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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTCGCTACTTCTTCCAACAACTCATTTCAGGAGTAAGCTACTGCCATTCAATGgtattagttgttatataatggcacatttttcatcatattgttattgtttactcataccatgcattgagctgagctgccttttttattcttattttcaag

Basic information

species Zea mays
transcript GRMZM2G171435_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G171435_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os03g55600.1 (Oryza sativa), 5'ss of exon 4
GCTCGCTACTTCTTCCAACAACTCATTTCAGGAGTAAGCTACTGCCATTCAATGgtattagttgttatataatggcacatttttcatcatattgttattgtttactcataccatgcattgagctgagctgccttttttattcttattttcaag
||||||||||||||||| || || || || ||||| |||||||||||||||||||||||  || ||| |  |||     | |||||||  ||||||||| | |||| |  |   |   | |||||| ||  | |  ||  ||  |||||||||
GCTCGCTACTTCTTCCAGCAGCTTATCTCGGGAGTCAGCTACTGCCATTCAATGgtatttcttattaca--atgattt-tctttcatctgattgttattctgtactaaggcatcgtggtaagctgaactatcctactttctcc-attttcaag

upper sequence: GRMZM2G171435_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA20G01240.1 (Glycine max), 5'ss of exon 4
GCTCGCTACTTCTTCCAACAACTCATTTCAGGAGTAAGCTACTGCCATTCAATGgtattagttgttatataatggcacatttttcatcat-attgttattgtttactcataccatgcattgagctgagctgccttttttattcttattt--tcaag
|| |||| ||||||||||||||| || ||||| || |||||||| ||| ||||||||         ||| | |    ||| |||  || | | | |||   |  |   |||    |       ||    ||  | | ||  ||||||||  | |||
GCACGCTTCTTCTTCCAACAACTTATATCAGGGGTTAGCTACTGTCATGCAATGgtac--------ata-agttcggcatctttagtctttacttttacaat--aggtataatgagttgctgacttcaatgtttctatttatcttatttaataaag

upper sequence: GRMZM2G171435_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA07G29500.1 (Glycine max), 5'ss of exon 4
GCTCGCTACTTCTTCCAACAACTCATTTCAGGAGTAAGCTACTGCCATTCAATGgtat-tagttgttatataatggcacatttttcatcatattgttattgtttactcataccatgcattgagctgagctgccttttttattcttattttcaag
|| |||| ||||||||||||||| || ||||| || |||||||| ||| ||||||||  ||  |     ||  |    | ||  || |   || | |||  |    |  |  | || ||   |   |  |  ||| |||| |            
GCACGCTTCTTCTTCCAACAACTTATATCAGGGGTTAGCTACTGTCATGCAATGgtacataagttcggcatctttagtctttactcttacaataggtataatgagttgctgacttgaat---gtctatttatcttatttaataaag--------

upper sequence: GRMZM2G171435_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA02G15330.1 (Glycine max), 5'ss of exon 4
GCTCGCTACTTCTTCCAACAACTCATTTCAGGAGTAAGCTACTGCCATTCAATGgtattag---ttgttatataatggcacatttttcatcatattgttattgtttactcataccatgcattgag----ctgagctgccttttt-tattcttattttcaag-----
|| |||| ||||||||||||||| || |||||||| |||||||| ||| ||||||||   |   |    | ||   | |     ||| | ||  |  ||  |    |     |  |     ||||    ||||  ||  ||| | ||||  | || |  |      
GCGCGCTTCTTCTTCCAACAACTTATATCAGGAGTTAGCTACTGTCATGCAATGgtacatgaattcaacacatgtagtctttacttttaccagttatttgcttcccagaagaaagaaagcatgagatgtctgacttgaatttctatatttgtcttctttaatgaag

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|211499753|gb|FL295241.1|FL295241
EST:     GCTACTTCTTCCAACAACTCATTTCAGGAGTAAGCTACTGCCATTCAATG                         CAAGTACTGCCACCGTGATTTGAAGCTGGAGAACACACTTCTAGATGGGAG
genomic: GCTACTTCTTCCAACAACTCATTTCAGGAGTAAGCTACTGCCATTCAATGgtattagttg ... tattttcaagCAAGTA-TGCCACCGTGATTTGAAGCTGGAGAACACACTTCTAGATGGGAG
EST: gi|32859143|gb|CD998824.1|CD998824
EST:     GCTACTTCTTCCAACAACTCATTTCAGGAGTAAGCTACTGCCATTCAATG                         CAAGTATGCCACCGTGATTTGAAGCTGGAGAACACACTTCTAGATGGGAGT
genomic: GCTACTTCTTCCAACAACTCATTTCAGGAGTAAGCTACTGCCATTCAATGgtattagttg ... tattttcaagCAAGTATGCCACCGTGATTTGAAGCTGGAGAACACACTTCTAGATGGGAGT
EST: gi|6022633|gb|AW067445.1|AW067445
EST:     GCTACTTCTTCCAACAACTCATTTCAGGAGTAAGCTACTGCCATTCAATG                         CAAGTATGCCACCGTGATTTGAAGCTGGAGAACACACTTCTAGATGGGAGT
genomic: GCTACTTCTTCCAACAACTCATTTCAGGAGTAAGCTACTGCCATTCAATGgtattagttg ... tattttcaagCAAGTATGCCACCGTGATTTGAAGCTGGAGAACACACTTCTAGATGGGAGT
EST: gi|148932906|gb|EE285698.2|EE285698
EST:     GCTACTTCTTCCAACAACTCATTTCAGGAGTAAGCTACTGCCATTCAATG                         CAAGTATGCCACCGTGATTTGAAGCTGGAGAACACACTTCTAGATGGGAGT
genomic: GCTACTTCTTCCAACAACTCATTTCAGGAGTAAGCTACTGCCATTCAATGgtattagttg ... tattttcaagCAAGTATGCCACCGTGATTTGAAGCTGGAGAACACACTTCTAGATGGGAGT
EST: gi|78107855|gb|DV526273.1|DV526273
EST:     GCTACTTCTTCCAACAACTCATTTCAGGAGTAAGCTACTGCCATTCAATG                         CAAGTATGCCACCGTGATTTGAAGCTGGAGAACACACTTCTAGATGGGAGT
genomic: GCTACTTCTTCCAACAACTCATTTCAGGAGTAAGCTACTGCCATTCAATGgtattagttg ... tattttcaagCAAGTATGCCACCGTGATTTGAAGCTGGAGAACACACTTCTAGATGGGAGT

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), 48 (downstream exon)
Score: 167

GCTCGCTACTTCTTCCAACAACTCATTTCAGGAGTAAGCTACTGCCATTCAATGgtattagttg ... tattttcaagCAAGTATGCCACCGTGATTTGAAGCTGGAGAACACACTTCTAGATGGGAGTGATGCTCCTCGCTTGAAGATATGTGACTTCGGTTATTCCAAG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 97

GCTCGCTACTTCTTCCAACAACTCATTTCAGGAGTAAGCTACTGCCATTCAATGgtattagttg ... tattttcaagCAAGTATGCCACCGTGATTTGAAGCTGGAGAACACACTTCTAGATGGGAGTGATGCTCCTCGCTTGAAGATATGTGACTTCGGTTATTCCAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 131

GCTCGCTACTTCTTCCAACAACTCATTTCAGGAGTAAGCTACTGCCATTCAATGgtattagttg ... tattttcaagCAAGTATGCCACCGTGATTTGAAGCTGGAGAACACACTTCTAGATGGGAGTGATGCTCCTCGCTTGAAGATATGTGACTTCGGTTATTCCAAG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 94

GCTCGCTACTTCTTCCAACAACTCATTTCAGGAGTAAGCTACTGCCATTCAATGgtattagttg ... tattttcaagCAAGTATGCCACCGTGATTTGAAGCTGGAGAACACACTTCTAGATGGGAGTGATGCTCCTCGCTTGAAGATATGTGACTTCGGTTATTCCAAG