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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCGCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCTgtaagagttaccactctatatattcctctcagtcatttggatgttaccattctaatttgatgagtgtggtaacaagttcctactcctctcaag

Basic information

species Zea mays
transcript GRMZM2G147721_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147721_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os01g50760.1 (Oryza sativa), 5'ss of exon 6
TCGCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCTgtaagagttaccactct---atatattcctctcagtcatttggatgttaccattctaatttg---atgagtgtggtaacaagt--tcctactcctctcaag-----
|| ||||| ||| |||||||||||||||||||| || ||||| || ||||| ||| || |||||| |||   ||  |||  |  || || ||    | | ||     |||| ||   ||   |||  | || ||   |  || |  |||  |      
TCACCGCCGCATTGTTCAGTACAAGACAGCTTACTACTCATTCTATCTTCCGgtaggatttaccattctcctatggattttttcca-tctttaaactctcacttcggtaatctgcgaatagttgtcatcactagcaataatatttttctttatccaag

upper sequence: GRMZM2G147721_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA15G12780.1 (Glycine max), 5'ss of exon 7
TCGCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCTgtaagagttaccactctatatattcctctcagtcatttggatgttaccattctaatttgatgagtgtgg--taacaagttcctactcctctcaag-------
 |  || |  || |||||||||||||| || |||||||| ||||||||||| |||||  |||    | | || |||  | |   || | | |         || |  |||  |   |||    |  |       ||||    ||||        
GCATCGACGTATTGTTCAGTACAAGACTGCATATTATTCCTTTTACCTTCCGgtaagtattaat-ttttgtacattttttttt-tcgtatagcctccctagttatggtttcttctttgtcccttttcctagagatactaacgtcaaatgattct

upper sequence: GRMZM2G147721_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA09G01820.3 (Glycine max), 5'ss of exon 7
TCGCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCTgtaagagttaccactc-tatatattcctct---cagtcatttggatgttaccattctaatttgatgagtgtggtaacaagttcctactcctctcaag--------
 |  || |  || |||||||||||||| || || ||||||||||||||||| |||||  |||   ||  || || ||  | |    || |      || ||    ||||  ||||     | |  ||   |     ||||  | ||||         
GCATCGACGTATAGTTCAGTACAAGACTGCATACTATTCATTTTACCTTCCAgtaagtattaattcttgtacatttttttttgtatagcctccctaatttttggtttcttctttgtcccttttcctagaga-----tactaatgtcaaatggttctt

upper sequence: GRMZM2G147721_T01 (Zea mays), 5'ss of exon 6
lower sequence: AT4G17190.1 (Arabidopsis thaliana), 5'ss of exon 6
TCGCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCTgtaagagttaccactctatatattcctctcagtcatttggatgttaccattctaatttgatgagtgtggtaacaagttcctactcctctcaag---------
 |  || |  || ||| ||||||| ||||||||||| |||||||| |||||||| ||   |   | ||  | | |   | |   | || |  |   |  ||      ||    |  ||  | |  || ||  | |       |           
CCATCGGCGTATTGTTGAGTACAAAACAGCTTATTACTCATTTTATCTTCCTgtgagtactctgaatccctctctctatatatat-atatatagagtcacacgtaggttcagaggttgcagca-taatttatttcgtaagctagacacattctg

upper sequence: GRMZM2G147721_T01 (Zea mays), 5'ss of exon 6
lower sequence: Vv19s0015g01010.t01 (Vitis vinifera), 5'ss of exon 7
TCGCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCTgtaag---agttacc---actctatatattcctctcagtcatttggatgtta--ccattctaatttgatgagtgtggtaac--aagtt-cctactcctctcaag
|| ||||| ||| ||||||||||| || |||||||| |||||||||||||| |||||   || |  |   |||    |   |  | |    || ||   |||||   ||| || ||||  |   | |  | ||  ||||| | |    || |    
TCACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCCAgtaagctaagctctctctactaagaacggttttgtattccactttattgttaaatcatgctgattttttatttttttttactgaagttacttgaggctat----

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|148986684|gb|EE030466.2|EE030466
EST:     GCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCT                         GTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGAT
genomic: GCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCTgtaagagtta ... tcctctcaagGTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGAT
EST: gi|60355786|gb|DN222759.1|DN222759
EST:     GCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCT                         GTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGAT
genomic: GCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCTgtaagagtta ... tcctctcaagGTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGAT
EST: gi|148995918|gb|EE035161.2|EE035161
EST:     GCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCT                         GTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGAT
genomic: GCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCTgtaagagtta ... tcctctcaagGTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGAT
EST: gi|149102315|gb|EE188183.2|EE188183
EST:     GCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCT                         GTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGAT
genomic: GCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCTgtaagagtta ... tcctctcaagGTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGAT
EST: gi|149081093|gb|EE170194.2|EE170194
EST:     GCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCT                         GTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGAT
genomic: GCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCTgtaagagtta ... tcctctcaagGTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGAT
EST: gi|148986685|gb|EE030467.2|EE030467
EST:     GCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCT                         GTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGAT
genomic: GCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCTgtaagagtta ... tcctctcaagGTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGAT
EST: gi|71437045|gb|DR818095.1|DR818095
EST:     GCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCT                         GTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGAT
genomic: GCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCTgtaagagtta ... tcctctcaagGTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGAT
EST: gi|148943253|gb|EC888314.2|EC888314
EST:     GCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCT                         GTTGCATGTGCATTGCTGC
genomic: GCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCTgtaagagtta ... tcctctcaagGTTGCATGTGCATTGCTGC
EST: gi|148943252|gb|EC888313.2|EC888313
EST:     TCAGTACAAGACAGCTTATTATTCATTTTCCCTTCCT                         GTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGAT
genomic: TCAGTACAAGACAGCTTATTATTCATTTTACCTTCCTgtaagagtta ... tcctctcaagGTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGAT
EST: gi|74235474|gb|DT643388.1|DT643388
EST:     GCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCT                         GTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGAT
genomic: GCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCTgtaagagtta ... tcctctcaagGTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGAT
EST: gi|111189546|gb|EE287682.1|EE287682
EST:     GCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCT                         GTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGAT
genomic: GCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCTgtaagagtta ... tcctctcaagGTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGAT

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), 47 (downstream exon)
Score: 49

TCGCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCTgtaagagtta ... tcctctcaagGTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGATGTAAAGAACATTCTTGTCGAAATGGGAACATACTTTCAAGTTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 63

TCGCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCTgtaagagtta ... tcctctcaagGTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGATGTAAAGAACATTCTTGTCGAAATGGGAACATACTTTCAAGTTCAG


Block sizes: 49 (upstream exon), 38 (downstream exon)
Score: 13

TCGCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCTgtaagagtta ... tcctctcaagGTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGATGTAAAGAACATTCTTGTCGAAATGGGAACATACTTTCAAGTTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 153

TCGCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCTgtaagagtta ... tcctctcaagGTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGATGTAAAGAACATTCTTGTCGAAATGGGAACATACTTTCAAGTTCAG