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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtgtctcattattaattcgtaattgatcattttgctatctaaaacacacctaatccttgcgctgtgcaccctcctaactgatttcagCAAACCGATGGAGCCTGATCGTCTTTTTGATTGTCTTCCAAGTACACTTCGACCATCGTCTGAATCTCAGCCCGAAGGTGGGAAAAACCCATCCGAGAAT

Basic information

species Zea mays
transcript GRMZM2G046590_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G046590_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os04g58880.1 (Oryza sativa), 3'ss of exon 3
gtttgtgtctcattattaattcgtaattgatcattttgctatctaaaacacacctaatccttgcgctgtgcaccctcctaactgatttcagCAAACCGATGGAGCCTGATCGTCTTTTTGATTGTCTTCCAAGTACACTTCGACCATCGTCTGAATCTCAGCCCGAAGGTGGGAAAAACCCATCCGAGAAT
  |||||||||||||||| ||  ||| ||     |||   | |  ||   || ||||  |||||  | ||||||||||| ||||||| ||||||||| || ||||||||||||||||||||||| ||||||||||| ||||||||||| ||||||||||| || |||||||| ||||||| |||  |   |
-gttgtgtctcattattagtt--taaatg-----tttttaaccccaacatcatctaa--cttgcattttgcaccctcctgactgattccagCAAACCTATCGAGCCTGATCGTCTTTTTGATTGCCTTCCAAGTACGCTTCGACCATCATCTGAATCTCATCCTGAAGGTGGAAAAAACCAATCACATTCT

upper sequence: GRMZM2G046590_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv08s0007g02340.t01 (Vitis vinifera), 3'ss of exon 3
---gtttgtgtctcattattaattcgtaattgatcattttgctatctaaaacacacctaatccttgc-gctgtgcaccct-----cctaactgatttcagCAAACCGATGGAGCCTGATCGTCTTTTTGATTGTCTTCCAAGTACACTTCGACCATCGTCTGAATCTCAGCCCGAAGGTGGGAAAAACCCATC--CGAGAAT
    |||  | ||  |    | |||  | |   ||| |  |   |    |||   | |     |||  ||||   |   |      ||    ||||||||||||||  |||| |||||||| ||||||||||| || ||     | || |||||||| || |  ||||  |  |      ||   || | |    | |||||
catattttggacttttggcaagttctaattctttcaatcagggttgagtaactgtcttttcatttgtagctgctgaagttgtatctcttttggatttcagCAAACCAGTGGAACCTGATCGCCTTTTTGATTGCCTCCCCCACTCTCTACGACCATCATCAGGGTCTC--CTGGGCATCAGGGTGAAGCTACTGGCAAGAAT
















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|211425858|gb|FL143031.1|FL143031
EST:     GCCCTTGTCAGGATGGAGGGTGAATTCCAGAATCAATTATCCCAGCGCAG                         CAAACCGATGGAGCCTGATCGNCTTTTTGATTGTCTTCCAAGTACACTTCG
genomic: GCCCTTGTCAGGATGGAGGGTGAATTCCAGAATCAATTATCCCAGCGCAGgtttgtgtct ... ctgatttcagCAAACCGATGGAGCCTGATCGTCTTTTTGATTGTCTTCCAAGTACACTTCG
EST: gi|71438744|gb|DR819794.1|DR819794
EST:     GCCCTTGTCAGGATGGAGGGTGAATTCCAGAATCAATTATCCCAGCGCAG                         CAAACCGATGGAGCCTGATCGTCTTTTTGATTGTCTTCCAAGTACACTTCG
genomic: GCCCTTGTCAGGATGGAGGGTGAATTCCAGAATCAATTATCCCAGCGCAGgtttgtgtct ... ctgatttcagCAAACCGATGGAGCCTGATCGTCTTTTTGATTGTCTTCCAAGTACACTTCG
EST: gi|211425849|gb|FL143022.1|FL143022
EST:     GCCCTTGTCANGATGGAGGGTGAATTCCAGAATCAATTATCCCAGCGCAG                         CAAACCGATGGAGCCTGATCGTCTTTTTGATTGTCTTCCAAGTACACTTCG
genomic: GCCCTTGTCAGGATGGAGGGTGAATTCCAGAATCAATTATCCCAGCGCAGgtttgtgtct ... ctgatttcagCAAACCGATGGAGCCTGATCGTCTTTTTGATTGTCTTCCAAGTACACTTCG
EST: gi|211428442|gb|FL143033.1|FL143033
EST:     GCCCTTGTCAGGATGGAGGGTGAATTCCAGAATCAATTATCCCAGCGCAG                         CAAACCGATGGAGCCTGATCGTCTTTTTGATTGTCTTCCAAGTACACTTCG
genomic: GCCCTTGTCAGGATGGAGGGTGAATTCCAGAATCAATTATCCCAGCGCAGgtttgtgtct ... ctgatttcagCAAACCGATGGAGCCTGATCGTCTTTTTGATTGTCTTCCAAGTACACTTCG
EST: gi|71432761|gb|DR813811.1|DR813811
EST:     GCCCTTGTCAGGATGGAGGGTGAATTCCAGAATCAATTATCCCAGCGCAG                         CAAACCGATGGAGCCTGATCGTCTTTTTGATTGTCTTCCAAGTACACTTCG
genomic: GCCCTTGTCAGGATGGAGGGTGAATTCCAGAATCAATTATCCCAGCGCAGgtttgtgtct ... ctgatttcagCAAACCGATGGAGCCTGATCGTCTTTTTGATTGTCTTCCAAGTACACTTCG
EST: gi|160481670|gb|EY254240.1|EY254240
EST:     GCCCTTGTCAGGATGGAGGGTGAATTCCAGAATCAATTATCCCAGCGCAG                         CAAACCGATGGAGCCTGATCGTCTTTTTGATTGTCTTCCAAGTACACTTCG
genomic: GCCCTTGTCAGGATGGAGGGTGAATTCCAGAATCAATTATCCCAGCGCAGgtttgtgtct ... ctgatttcagCAAACCGATGGAGCCTGATCGTCTTTTTGATTGTCTTCCAAGTACACTTCG
EST: gi|211425850|gb|FL143023.1|FL143023
EST:     GCCCTTGTCAGGATGGAGGGTGAATTCCAGAATCAATTATCCCAGCGCAG                         CAAACCGATGGAGCCTGATCCGTCTTTTTGATTGTCTTTCCAAG
genomic: GCCCTTGTCAGGATGGAGGGTGAATTCCAGAATCAATTATCCCAGCGCAGgtttgtgtct ... ctgatttcagCAAACCGATGGAGCCTGATC-GTCTTTTTGATTGTCTT-CCAAG
EST: gi|211425855|gb|FL143028.1|FL143028
EST:     GCCCTTGTCAGGATGGAGGGTGAATTCCAGAATCAATTATCCCAGCGCAG                         CAAACCGATGGAGCCTGATCGTCTTTTTGATTGTCTTCCAAGNACACTTCG
genomic: GCCCTTGTCAGGATGGAGGGTGAATTCCAGAATCAATTATCCCAGCGCAGgtttgtgtct ... ctgatttcagCAAACCGATGGAGCCTGATCGTCTTTTTGATTGTCTTCCAAGTACACTTCG
EST: gi|60358995|gb|DN225968.1|DN225968
EST:     GCCCTTGTCAGGATGGAGGGTGAATTCCAGAATCAATTATCCCAGCGCAG                         CAAACCGATGGAGCCTGATCGTCTTTTTGATTGTCTTCCAAGTACACTTCG
genomic: GCCCTTGTCAGGATGGAGGGTGAATTCCAGAATCAATTATCCCAGCGCAGgtttgtgtct ... ctgatttcagCAAACCGATGGAGCCTGATCGTCTTTTTGATTGTCTTCCAAGTACACTTCG
EST: gi|148983420|gb|EE029420.2|EE029420
EST:     GCCCTTGTCAGGATGGAGGGTGAATTCCAGAATCAATTATCCCAGCGCAG                         CAAACCGATGGAGCCTGATCGTCTTTTTGATTGTCTTCCAAGTACACTTCG
genomic: GCCCTTGTCAGGATGGAGGGTGAATTCCAGAATCAATTATCCCAGCGCAGgtttgtgtct ... ctgatttcagCAAACCGATGGAGCCTGATCGTCTTTTTGATTGTCTTCCAAGTACACTTCG
EST: gi|149103987|gb|EE289410.2|EE289410
EST:     GCCCTTGTCAGGATGGAGGGTGAATTCCAGAATCAATTATCCCAGCGCAG                         CAAACCGATGGAGCCTGATCGTCTTTTTGATTGTCTTCCAAGTACACTTCG
genomic: GCCCTTGTCAGGATGGAGGGTGAATTCCAGAATCAATTATCCCAGCGCAGgtttgtgtct ... ctgatttcagCAAACCGATGGAGCCTGATCGTCTTTTTGATTGTCTTCCAAGTACACTTCG
EST: gi|78117266|gb|DV535653.1|DV535653
EST:     GCCCTTGTCAGGATGGAGGGTGAATTCCAGAATCAATTATCCCAGCGCAG                         CAAACCGATGGAGCCTGATCGTCTTTTTGATTGTCTTCCAAGTACACTTCG
genomic: GCCCTTGTCAGGATGGAGGGTGAATTCCAGAATCAATTATCCCAGCGCAGgtttgtgtct ... ctgatttcagCAAACCGATGGAGCCTGATCGTCTTTTTGATTGTCTTCCAAGTACACTTCG
EST: gi|211425854|gb|FL143027.1|FL143027
EST:     GCCCTTGTCAGGATGGAGGGTGAATTCCAGAATCAATTATCCCAGCGCAG                         CAAACCGATGGAGCCTGATCGTCTTTTTGATTGTCTTCCAAGTACACTTCG
genomic: GCCCTTGTCAGGATGGAGGGTGAATTCCAGAATCAATTATCCCAGCGCAGgtttgtgtct ... ctgatttcagCAAACCGATGGAGCCTGATCGTCTTTTTGATTGTCTTCCAAGTACACTTCG
EST: gi|6626352|gb|AW257884.1|AW257884
EST:     GCCCTTGTCAGGATGGAGGGTGAATTCCAGAATCAATTATCCCAGCGCAG                         CAAACCGATGGAGCCTGATCGTCTTTTTGATTGTCTTCCAAGTACACTTCG
genomic: GCCCTTGTCAGGATGGAGGGTGAATTCCAGAATCAATTATCCCAGCGCAGgtttgtgtct ... ctgatttcagCAAACCGATGGAGCCTGATCGTCTTTTTGATTGTCTTCCAAGTACACTTCG
EST: gi|211428443|gb|FL143034.1|FL143034
EST:     CTTGTCCAGGGATGGGAGGGTGAATTCCAGAATCAATTATCCCAGCGCAG                         CAAACCGATGGNAGCCTGATCGTCCTTTTTGATTGTCTTCCAAGTACACTT
genomic: CTTGTC-AGG-ATGG-AGGGTGAATTCCAGAATCAATTATCCCAGCGCAGgtttgtgtct ... ctgatttcagCAAACCGATGG-AGCCTGATCGTC-TTTTTGATTGTCTTCCAAGTACACTT
EST: gi|211425856|gb|FL143029.1|FL143029
EST:     GCCCTTGTCAGGATGGAGGGTGAATTCCAGAATCAATTATCCCAGCGCAG                         CAAACCGATGGAGCCTGATCGTCTTTTTGATTGTCTTCCAAGTACACTTCG
genomic: GCCCTTGTCAGGATGGAGGGTGAATTCCAGAATCAATTATCCCAGCGCAGgtttgtgtct ... ctgatttcagCAAACCGATGGAGCCTGATCGTCTTTTTGATTGTCTTCCAAGTACACTTCG
EST: gi|211425853|gb|FL143026.1|FL143026
EST:     GCCCTTGTCAGGATGGAGGGTGAATTCCAGAATCAATTATCCCAGCGCAG                         CAAACCGATGGAGCCTGATCGTCTTTTTGATTGTCTTCCAAGTACACTTCG
genomic: GCCCTTGTCAGGATGGAGGGTGAATTCCAGAATCAATTATCCCAGCGCAGgtttgtgtct ... ctgatttcagCAAACCGATGGAGCCTGATCGTCTTTTTGATTGTCTTCCAAGTACACTTCG
EST: gi|211425852|gb|FL143025.1|FL143025
EST:     GCCCTTGTCAGGATGGAGGGTGAATTCCAGAATCAATTATCCCAGCGCAG                         CAAACCGATGGAGCCTGATCGTCTTTTTGATTGTCTTCCAAGTACACTTCG
genomic: GCCCTTGTCAGGATGGAGGGTGAATTCCAGAATCAATTATCCCAGCGCAGgtttgtgtct ... ctgatttcagCAAACCGATGGAGCCTGATCGTCTTTTTGATTGTCTTCCAAGTACACTTCG
EST: gi|149089875|gb|EE179160.2|EE179160
EST:     GCCCTTGTCAGGATGGAGGGTGAATTCCAGAATCAATTATCCCAGCGCAG                         CAAACCGATGGAGCCTGATCGTCTTTTTGATTGTCTTCCAAGTACACTTCG
genomic: GCCCTTGTCAGGATGGAGGGTGAATTCCAGAATCAATTATCCCAGCGCAGgtttgtgtct ... ctgatttcagCAAACCGATGGAGCCTGATCGTCTTTTTGATTGTCTTCCAAGTACACTTCG
EST: gi|149088666|gb|EE177784.2|EE177784
EST:     GCCCTTGTCAGGATGGAGGGTGAATTCCAGAATCAATTATCCCAGCGCAG                         CAAACCGATGGAGCCTGATCGTCTTTTTGATTGTCTTCCAAGTACACTTCG
genomic: GCCCTTGTCAGGATGGAGGGTGAATTCCAGAATCAATTATCCCAGCGCAGgtttgtgtct ... ctgatttcagCAAACCGATGGAGCCTGATCGTCTTTTTGATTGTCTTCCAAGTACACTTCG
EST: gi|149090520|gb|EE179830.2|EE179830
EST:     GCCCTTGTCAGGATGGAGGGTGAATTCCAGAATCAATTATCCCAGCGCAG                         CAAACCGATGGAGCCTGATCGTCTTTTTGATTGTCTTCCAAGTACACTTCG
genomic: GCCCTTGTCAGGATGGAGGGTGAATTCCAGAATCAATTATCCCAGCGCAGgtttgtgtct ... ctgatttcagCAAACCGATGGAGCCTGATCGTCTTTTTGATTGTCTTCCAAGTACACTTCG

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: 241

ACCGTAGTAGCGATGGGGTGCTCAACCACGTAAACGCGCTCCTTTCTAAGGCCCTTGTCAGGATGGAGGGTGAATTCCAGAATCAATTATCCCAGCGCAGgtttgtgtct ... ctgatttcagCAAACCGATGGAGCCTGATCGTCTTTTTGATTGTCTTCCAAGTACACTTCGACCATCGTCTGAATCTCAGCCCGAAGGTGGGAAAAACCCATCCGAGAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 212

ACCGTAGTAGCGATGGGGTGCTCAACCACGTAAACGCGCTCCTTTCTAAGGCCCTTGTCAGGATGGAGGGTGAATTCCAGAATCAATTATCCCAGCGCAGgtttgtgtct ... ctgatttcagCAAACCGATGGAGCCTGATCGTCTTTTTGATTGTCTTCCAAGTACACTTCGACCATCGTCTGAATCTCAGCCCGAAGGTGGGAAAAACCCATCCGAGAAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 199

ACCGTAGTAGCGATGGGGTGCTCAACCACGTAAACGCGCTCCTTTCTAAGGCCCTTGTCAGGATGGAGGGTGAATTCCAGAATCAATTATCCCAGCGCAGgtttgtgtct ... ctgatttcagCAAACCGATGGAGCCTGATCGTCTTTTTGATTGTCTTCCAAGTACACTTCGACCATCGTCTGAATCTCAGCCCGAAGGTGGGAAAAACCCATCCGAGAAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 211

ACCGTAGTAGCGATGGGGTGCTCAACCACGTAAACGCGCTCCTTTCTAAGGCCCTTGTCAGGATGGAGGGTGAATTCCAGAATCAATTATCCCAGCGCAGgtttgtgtct ... ctgatttcagCAAACCGATGGAGCCTGATCGTCTTTTTGATTGTCTTCCAAGTACACTTCGACCATCGTCTGAATCTCAGCCCGAAGGTGGGAAAAACCCATCCGAGAAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctatctaaaacacacctaatccttgcgctgtgcaccctcctaactgatttcagCAAACCGATGGAGCCTGATCGTCTTTTTGATTGTCTTCCAAGTACACTTCGACCATCGTCTGAATCTCAGCCCGAAGGTGGGAAAAACCCATCCGAGAAT
     tctaaaa  TA-rich tract