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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacattcactttctcgccagattcactattctactttatcaatattacttattctgaaatctaacttgtcctggcagGTCTCCTATTTTCAGTACTTATTACTGCTGTTTTAACTGATGCGATAAAGGATGGTGTTGGGCGACCACGTCCTGATTTCTTCTGGCGTTGCTTCCCTGA

Basic information

species Zea mays
transcript GRMZM2G077187_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G077187_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g49820.1 (Oryza sativa), 3'ss of exon 3
----gtacattcactttctcgccagattcactattctactttatcaatatt---acttatt--ctgaaatctaact-tgtcctggcagGTCTCCTATTTTCAGTACTTATTACTGCTGTTTTAACTGATGCGATAAAGGATGGTGTTGGGCGACCACGTCCTGATTTCTTCTGGCGTTGCTTCCCTGA
    |  |||   ||||||   | | ||   | | ||| | ||   || ||   | || ||  |||||| ||| |  || ||| |||||||||||||||||||| ||||| || || ||  |||||||||| || || ||||| ||||| ||||| ||||| |||||||| ||||| || || |||||
gtgagctcatgttctttctattctgttttgttttgctagtctacacattttgtaatttcttatctgaaacctagcaatgcccttgcagGTCTCCTATTTTCAGTTCTTATCACGGCGGTAATAACTGATGCCATTAAAGATGGGGTTGGTCGACCGCGTCCAGATTTCTTTTGGCGCTGTTTTCCTGA

upper sequence: GRMZM2G077187_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA09G18450.2 (Glycine max), 3'ss of exon 3
---------------gtacattcactttctcgccagattcactattctactttatcaatattacttattctgaaatctaacttgtcctggcagGTCTCCTATTTTCAGTACTTATTACTGCTGTTTTAACTGATGCGATAAAGGATGGTGTTGGGCGACCACGTCCTGATTTCTTCTGGCGTTGCTTCCCTGA
                || |  |  || ||  ||  |||    ||   |||||   | ||        | || | |   |  ||      |||| ||  ||||||| ||||| |||||||| ||  |||| ||||| || || ||||||||||| || ||||| || ||||||||||||||||| ||||||||
gtacttttctgtcttttagaaacttttcctaaccttattttgcatatcactttgcta-tagcctaacctatgtattgccaaatgcatattcagGCCTTTTATTTTCTGTACTCATTACTGCGGTGATAACGGATGCTATCAAAGATGGTGTTGGACGGCCACGCCCAGATTTCTTCTGGCGTTGTTTCCCTGA

upper sequence: GRMZM2G077187_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA20G25650.1 (Glycine max), 3'ss of exon 3
gtacattcactt-tctcgccagattcactat-tctactttatcaatattacttattctgaaatcta--acttgtcctggcagGTCTCCTATTTTCAGTACTTATTACTGCTGTTTTAACTGATGCGATAAAGGATGGTGTTGGGCGACCACGTCCTGATTTCTTCTGGCGTTGCTTCCCTGA
|||||||       || |  |  ||  || | ||    ||||||  |||    || |||||| |||   ||        |||| || |||||||| ||||| |||||||| ||  | |||||||| || ||||||| |||||| || ||| | || || |||||||||||||| ||||||||
gtacatttctgaaccttggaatgttttctctgtccttcttatca-cattgga-atactgaaacctattgctaaatgcaccagGCCTTCTATTTTCTGTACTCATTACTGCGGTGATGACTGATGCTATCAAGGATGCTGTTGGACGGCCAAGGCCAGACTTCTTCTGGCGTTGTTTCCCTGA

upper sequence: GRMZM2G077187_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA10G41580.1 (Glycine max), 3'ss of exon 3
gtacattcactt-tctcgccagattcactattctactttatcaatattactt----attctgaaatcta--acttgtcctggcagGTCTCCTATTTTCAGTACTTATTACTGCTGTTTTAACTGATGCGATAAAGGATGGTGTTGGGCGACCACGTCCTGATTTCTTCTGGCGTTGCTTCCCTGA
|||||||       ||    || ||  || |     | | |  | || || |    || |||||| |||   ||     |  |||| || |||||||| ||||| |||||||| ||  | |||||||| || ||||||| |||||| || ||| | || || |||||||||||||| ||||||||
gtacatttctgaaccttagaaggttttctctgtccttatttgcacatcacatcggaatactgaaacctattgctaaatgtatcagGCCTTCTATTTTCCGTACTCATTACTGCGGTGATGACTGATGCTATCAAGGATGCTGTTGGACGGCCAAGGCCAGACTTCTTCTGGCGTTGTTTCCCTGA

upper sequence: GRMZM2G077187_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT1G15080.1 (Arabidopsis thaliana), 3'ss of exon 3
gtacattcactttctcgcca----gattcactattctactttatcaatattacttattctgaaatctaactt-----gtcctgg-cagGTCTCCTATTTTCAGTACTTATTACTGCTGTTTTAACTGATGCGATAAAGGATGGTGTTGGGCGACCACGTCCTGATTTCTTCTGGCGTTGCTTCCCTGA
|||| |     ||||  | |    | ||||   ||| | ||         |  | ||| |||  | |    |     ||| |   |||| ||  | || || |||||||| || | |||  |||| ||||| |||||||| | |||||| ||||| |||||||||||||| |||||||| ||||||||
gtacctctttcttcttccaattgtgtttcatgtttcgaattctctgtagctcttgattttgaggtgtgttctcttgggtcttcttcagGGCTTTTGTTCTCTGTACTTATAACCGGTGTCATAACCGATGCTATAAAGGACGCTGTTGGTCGACCTCGTCCTGATTTCTTTTGGCGTTGTTTCCCTGA

upper sequence: GRMZM2G077187_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ17723 (Selaginella moellendorffii), 3'ss of exon 2
gtacattcactttctcgccagattcactattctactttatcaatattacttattctgaaatctaacttgtcctgg----------cagGTCTCCTATTTTCAGTACTTATTACTGCTGTTTTAACTGATGCGATAAAGGATGGTGTTGGGCGACCACGTCCTGATTTCTTCTGGCGTTGCTTCCCTGA
|||   | | |||     ||   || || |   ||      || |   |  | |  | || |||  |||| || |          ||||  | || ||  | || ||||||||||||||| | ||||||||||| || || |  ||||| || ||| | ||||||||||||||||| || || || ||
gtaagcttatttttctttcat-ctctctctcgaaccaagagaagagctcggactaagtaaactatgttgttcttgttttttactacagGCTTGCTTTTCGCGGTGCTTATTACTGCTGTTCTTACTGATGCGATCAAAGACGCAGTTGGACGTCCAAGGCCTGATTTCTTCTGGCGGTGTTTTCCAGA

upper sequence: GRMZM2G077187_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ16251 (Selaginella moellendorffii), 3'ss of exon 2
gtacattcactttctcgccagattcactattctactttatcaatattacttattctgaaatctaacttgtcctgg-----------cagGTCTCCTATTTTCAGTACTTATTACTGCTGTTTTAACTGATGCGATAAAGGATGGTGTTGGGCGACCACGTCCTGATTTCTTCTGGCGTTGCTTCCCTGA
|||   | | |||     ||   || || |   ||      || |   |  | |  | || |||  |||| || |           ||||  | || ||  | || ||||||||||||||| | ||||||||||| || || |  ||||| || ||| | ||||||||||||||||| || || || ||
gtaagcttatttttctttcat-ctctctctcgaaccaagagaagagctcggactaagtaaactatgttgttcttgtttttttactacagGCTTGCTTTTCGCGGTGCTTATTACTGCTGTTCTTACTGATGCGATCAAAGACGCAGTTGGACGTCCAAGGCCTGATTTCTTCTGGCGGTGTTTTCCAGA

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|78124930|gb|DV543314.1|DV543314
EST:     TATGATCTGCATCATGCCATACTAG                         GTCTCCTATTTTCAGTACTTATTACTGCTGTTTTAACTGATGCGATAAAGG
genomic: TATGATCTGCATCATGCCATACTAGgtacattcac ... gtcctggcagGTCTCCTATTTTCAGTACTTATTACTGCTGTTTTAACTGATGCGATAAAGG
EST: gi|76286378|gb|DV025946.1|DV025946
EST:     GATATACTTTAAGAAGAGAAATGTATATGATCTGCATCATGCCATACTAG                         GTCTCCTATTTTCAGTACTTATTACTGCTGTTTTAACTGATGCGATAAAGG
genomic: GATATACTTTAAGAAGAGAAATGTATATGATCTGCATCATGCCATACTAGgtacattcac ... gtcctggcagGTCTCCTATTTTCAGTACTTATTACTGCTGTTTTAACTGATGCGATAAAGG
EST: gi|14243380|gb|BG841070.2|BG841070
EST:     GATATACTTTAAGAAGAGAAATGTATATGATCTGCATCATGCCATACTAG                         GTCTCCTATTTTCAGTACTTATTACTGCTGTTTTAACTGATGCGATAAAGG
genomic: GATATACTTTAAGAAGAGAAATGTATATGATCTGCATCATGCCATACTAGgtacattcac ... gtcctggcagGTCTCCTATTTTCAGTACTTATTACTGCTGTTTTAACTGATGCGATAAAGG
EST: gi|61119018|gb|DN559979.1|DN559979
EST:     GATATACTTTAAGAAGAGAAATGTATATGATCTGCATCATGCCATACTAG                         GTCTCCTATTTTCGGTACTTATTACTGCTGTTTTAACTGATGCGATAAAGG
genomic: GATATACTTTAAGAAGAGAAATGTATATGATCTGCATCATGCCATACTAGgtacattcac ... gtcctggcagGTCTCCTATTTTCAGTACTTATTACTGCTGTTTTAACTGATGCGATAAAGG
EST: gi|78079032|gb|DV507444.1|DV507444
EST:     GATATACTTTAAGAAGAGAAATGTATATGATCTGCATCATGCCATACTAG                         GTCTCCTATTTTCAGTACTTATTACTGCTGTTTTAACTGATGCGATAAAGG
genomic: GATATACTTTAAGAAGAGAAATGTATATGATCTGCATCATGCCATACTAGgtacattcac ... gtcctggcagGTCTCCTATTTTCAGTACTTATTACTGCTGTTTTAACTGATGCGATAAAGG
EST: gi|86467943|gb|DY234313.1|DY234313
EST:     GATATACTTTAAGAAGAGAAATGTATATGATCTGCATCGTGCCATACTAG                         GTCTCCTATTTTC
genomic: GATATACTTTAAGAAGAGAAATGTATATGATCTGCATCATGCCATACTAGgtacattcac ... gtcctggcagGTCTCCTATTTTC
EST: gi|76289091|gb|DV028659.1|DV028659
EST:     GATATACTTTAAGAAGAGAAATGTATATGATCTGCATCATGCCATACTAG                         GTCTCCTATTTTCAGTACTTATTACTGCTGTTTTAACTGATGCGATAAAGG
genomic: GATATACTTTAAGAAGAGAAATGTATATGATCTGCATCATGCCATACTAGgtacattcac ... gtcctggcagGTCTCCTATTTTCAGTACTTATTACTGCTGTTTTAACTGATGCGATAAAGG
EST: gi|24934529|gb|CA452747.1|CA452747
EST:     GATATACTTTAAGAAGAGAAATGTATATGATCTGCATCATGCCATACTAG                         GTCTCCTATTTTCAGT
genomic: GATATACTTTAAGAAGAGAAATGTATATGATCTGCATCATGCCATACTAGgtacattcac ... gtcctggcagGTCTCCTATTTTCAGT

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: 39 (upstream exon), 41 (downstream exon)
Score: 3

ATAATTGGTATCATTGGGCCTATGGTTATCATAACAGTGATATACTTTAAGAAGAGAAATGTATATGATCTGCATCATGCCATACTAGgtacattcac ... gtcctggcagGTCTCCTATTTTCAGTACTTATTACTGCTGTTTTAACTGATGCGATAAAGGATGGTGTTGGGCGACCACGTCCTGATTTCTTCTGGCGTTGCTTCCCTGA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 203

ATAATTGGTATCATTGGGCCTATGGTTATCATAACAGTGATATACTTTAAGAAGAGAAATGTATATGATCTGCATCATGCCATACTAGgtacattcac ... gtcctggcagGTCTCCTATTTTCAGTACTTATTACTGCTGTTTTAACTGATGCGATAAAGGATGGTGTTGGGCGACCACGTCCTGATTTCTTCTGGCGTTGCTTCCCTGA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 237

ATAATTGGTATCATTGGGCCTATGGTTATCATAACAGTGATATACTTTAAGAAGAGAAATGTATATGATCTGCATCATGCCATACTAGgtacattcac ... gtcctggcagGTCTCCTATTTTCAGTACTTATTACTGCTGTTTTAACTGATGCGATAAAGGATGGTGTTGGGCGACCACGTCCTGATTTCTTCTGGCGTTGCTTCCCTGA


Block sizes: 43 (upstream exon), 31 (downstream exon)
Score: 12

ATAATTGGTATCATTGGGCCTATGGTTATCATAACAGTGATATACTTTAAGAAGAGAAATGTATATGATCTGCATCATGCCATACTAGgtacattcac ... gtcctggcagGTCTCCTATTTTCAGTACTTATTACTGCTGTTTTAACTGATGCGATAAAGGATGGTGTTGGGCGACCACGTCCTGATTTCTTCTGGCGTTGCTTCCCTGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcactattctactttatcaatattacttattctgaaatctaacttgtcctggcagGTCTCCTATTTTCAGTACTTATTACTGCTGTTTTAACTGATGCGATAAAGGATGGTGTTGGGCGACCACGTCCTGATTTCTTCTGGCGTTGCTTCCCTGA
                                    atctaac  putative branch site (score: 12)
                                          cttgtcct  CT-rich tract
         tactttatcaatatta  TA-rich tract