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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTAGTAGATTACCACGGATGTGATTTCTTTCCAGAACGTTGGTTTGACCTCGTAGTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGGgtaggtaggtaatccaagttgaattcgacgtaagtgcattctagtcacctcatcctgcatccttatatttgggactaaacttgtacag

Basic information

species Zea mays
transcript GRMZM2G032699_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G032699_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os07g22950.1 (Oryza sativa), 5'ss of exon 2
CTAGTAGATTACCACGGATGTGATTTCTTTCCAGAACGTTGGTTTGACCTCGTAGTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGGgtaggtaggtaatcca-agttgaatt-cgacgtaagtgc-attctagtcacctcatcctgcatccttatatttgggactaaacttgtacag
    |||||||||| ||||||||||||||||||||||||||||||||||| |||||||||||||| || || ||||||||||||||||||||| ||||  | |||||  | || || |  || |     ||  |  ||      ||| ||        ||| |  || |   |  || |    ||  ||||
----TAGATTACCATGGATGTGATTTCTTTCCAGAACGTTGGTTTGACCTTGTAGTTGTGCTCCAAACAGATAACTCAATTCTGCATGATCGCTTGACTAGCAGgtaattcatgcagaactgcacaatcacccacctgttggaatagccattatgaaatgcttatttctgactaagagttctatt-cacag

upper sequence: GRMZM2G032699_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os07g22950.3 (Oryza sativa), 5'ss of exon 2
CTAGTAGATTACCACGGATGTGATTTCTTTCCAGAACGTTGGTTTGACCTCGTAGTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGGgtaggtaggtaatcca-agttgaatt-cgacgtaagtgc-attctagtcacctcatcctgcatccttat-atttgggactaaacttgtacag--------------------------------------------------
    |||||||||| ||||||||||||||||||||||||||||||||||| |||||||||||||| || || ||||||||||||||||||||| ||||  | |||||  | || || |  || |     ||  |  ||      ||| ||        ||| |  || | | |  |   |  | |   | ||                                                  
----TAGATTACCATGGATGTGATTTCTTTCCAGAACGTTGGTTTGACCTTGTAGTTGTGCTCCAAACAGATAACTCAATTCTGCATGATCGCTTGACTAGCAGgtaattcatgcagaactgcacaatcacccacctgttggaatagccattatgaaatgcttatttctgactaagagttctattcacagaggttatatgggtgccaagctcacaaacaacatagaatgtgaaattttccag

upper sequence: GRMZM2G032699_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os07g22950.2 (Oryza sativa), 5'ss of exon 2
------------------------------------------CTAGTAGATTACCACGGATGTGATTTCTTTCCAGAACGTTGGTTTGACCTCGTAGTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGGgtaggtaggtaatccaagttgaattcgacgtaagtgcattctagtcacctcatcctgcatccttatatttgggactaaacttgtacag
                                          |||||||||||||| ||||||||||||||||||||||||||||||||||| |||||||||||||| || |                                                                                                                      
GTTTGCGATGAGCTTGAGGACGTGATGGAAGAAGgtggtatactagtagattaccatggatgtgatttctttccagaacgttggtttgaccttgtagttgtgctccaaacag----------------------------------------------------------------------------------------------------------------------

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|211450962|gb|FK989163.1|FK989163
EST:     CGTAGTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGGGTAG                      
genomic: CGTAGTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGAC--G--Ggtaggtaggt ... acttgta
EST: gi|60341109|gb|DN208082.1|DN208082
EST:     CGTAGTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGG                         G
genomic: CGTAGTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGGgtaggtaggt ... acttgtacag-
EST: gi|60341109|gb|DN208082.1|DN208082
EST:     CGTAGTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGG                         G
genomic: CGTAGTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGGgtaggtaggt ... acttgtacag-
EST: gi|60341109|gb|DN208082.1|DN208082
EST:     CGTAGTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGG                         G
genomic: CGTAGTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGGgtaggtaggt ... acttgtacag-
EST: gi|6695878|gb|AW288986.1|AW288986
EST:     CGTAGTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGG                         G
genomic: CGTAGTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGGgtaggtaggt ... acttgtacag-
EST: gi|6695878|gb|AW288986.1|AW288986
EST:     CGTAGTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGG                         G
genomic: CGTAGTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGGgtaggtaggt ... acttgtacag-
EST: gi|6695878|gb|AW288986.1|AW288986
EST:     CGTAGTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGG                         G
genomic: CGTAGTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGGgtaggtaggt ... acttgtacag-
EST: gi|60359354|gb|DN226327.1|DN226327
EST:     CGTAGTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGG                         G
genomic: CGTAGTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGGgtaggtaggt ... acttgtacag-
EST: gi|60359354|gb|DN226327.1|DN226327
EST:     CGTAGTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGG                         G
genomic: CGTAGTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGGgtaggtaggt ... acttgtacag-
EST: gi|60359354|gb|DN226327.1|DN226327
EST:     CGTAGTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGG                         G
genomic: CGTAGTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGGgtaggtaggt ... acttgtacag-
EST: gi|60359354|gb|DN226327.1|DN226327
EST:     CGTAGTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGG                         G
genomic: CGTAGTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGGgtaggtaggt ... acttgtacag-
EST: gi|60359354|gb|DN226327.1|DN226327
EST:     CGTAGTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGG                         G
genomic: CGTAGTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGGgtaggtaggt ... acttgtacag-
EST: gi|211226976|gb|FL456590.1|FL456590
EST:     CGTAGTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGG                         AGGTTACATGGGTTCCAAACTCGCCAACAACATAGAGTGCGAAATCTTCCA
genomic: CGTAGTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGGgtaggtaggt ... acttgtacagAGGTTACATGGGTTCCAAACTCGCCAACAACATAGAGTGCGAAATCTTCCA
EST: gi|5525640|gb|AI861533.1|AI861533
EST:     CGTAGTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGG                         G
genomic: CGTAGTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGGgtaggtaggt ... acttgtacag-
EST: gi|5525640|gb|AI861533.1|AI861533
EST:     CGTAGTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGG                         G
genomic: CGTAGTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGGgtaggtaggt ... acttgtacag-
EST: gi|5525640|gb|AI861533.1|AI861533
EST:     CGTAGTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGG                         G
genomic: CGTAGTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGGgtaggtaggt ... acttgtacag-
EST: gi|6194875|gb|AW146979.1|AW146979
EST:     CGTAGTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGGGCAG                      
genomic: CGTAGTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGAC--G--Ggtaggtaggt ... acttgta
EST: gi|60358371|gb|DN225344.1|DN225344
EST:     CGTAGTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGG                         AGGTTACATGGGTTCCAAACTCGCCAACAACATAGAGTGCGAAATCTTCCA
genomic: CGTAGTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGGgtaggtaggt ... acttgtacagAGGTTACATGGGTTCCAAACTCGCCAACAACATAGAGTGCGAAATCTTCCA
EST: gi|37387580|gb|CF630987.1|CF630987
EST:     CGTAGTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGG                         G
genomic: CGTAGTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGGgtaggtaggt ... acttgtacag-
EST: gi|37387580|gb|CF630987.1|CF630987
EST:     CGTAGTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGG                         G
genomic: CGTAGTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGGgtaggtaggt ... acttgtacag-
EST: gi|37387580|gb|CF630987.1|CF630987
EST:     CGTAGTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGG                         G
genomic: CGTAGTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGGgtaggtaggt ... acttgtacag-
EST: gi|37387580|gb|CF630987.1|CF630987
EST:     CGTAGTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGG                         G
genomic: CGTAGTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGGgtaggtaggt ... acttgtacag-
EST: gi|37387580|gb|CF630987.1|CF630987
EST:     CGTAGTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGG                         G
genomic: CGTAGTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGGgtaggtaggt ... acttgtacag-

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: 24 (upstream exon), 41 (downstream exon)
Score: 4

CTAGTAGATTACCACGGATGTGATTTCTTTCCAGAACGTTGGTTTGACCTCGTAGTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGGgtaggtaggt ... acttgtacagAGGTTACATGGGTTCCAAACTCGCCAACAACATAGAGTGCGAAATCTTCCAAGTGCTCCTCGAGGAGGCGAGGGAGAGCTACAGAGAGGACATCGTGATG


Block sizes: 39 (upstream exon), 24 (downstream exon)
Score: 8

CTAGTAGATTACCACGGATGTGATTTCTTTCCAGAACGTTGGTTTGACCTCGTAGTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGGgtaggtaggt ... acttgtacagAGGTTACATGGGTTCCAAACTCGCCAACAACATAGAGTGCGAAATCTTCCAAGTGCTCCTCGAGGAGGCGAGGGAGAGCTACAGAGAGGACATCGTGATG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 15

CTAGTAGATTACCACGGATGTGATTTCTTTCCAGAACGTTGGTTTGACCTCGTAGTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGGgtaggtaggt ... acttgtacagAGGTTACATGGGTTCCAAACTCGCCAACAACATAGAGTGCGAAATCTTCCAAGTGCTCCTCGAGGAGGCGAGGGAGAGCTACAGAGAGGACATCGTGATG


Block sizes: 26 (upstream exon), 26 (downstream exon)
Score: 3

CTAGTAGATTACCACGGATGTGATTTCTTTCCAGAACGTTGGTTTGACCTCGTAGTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGGgtaggtaggt ... acttgtacagAGGTTACATGGGTTCCAAACTCGCCAACAACATAGAGTGCGAAATCTTCCAAGTGCTCCTCGAGGAGGCGAGGGAGAGCTACAGAGAGGACATCGTGATG