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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGCGATCTGTATCGACCATCTTGTATCTTGTGTCACTTCAAGATCTTACCAACTGCCCTTTTCGGGTTGTTGATGAGATAAATCAAGgtaacacaactgaattgcttcatttctccaactgtatgactgctaacttgtataggtattgaggtggtctaatgcattcatccgaatatgcag

Basic information

species Zea mays
transcript GRMZM2G440916_T01
intron # 26
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G440916_T01 (Zea mays), 5'ss of exon 26
lower sequence: LOC_Os05g51790.2 (Oryza sativa), 5'ss of exon 26
GAGCGATCTGTATCGACCATCTTGTATCTTGTGTCACTTCAAGATCTTACCAACTGCCCTTTTCGGGTTGTTGATGAGATAAATCAAGgtaacacaac--tgaattgcttcatttctcca----------actgt------atgactgctaacttgtataggtattgaggtggtctaatgcattcatccgaatatgcag
|||||||| || || |||||| |||| ||||| |||||||||||||||||||||||||| |||||||| |||||||||||||||||||| ||  ||||  | |   | ||   ||| | |           ||||      |||| | |||  ||||  | | |||     |||   |    ||   |||||  |||||
GAGCGATCAGTTTCAACCATCCTGTACCTTGTATCACTTCAAGATCTTACCAACTGCCCCTTTCGGGTCGTTGATGAGATAAATCAAGgcaagccaaccctcacaagtttttgttccctatgcactcaatgctgttataaaatgattactagtttgttgaagcattacaaaggt---aactgtttccccgaaattgcag

upper sequence: GRMZM2G440916_T01 (Zea mays), 5'ss of exon 26
lower sequence: GLYMA20G34020.1 (Glycine max), 5'ss of exon 27
GAGCGATCTGTATCGACCATCTTGTATCTTGTGTCACTTCAAGATCTTACCAACTGCCCTTTTCGGGTTGTTGATGAGATAAATCAAGgtaacacaactgaattgcttcatttctccaactgtatgactgctaacttgtataggtattgaggtggtctaatgcattcatccgaatatgcag
|| || || || || || ||  | |||||||| || |||||||||||||| |||||||| ||| | || ||||||||||| || ||||||      ||||  |      | ||||     |  ||     | | ||  | ||   | ||   | | ||  ||  || ||| |         
GAACGCTCAGTTTCAACTATTGTTTATCTTGTTTCCCTTCAAGATCTTACAAACTGCCCATTTAGAGTCGTTGATGAGATCAACCAAGgtg-tgttactgtttgaagaaaattctt----tccattgacaccagctc-tctaaagactgtctttgactg-tgtttttatcag---------

upper sequence: GRMZM2G440916_T01 (Zea mays), 5'ss of exon 26
lower sequence: AT5G15920.1 (Arabidopsis thaliana), 5'ss of exon 2
------------GAGCGATCTGTATCGACCATCTTGTATCTTGTGTCACTTCAAGATCTTACCAACTGCCCTTTTCGGGTTGTTGATGAGATAAATCAAGgtaacacaactgaattgcttcatttctccaactgtatgactgctaacttgtataggtattgaggtggtctaatgcattcatccgaatatgcag
            ||||| ||||| || || ||| | || || || || ||||||||||| || ||||| |||||  |||||||||||||||| ||||||||||| | |    || || ||  ||| |  ||    |  ||||         ||  ||    ||    |  ||   || |||  |  | |||||
CAATCTGGAGGAGAGCGTTCTGTCTCAACTATCCTTTACCTCGTCTCTCTTCAAGATCTGACAAACTGTCCTTTCAGGGTTGTTGATGAGATTAATCAAGgtaa-aaagtgtaaatgttt--tttttttaatgtaaaaactgtctcgaaacattagt-caaagtctcttaaaaatatacatttgcttgtgcag

upper sequence: GRMZM2G440916_T01 (Zea mays), 5'ss of exon 26
lower sequence: Vv13s0064g00180.t01 (Vitis vinifera), 5'ss of exon 26
GAGCGATCTGTATCGACCATCTTGTATCTTGTGTCACTTCAAGATCTTACCAACTGCCCTTTTCGGGTTGTTGATGAGATAAATCAAGgtaa--cacaactgaattgcttcatttctccaactgtatgactgctaacttgtataggtatt-gaggtgg--tctaatgcattcatccgaatatgcag
||||| || ||  | || ||  |||||||||| || || |||||||| || |||||||||||| |||| ||||||||||||||||||||| |   | ||   ||| |  | ||| || |  |  |   |     ||  | ||  |   ||  || ||   | || |   ||  |||   ||     
GAGCGCTCAGTTGCAACTATTCTGTATCTTGTTTCTCTACAAGATCTCACAAACTGCCCTTTTAGGGTGGTTGATGAGATAAATCAAGgtgagttaaaatataatggtgttattgcttcgtcattgcaa-----aatatatactgcctttcaagatgacttttattttgtttttccccctag----

upper sequence: GRMZM2G440916_T01 (Zea mays), 5'ss of exon 26
lower sequence: EFJ24458 (Selaginella moellendorffii), 5'ss of exon 25
GAGCGATCTGTATCGACCATCTTGTATCTTGTGTCACTTCAAGATCTTACCAACTGCCCTTTTCGGGTTGTTGATGAGATAAATCAAGgtaacacaactgaattgcttcatttctccaactgtatgactgctaacttgtataggtattgaggtggtctaatgcattcatccgaatatgcag
|| || || || || || ||  | || ||||| ||||| ||||| |||||| |||| || ||||| ||||| ||||||||||| ||||||| |   |||||  |   |  || |    | | | | || | |   |||   ||                                      
GAACGCTCGGTGTCAACTATACTCTACCTTGTCTCACTCCAAGACCTTACCCACTGTCCGTTTCGTGTTGTGGATGAGATAAACCAAGgtatcctgactgagatttctggttgc---gaatctttaacaggt---ttgatcag--------------------------------------

upper sequence: GRMZM2G440916_T01 (Zea mays), 5'ss of exon 26
lower sequence: EFJ13183 (Selaginella moellendorffii), 5'ss of exon 24
GAGCGATCTGTATCGACCATCTTGTATCTTGTGTCACTTCAAGATCTTACCAACTGCCCTTTTCGGGTTGTTGATGAGATAAATCAAGgtaacacaactgaattgcttcatttctccaactgtatgactgctaacttgtataggtattgaggtggtctaatgcattcatccgaatatgcag
|| || || || || || ||  | || ||||| ||||| ||||| |||||| |||| || ||||| ||||| ||||||||||| ||||||| |    ||||   ||||  |   | | | | | | || | |   |||   ||                                      
GAACGCTCGGTGTCAACTATTCTCTACCTTGTCTCACTCCAAGACCTTACCCACTGTCCGTTTCGTGTTGTGGATGAGATAAACCAAGgtatcctggctga---gctttctggttgcgaatctttaacaggt---ttgatcag--------------------------------------

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|32794483|gb|CD946719.1|CD946719
EST:     GATCTTACCAACTGCCCTTTTCGGGTTGTTGATGAGATAAATCAAG                         GAATGGACCCCATAAACGAGAGGAAAATGTTTCAGCAGCTTGTCAGAGCTG
genomic: GATCTTACCAACTGCCCTTTTCGGGTTGTTGATGAGATAAATCAAGgtaacacaac ... gaatatgcagGAATGGACCCCATAAACGAGAGGAAAATGTTTCAGCAGCTTGTCAGAGCTG
EST: gi|33097205|gb|CF057165.1|CF057165
EST:     GAGATAAATCAAG                         GAATGGACCCCATAAACGAGAGGAAAATGTTTCAGCAGCTTGTCAGAGCTG
genomic: GAGATAAATCAAGgtaacacaac ... gaatatgcagGAATGGACCCCATAAACGAGAGGAAAATGTTTCAGCAGCTTGTCAGAGCTG
EST: gi|32930688|gb|CF035500.1|CF035500
EST:     TCAAGATCTTACCAACTGCCCTTTTCGGGTTGTTGATGAGATAAATCAAG                         GAATGGACCCCATAAACGAGAGGAAAATGTTTCAGCAGCTTGTCAGAGCTG
genomic: TCAAGATCTTACCAACTGCCCTTTTCGGGTTGTTGATGAGATAAATCAAGgtaacacaac ... gaatatgcagGAATGGACCCCATAAACGAGAGGAAAATGTTTCAGCAGCTTGTCAGAGCTG
EST: gi|211323885|gb|FK953781.1|FK953781
EST:     TCAAGATCTTACCAACTGCCCTTTTCGGGTTGTTGATGAGATAAATCAAG                         GAATGGACCCCATAAACGAGAGGAAAATGTTTCAGCAGCTTGTCAGAGCTG
genomic: TCAAGATCTTACCAACTGCCCTTTTCGGGTTGTTGATGAGATAAATCAAGgtaacacaac ... gaatatgcagGAATGGACCCCATAAACGAGAGGAAAATGTTTCAGCAGCTTGTCAGAGCTG
EST: gi|33092036|gb|CF052030.1|CF052030
EST:     TCAAGATCTTACCAACTGCCCTTTTCGGGTTGTTGATGAGATAAATCAAG                         GAATGGACCCCATAAACGAGAGGAAAATGTTTCAGCAGCTTGTCAGAGCTG
genomic: TCAAGATCTTACCAACTGCCCTTTTCGGGTTGTTGATGAGATAAATCAAGgtaacacaac ... gaatatgcagGAATGGACCCCATAAACGAGAGGAAAATGTTTCAGCAGCTTGTCAGAGCTG
EST: gi|211323884|gb|FK953780.1|FK953780
EST:     TCAAGATCTTACCAACTGCCCTTTTCGGGTTGTTGATGAGATAAATCAAG                         GAATGGACCCCATAAACGAGAGGAAAATGTTTCAGCAGCTTGTCAGAGCTG
genomic: TCAAGATCTTACCAACTGCCCTTTTCGGGTTGTTGATGAGATAAATCAAGgtaacacaac ... gaatatgcagGAATGGACCCCATAAACGAGAGGAAAATGTTTCAGCAGCTTGTCAGAGCTG
EST: gi|78075393|gb|DV503827.1|DV503827
EST:     TCAAGATCTTACCAACTGCCCTTTTCGGGTTGTTGATGAGATAAATCAAG                         GAATGGACCCCATAAACGAGAGGAAAATGTTTCAGCAGCTTGTCAGAGCTG
genomic: TCAAGATCTTACCAACTGCCCTTTTCGGGTTGTTGATGAGATAAATCAAGgtaacacaac ... gaatatgcagGAATGGACCCCATAAACGAGAGGAAAATGTTTCAGCAGCTTGTCAGAGCTG

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: 49 (upstream exon), 49 (downstream exon)
Score: 291

GAGCGATCTGTATCGACCATCTTGTATCTTGTGTCACTTCAAGATCTTACCAACTGCCCTTTTCGGGTTGTTGATGAGATAAATCAAGgtaacacaac ... gaatatgcagGAATGGACCCCATAAACGAGAGGAAAATGTTTCAGCAGCTTGTCAGAGCTGCCAGCCAAATTAACACGCCGCA


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 42

GAGCGATCTGTATCGACCATCTTGTATCTTGTGTCACTTCAAGATCTTACCAACTGCCCTTTTCGGGTTGTTGATGAGATAAATCAAGgtaacacaac ... gaatatgcagGAATGGACCCCATAAACGAGAGGAAAATGTTTCAGCAGCTTGTCAGAGCTGCCAGCCAAATTAACACGCCGCA


Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 47

GAGCGATCTGTATCGACCATCTTGTATCTTGTGTCACTTCAAGATCTTACCAACTGCCCTTTTCGGGTTGTTGATGAGATAAATCAAGgtaacacaac ... gaatatgcagGAATGGACCCCATAAACGAGAGGAAAATGTTTCAGCAGCTTGTCAGAGCTGCCAGCCAAATTAACACGCCGCA


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 79

GAGCGATCTGTATCGACCATCTTGTATCTTGTGTCACTTCAAGATCTTACCAACTGCCCTTTTCGGGTTGTTGATGAGATAAATCAAGgtaacacaac ... gaatatgcagGAATGGACCCCATAAACGAGAGGAAAATGTTTCAGCAGCTTGTCAGAGCTGCCAGCCAAATTAACACGCCGCA