTCATCCAGAAAGTTGGAATCCCATGTGGTCTGTATCAAG

upper sequence: GRMZM2G116919_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA07G05170.1 (Glycine max), 3'ss of exon 6
ccaccccggcaaatgcggagaggctgctttgaacctgggacctagtgattcagtgagatagctctttgaaataacgctcattatttcattgcttttgcagTTCATCCTGAATCTTGGAATCCGATGTGGTCTGTTGCAAG
       |  |  |     |  |  ||    |||        |  ||| | |   | ||  |  |||  ||||   ||      ||   | |||||||||||||||| |||  ||||||||| |||||||||||  ||||
---gtaagctattttttctgttgtagcacaaaacaattagtatcatgagtaacccatattacaattt--aatatttctgcgggatttgctacttttgcagTTCATCCAGAAAGTTGGAATCCCATGTGGTCTGTATCAAG

upper sequence: GRMZM2G116919_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA07G05170.2 (Glycine max), 3'ss of exon 5
--ccaccccggcaaatgcggagaggctgctttgaacctgggacctagtgattcagtgagatagctctttgaaataacgctcattatttcattgcttttgcagTTCATCCTGAATCTTGGAATCCGATGTGGTCTGTTGCAAG
   |     |  |  |     |  |  ||    |||        |  ||| | |   | ||  |  |||  ||||   ||      ||   | |||||||||||||||| |||  ||||||||| |||||||||||  ||||
tgactgtaagctattttttctgttgtagcacaaaacaattagtatcatgagtaacccatattacaattt--aatatttctgcgggatttgctacttttgcagTTCATCCAGAAAGTTGGAATCCCATGTGGTCTGTATCAAG

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|37421879|gb|CF648643.1|CF648643
EST:     GAGCGGCAGATTTGCGCCACACAAAAGAATATGCTTGTCAATGAGTGACT                         TTCATCCTGAATCTTGGAATCCGATGTGGTCTGTTGCAAG
genomic: GAGCGGCAGATTTGCGCCACACAAAAGAATATGCTTGTCAATGAGTGACTgtaagttctg ... gcttttgcagTTCATCCTGAATCTTGGAATCCGATGTGGTCTGTTGCAAG
EST: gi|76917612|gb|DV166918.1|DV166918
EST:     GAGCGGCAGATTTGCGCCACACAAAAGAATATGCTTGTCAATGAGTGACT                         TTCATCCTGAATCTTGGAATCCGATGTGGTCTGTTGCAAG
genomic: GAGCGGCAGATTTGCGCCACACAAAAGAATATGCTTGTCAATGAGTGACTgtaagttctg ... gcttttgcagTTCATCCTGAATCTTGGAATCCGATGTGGTCTGTTGCAAG
EST: gi|50332246|gb|CO527372.1|CO527372
EST:     GAGCGGCAGATTTGCGCCACACAAAAGAATATGCTTGTCAATGAGTGACT                         TTCATCCTGAATCTTGGAATCCGATGTGGTCTGTTGCAAG
genomic: GAGCGGCAGATTTGCGCCACACAAAAGAATATGCTTGTCAATGAGTGACTgtaagttctg ... gcttttgcagTTCATCCTGAATCTTGGAATCCGATGTGGTCTGTTGCAAG
EST: gi|78544504|gb|DV622002.1|DV622002
EST:     GAGCGGCAGATTTGCGCCACACAAAAGAATATGCTTGTCAATGAGTGACT                         TTCATCCTGAATCTTGGAATCCGATGTGGTCTGTTGCAAG
genomic: GAGCGGCAGATTTGCGCCACACAAAAGAATATGCTTGTCAATGAGTGACTgtaagttctg ... gcttttgcagTTCATCCTGAATCTTGGAATCCGATGTGGTCTGTTGCAAG
EST: gi|34391285|gb|CF384513.1|CF384513
EST:     GAGCGGCAGATTTGCGCCACACAAAAGAATATGCTTGTCAATGAGTGACT                         TTCATCCTGGATCTTGGAATCCGATGTGGTCTGTTGCAAG
genomic: GAGCGGCAGATTTGCGCCACACAAAAGAATATGCTTGTCAATGAGTGACTgtaagttctg ... gcttttgcagTTCATCCTGAATCTTGGAATCCGATGTGGTCTGTTGCAAG
EST: gi|78123531|gb|DV541915.1|DV541915
EST:     GAGCGGCAGATTTGCGCCACACAAAAGAATATGCTTGTCAATGAGTGACT                         TTCATCCTGAATCTTGGAATCCGATGTGGTCTGTTGCAAG
genomic: GAGCGGCAGATTTGCGCCACACAAAAGAATATGCTTGTCAATGAGTGACTgtaagttctg ... gcttttgcagTTCATCCTGAATCTTGGAATCCGATGTGGTCTGTTGCAAG
EST: gi|71420480|gb|DR805114.1|DR805114
EST:     GAGCGGCAGATTTGCGCCACACAAAAGAATATGCTTGTCAATGAGCGACT                         TTCATCCTGAATCTTGGAATCCGATGTGGTCTGTTGCAAG
genomic: GAGCGGCAGATTTGCGCCACACAAAAGAATATGCTTGTCAATGAGTGACTgtaagttctg ... gcttttgcagTTCATCCTGAATCTTGGAATCCGATGTGGTCTGTTGCAAG
EST: gi|31364477|gb|CD448832.1|CD448832
EST:     GAGCGGCAGATTTGCGCCACACAAAAGAATATGCTTGTCAATGAGTGACT                         TTCATCCTGAATCTTGGAATCCCATGTGGTCTGTTGCAAG
genomic: GAGCGGCAGATTTGCGCCACACAAAAGAATATGCTTGTCAATGAGTGACTgtaagttctg ... gcttttgcagTTCATCCTGAATCTTGGAATCCGATGTGGTCTGTTGCAAG
EST: gi|4804485|gb|AI665355.2|AI665355
EST:     AATATGCTTGTCAATGAGTGACT                         TTCATCCTGAATCTTGGAATCCGATGTGGTCTGTTGCAAG
genomic: AATATGCTTGTCAATGAGTGACTgtaagttctg ... gcttttgcagTTCATCCTGAATCTTGGAATCCGATGTGGTCTGTTGCAAG
EST: gi|37382371|gb|CF628128.1|CF628128
EST:     GAGCGGCAGATTTGCGCCACACAAAAGAATATGCTTGTCAATGAGTGACT                         TTCATCCTGAATCTTGGAATCCCATGTGGTCTGTTGCAAG
genomic: GAGCGGCAGATTTGCGCCACACAAAAGAATATGCTTGTCAATGAGTGACTgtaagttctg ... gcttttgcagTTCATCCTGAATCTTGGAATCCGATGTGGTCTGTTGCAAG
EST: gi|5343079|gb|AI795489.1|AI795489
EST:     GAGCGGCAGATTTGCGCCACACAAAAGAATATGCTTGTCAATGAGTGACT                         TTCATCCTGAATCTTGGAATCCGATGTGGTCTGTTGCAAG
genomic: GAGCGGCAGATTTGCGCCACACAAAAGAATATGCTTGTCAATGAGTGACTgtaagttctg ... gcttttgcagTTCATCCTGAATCTTGGAATCCGATGTGGTCTGTTGCAAG
EST: gi|71756603|gb|DR954540.1|DR954540
EST:     GAGCGGCAGATTTGCGCCACACAAAAGAATATGCTTGTCAATGAGTGACT                         TTCATCCTGAATCTTGGAATCCGATGTGGTCTGTTGCAAG
genomic: GAGCGGCAGATTTGCGCCACACAAAAGAATATGCTTGTCAATGAGTGACTgtaagttctg ... gcttttgcagTTCATCCTGAATCTTGGAATCCGATGTGGTCTGTTGCAAG
EST: gi|8103224|gb|AW927877.1|AW927877
EST:     GAGCGGCAGATTTGCGCCACACAAAAGAATATGCTTGTCAATGAGTGACT                         TTCATCCTGAATCTTGGAATCCCATGTGGTCTGTTGCAAG
genomic: GAGCGGCAGATTTGCGCCACACAAAAGAATATGCTTGTCAATGAGTGACTgtaagttctg ... gcttttgcagTTCATCCTGAATCTTGGAATCCGATGTGGTCTGTTGCAAG
EST: gi|60346203|gb|DN213176.1|DN213176
EST:     GAGCGGCAGATTTGCGCCACACAAAAGAATATGCTTGTCAATGAGTGACT                         TTCATCCTGAATCTTGGAATCCGATGTGGTCTGTTGCAAG
genomic: GAGCGGCAGATTTGCGCCACACAAAAGAATATGCTTGTCAATGAGTGACTgtaagttctg ... gcttttgcagTTCATCCTGAATCTTGGAATCCGATGTGGTCTGTTGCAAG
EST: gi|78024877|gb|DV493264.1|DV493264
EST:     GCCACACAAAAGAATATGCTTGTCAATGAGTGACT                         TTCATCCTGAATCTTGGAATCCGATGTGGTCTGTTGCAAG
genomic: GCCACACAAAAGAATATGCTTGTCAATGAGTGACTgtaagttctg ... gcttttgcagTTCATCCTGAATCTTGGAATCCGATGTGGTCTGTTGCAAG
EST: gi|71320224|gb|DR796871.1|DR796871
EST:     GAGCGGCAGATTTGCGCCACACAAAAGAATATGCTTGTCAATGAGTGACT                         TTCATCCTGAATCTTGGAATCCGATGTGGTCTGTTGCAAG
genomic: GAGCGGCAGATTTGCGCCACACAAAAGAATATGCTTGTCAATGAGTGACTgtaagttctg ... gcttttgcagTTCATCCTGAATCTTGGAATCCGATGTGGTCTGTTGCAAG
EST: gi|9742575|gb|BE518723.1|BE518723
EST:     GAGCGGCAGATTTGCGCCACACAAAAGAATATGCTTGTCAATGAGTGACT                         TTCATCCTGAATCTTGGAATCCGATGTGGTCTGTTGCAAG
genomic: GAGCGGCAGATTTGCGCCACACAAAAGAATATGCTTGTCAATGAGTGACTgtaagttctg ... gcttttgcagTTCATCCTGAATCTTGGAATCCGATGTGGTCTGTTGCAAG
EST: gi|60341447|gb|DN208420.1|DN208420
EST:     GAGCGGCAGATTTGCGCCACACAAAAGAATATGCTTGTCAATGAGTGACT                         TTCATCCTGAATCTTGGAATCCGATGTGGTCTGTTGCAAG
genomic: GAGCGGCAGATTTGCGCCACACAAAAGAATATGCTTGTCAATGAGTGACTgtaagttctg ... gcttttgcagTTCATCCTGAATCTTGGAATCCGATGTGGTCTGTTGCAAG
EST: gi|16920917|gb|BM074893.1|BM074893
EST:     GAGCGGCAGATTTGCGCCACACAAAAGAATATGCTTGTCAATGAGTGACT                         TTCATCCTGAATCTTGGAATCCGATGTGGTCTGTTGCAAG
genomic: GAGCGGCAGATTTGCGCCACACAAAAGAATATGCTTGTCAATGAGTGACTgtaagttctg ... gcttttgcagTTCATCCTGAATCTTGGAATCCGATGTGGTCTGTTGCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgattcagtgagatagctctttgaaataacgctcattatttcattgcttttgcagTTCATCCTGAATCTTGGAATCCGATGTGGTCTGTTGCAAG
                       aaataac  putative branch site (score: 2)
                                           ttgctttt  putative PPT
                                  attatttcatt  TA-rich tract