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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgtggattagattggattttatgggtgatcgatttgattgtggagtcgggattgatcgcactttcttttgctctgtgtgagtgccgcctgtgcaatattttttgtgtgtgtgcgaattccgtttctgatggcggtgcaagcgtgcagATGTGCTTCGATTGCAACGCCAAGAACCCGACGTGGGCGTCCGTCACCTACGGCGTCTTCCTCTGCATCGACTGCTCGGCGGCGCACCGCAGCCTCGGCG

Basic information

species Zea mays
transcript GRMZM2G094390_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G094390_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os10g42420.1 (Oryza sativa), 3'ss of exon 1
gtactgtggattagattggattttatgggtgatcgatttgattgtggagtcgggattgatcgcactttcttttgctctgtgtgagtgccgcctgtgcaatattttttgtgtgtgtgcgaattccgtttctgatggcggtgcaagcgtgcagATGTGCTTCGATTGCAACGCCAAGAACCCGACGTGGGCGTCCGTCACCTACGGCGTCTTCCTCTGCATCGACTGCTCGGCGGCGCACCGCAGCCTCGGCG
                                       | |||||     | ||  ||  |   | |  | |  |  |||||| |             | | | ||  | ||   | |  |   | | ||     |   | |   |||||||||||||||| |||||||||||||||||||| ||||| |||||||||||||||||||||||||||||||||||||| || |  ||||| ||||||||||
---------------------------------------ggttgtgtgtgtgagagagactgtgttcttctgtaattcgtgtgattttt----------tttctcttacgagtcgactatatttatatgtgcgtatgc--ctaatttgcagATGTGCTTCGACTGCAACGCCAAGAACCCGACCTGGGCCTCCGTCACCTACGGCGTCTTCCTCTGCATCGACTGCTCTGCCGTCCACCGTAGCCTCGGCG

upper sequence: GRMZM2G094390_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA08G36700.2 (Glycine max), 3'ss of exon 1
-------------------------gtactgtggattagattggat--tttatgggtgatcgatttgatt--gtggagtcgggattgatcgcactttcttt-tgctctgtgtga----gtgccgcctgtgcaatattttt-tgtgtgtgtgcgaattccgtttctg-atggcggtgcaagcgtg-------cagATGTGCTTCGATTGCAACGCCAAGAACCCGACGTGGGCGTCCGTCACCTACGGCGTCTTCCTCTGCATCGACTGCTCGGCGGCGCACCGCAGCCTCGGCG
                           | | |  ||| || || ||  |   ||| |    |||||  ||   |  |||  | | |  |||    |  ||| || | |  | ||    ||  |   | |||||||  | |   |||| ||  || ||  |  |  | ||||   |      ||        |||||||| ||||||||||| || |||||||| || |||||||||||||| || ||  |||| ||||||||||| ||||| || |  |||||||| |||||||
gtttggtttttgtaattttgaatttcgaatttcaatttgagtgcataatcgttggttccgtgatttcgttttatacagtttgaaattttcgtttgtggtttctgatttacgagatctggtttcagatctgcaatacctgtgcttgtgcgtttgatttttgaattggtatggtttttttgttgtttttttttcagATGTGTTTCGATTGCAATGCGAAGAACCCTACCTGGGCGTCCGTCACGTATGGGATCTTTCTCTGCATCGATTGCTCCGCCGTACACCGCAGTCTCGGCG

upper sequence: GRMZM2G094390_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA01G12340.2 (Glycine max), 3'ss of exon 1
------------------gtactgtggattagattggat--tttatgggtgatcgatttgatt--gtggagtcgggattgatcgcactttcttt-tgctctgtgtga----gtgccgcctgtgcaatattttttgt-gtgtgtgcgaattccgtttctg-atggcggtgcaagcgtg-------cagATGTGCTTCGATTGCAACGCCAAGAACCCGACGTGGGCGTCCGTCACCTACGGCGTCTTCCTCTGCATCGACTGCTCGGCGGCGCACCGCAGCCTCGGCG
                    | | |  ||| || || ||  |   ||| |    |||||  ||   |  |||| | | |  |||    |  ||| || | |  | ||    ||  |   | ||  |||    | || ||||||  || ||  |  | || |||||  |       |        |||||||| ||||||||||| || |||||||| || |||||||||||||| || ||  |||||||||||||||| ||||| || |  |||||||| |||||||
gttttttgtttataattttgaatttcaatttgagtgcataatcgttggttccgtgatttcgtttaatatagtctgaacttttcgtttgtggtttctgatttacgagatctggtttcagatctgtgatacccgtggtagtgtgtttgatttttgaatttgtatggcttttttttttttttaatttcagATGTGTTTCGATTGCAATGCGAAGAACCCTACCTGGGCGTCCGTCACGTATGGGATCTTCCTCTGCATCGATTGCTCCGCCGTTCACCGCAGTCTCGGCG

upper sequence: GRMZM2G094390_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT2G35210.2 (Arabidopsis thaliana), 3'ss of exon 1
gtactgtggattagattggattttatgggtgatcgatttgattgtggagtcgggattgatc-gcactttcttttgctctgtgtgagtgccgcctgtgcaatattttttgtgtgtgtgcgaattccgtttctgatggcggtgcaagcgtgcagATGTGCTTCGATTGCAACGCCAAGAACCCGACGTGGGCGTCCGTCACCTACGGCGTCTTCCTCTGCATCGACTGCTCGGCGGCGCACCGCAGCCTCGGCG
                                           ||   ||      || ||  ||   ||| | | |  |  | ||  |     || |    |   |    | ||  |  |||  |  | |      |         ||||||| || || |||||||| || |||||||| || ||||| ||||| || |||||  |||| ||||||||||| ||||| || |  || || || || ||||
-------------------------------------------gtaatgttaacgatgttctacagaatctatagattcgattaagatctcgaagttcg---tcgatcagatctg-acagatttaggatttatctttgaatattttttgcagATTTGTTTTGATTGCAATGCGAAGAACCCAACATGGGCTTCCGTTACTTACGGGATCTTTCTCTGCATCGATTGCTCAGCTGTTCATCGGAGTCTTGGCG

upper sequence: GRMZM2G094390_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv02s0012g01330.t01 (Vitis vinifera), 3'ss of exon 1
gtactgtggattagattggattttatgggtgatcgatttgattgtggagtcgggattgatcgcactttcttttgctctgtg--tgagtgccgcctgtgcaatattttttgtgtgtgtgcgaattccgtttctgatggcggtgca----agcgtgcagATGTGCTTCGATTGCAACGCCAAGAACCCGACGTGGGCGTCCGTCACCTACGGCGTCTTCCTCTGCATCGACTGCTCGGCGGCGCACCGCAGCCTCGGCG
    | ||   |  | || ||||  | |  |     ||  ||  |    |  |  || ||     ||| |  |  |||||   ||||  | |  |  |   |     ||  | |  || ||  || |||| | ||   | | |      |  |  ||||||| || ||||| || || ||||||||||| |||||||||||||| || ||  |||||||||||||||||||||| || | |||  | || || || |
---gtctgttctttactgaatttcttcgcggtatttttaaatgttttcttttgtttttattttggtttttggttttctgttcttgagatctggttcagatctggaggtttcgcgattg-gatctcggttttttattttgtttctttttggtttttagATGTGTTTTGATTGTAATGCGAAGAACCCGACTTGGGCGTCCGTCACGTATGGGATCTTCCTCTGCATCGACTGCTCCGCCGTGCATAGGAGTCTTGGGG

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|211011501|gb|FL284249.1|FL284249
EST:     CAGATAAGAACGCCGTCTTCCGCAAGCTTCGCGCCAAATCGGACAACAAG                         ATGTGCTTCGATTGCAACGCCAAGAACCCGACGTGGGCGTCCGTCACCTAC
genomic: CAGATAAGAACGCCGTCTTCCGCAAGCTTCGCGCCAAATCGGACAACAAGgtactgtgga ... aagcgtgcagATGTGCTTCGATTGCAACGCCAAGAACCCGACGTGGGCGTCCGTCACCTAC
EST: gi|37422203|gb|CF648807.1|CF648807
EST:     CAGATAAGAACGCCGTCTTCCGCAAGCTTCGCGCCAAATCGGACAACAAG                         ATGTGCTTCGATTGCAACGCCAAGAACCCGACGTGGGCGTCCGTCACCTAC
genomic: CAGATAAGAACGCCGTCTTCCGCAAGCTTCGCGCCAAATCGGACAACAAGgtactgtgga ... aagcgtgcagATGTGCTTCGATTGCAACGCCAAGAACCCGACGTGGGCGTCCGTCACCTAC
EST: gi|211008716|gb|FL284228.1|FL284228
EST:     CAGATAAGAACGCCGTCTTCCGCAAGCTTCGCGCCAAATCGGACAACAAG                         ATGTGCTTCGATTGCAACGCCAAGAACCCGACGTGGGCGTCCGTCACCTAC
genomic: CAGATAAGAACGCCGTCTTCCGCAAGCTTCGCGCCAAATCGGACAACAAGgtactgtgga ... aagcgtgcagATGTGCTTCGATTGCAACGCCAAGAACCCGACGTGGGCGTCCGTCACCTAC
EST: gi|211011498|gb|FL284246.1|FL284246
EST:     CAGATAAGAACGCCGTCTTCCGCAAGCTTCGCGCCAAATCGGACAACAAG                         ATGTGCTTCGATTGCAACGCCAAGAACCCGACGTGGGCGTCCGTCACCTAC
genomic: CAGATAAGAACGCCGTCTTCCGCAAGCTTCGCGCCAAATCGGACAACAAGgtactgtgga ... aagcgtgcagATGTGCTTCGATTGCAACGCCAAGAACCCGACGTGGGCGTCCGTCACCTAC
EST: gi|211005952|gb|FL284225.1|FL284225
EST:     CAGATAAGAACGCCGTCTTCCGCAAGCTTCGCGCCAAATCGGACAACAAG                         ATGTGCTTCGATTGCAACGCCAAGAACCCGACGTGGGCGTCCGTCACCTAC
genomic: CAGATAAGAACGCCGTCTTCCGCAAGCTTCGCGCCAAATCGGACAACAAGgtactgtgga ... aagcgtgcagATGTGCTTCGATTGCAACGCCAAGAACCCGACGTGGGCGTCCGTCACCTAC
EST: gi|211005945|gb|FL284218.1|FL284218
EST:     CAGATAAGAACGCCGTCTTCCGCAAGCTTCGCGCCAAATCGGACAACAAG                         ATGTGCTTCGATTGCAACGCCAAGAACCCGACGTGGGCGTCCGTCACCTAC
genomic: CAGATAAGAACGCCGTCTTCCGCAAGCTTCGCGCCAAATCGGACAACAAGgtactgtgga ... aagcgtgcagATGTGCTTCGATTGCAACGCCAAGAACCCGACGTGGGCGTCCGTCACCTAC
EST: gi|211008725|gb|FL284237.1|FL284237
EST:     CAGATAANAACGCCGTCTTCCGCAAGCTTCGCGCCAAATCGGACAACAAG                         ATGTGCTTCGATTGCAACGCCAAGAACCCGACGTGGGCGTCCGTCACCTAC
genomic: CAGATAAGAACGCCGTCTTCCGCAAGCTTCGCGCCAAATCGGACAACAAGgtactgtgga ... aagcgtgcagATGTGCTTCGATTGCAACGCCAAGAACCCGACGTGGGCGTCCGTCACCTAC
EST: gi|211008727|gb|FL284239.1|FL284239
EST:     CAGATAAGAACGCCGTCTTCCGCAAGCTTCGCGCCAAATCGGACAACAAG                         ATGTGCTTCGATTGCAACGCCAAGAACCCGACGTGGGCGTCCGTCACCTAC
genomic: CAGATAAGAACGCCGTCTTCCGCAAGCTTCGCGCCAAATCGGACAACAAGgtactgtgga ... aagcgtgcagATGTGCTTCGATTGCAACGCCAAGAACCCGACGTGGGCGTCCGTCACCTAC
EST: gi|89755431|gb|DY685850.1|DY685850
EST:     CAGATAAGAACGCCGTCTTCCGCAAGCTTCGCGCCAAATCGGACAACAAG                         ATGTGCTTCGATTGCAACGCCAAGAACCCGACGTGGGCGTCCGTCACCTAC
genomic: CAGATAAGAACGCCGTCTTCCGCAAGCTTCGCGCCAAATCGGACAACAAGgtactgtgga ... aagcgtgcagATGTGCTTCGATTGCAACGCCAAGAACCCGACGTGGGCGTCCGTCACCTAC
EST: gi|93282709|gb|EB674973.1|EB674973
EST:     CAGATAAGAACGCCGTCTTCCGCAAGCTTCGCGCCAAATCGGACAACAAG                         ATGTGCTTCGATTGCAACGCCAAGAACCCGACGTGGGCGTCCGTCACCTAC
genomic: CAGATAAGAACGCCGTCTTCCGCAAGCTTCGCGCCAAATCGGACAACAAGgtactgtgga ... aagcgtgcagATGTGCTTCGATTGCAACGCCAAGAACCCGACGTGGGCGTCCGTCACCTAC
EST: gi|101394873|gb|EB819371.1|EB819371
EST:     CAGATAAGAACGCCGTCTTCCGCAAGCTTCGCGCCAAATCGGACAACAAG                         ATGTGCTTCGATTGCAACGCCAAGAACCCGACGTGGGCGTCCGTCACCTAC
genomic: CAGATAAGAACGCCGTCTTCCGCAAGCTTCGCGCCAAATCGGACAACAAGgtactgtgga ... aagcgtgcagATGTGCTTCGATTGCAACGCCAAGAACCCGACGTGGGCGTCCGTCACCTAC
EST: gi|6578063|gb|AW244200.1|AW244200
EST:     CAGATAAGAACGCCGTCTTCCGCAAGCTTCGCGCCAAATCGGACAACAAG                         ATGTGCTTCGATTGCAACGCCAAGAACCCGACGTGGGCGTCCGTCACCTAC
genomic: CAGATAAGAACGCCGTCTTCCGCAAGCTTCGCGCCAAATCGGACAACAAGgtactgtgga ... aagcgtgcagATGTGCTTCGATTGCAACGCCAAGAACCCGACGTGGGCGTCCGTCACCTAC
EST: gi|211005949|gb|FL284222.1|FL284222
EST:     CAGATAAGAACGCCGTCTTCCGCAAGCTTCGCGCCAAATCGGACAACAAG                         ATGTGCTTCGATTGCAACGCCAAGAACCCGACGTGGGCGTCCGTCACCTAC
genomic: CAGATAAGAACGCCGTCTTCCGCAAGCTTCGCGCCAAATCGGACAACAAGgtactgtgga ... aagcgtgcagATGTGCTTCGATTGCAACGCCAAGAACCCGACGTGGGCGTCCGTCACCTAC
EST: gi|50326040|gb|CO521166.1|CO521166
EST:     CAGATAAGAACGCCGTCTTCCGCAAGCTTCGCGCCAAATCGGACAACAAG                         ATGTGCTTCGATTGCAACGCCAAGAACCCGACGTGGGCGTCCGTCACCTAC
genomic: CAGATAAGAACGCCGTCTTCCGCAAGCTTCGCGCCAAATCGGACAACAAGgtactgtgga ... aagcgtgcagATGTGCTTCGATTGCAACGCCAAGAACCCGACGTGGGCGTCCGTCACCTAC
EST: gi|211011496|gb|FL284244.1|FL284244
EST:     CAGATAAGAACGCCGTCTTCCGCAAGCTTCGCGCCAAATCGGACAACAAG                         ATGTGCTTCGATTGCAACGCCAAGAACCCGACGTGGGCGTCCGTCACCTAC
genomic: CAGATAAGAACGCCGTCTTCCGCAAGCTTCGCGCCAAATCGGACAACAAGgtactgtgga ... aagcgtgcagATGTGCTTCGATTGCAACGCCAAGAACCCGACGTGGGCGTCCGTCACCTAC
EST: gi|91868839|gb|EB400177.1|EB400177
EST:     CAGATAAGAACGCCGTCTTCCGCAAGCTTCGCGCCAAATCGGACAACAAG                         ATGTGCTTCGATTGCAACGCCAAGAACCCGACGTGGGCGTCCGTCACCTAC
genomic: CAGATAAGAACGCCGTCTTCCGCAAGCTTCGCGCCAAATCGGACAACAAGgtactgtgga ... aagcgtgcagATGTGCTTCGATTGCAACGCCAAGAACCCGACGTGGGCGTCCGTCACCTAC
EST: gi|211011493|gb|FL284241.1|FL284241
EST:     CAGATAAGAACGCCGTCTTCCGCAAGCTTCGCGCCAAATCGGACAACAAG                         ATGTGCTTCGATTGCAACGCCAAGAACCCGACGTGGGCGTCCGTCACCTAC
genomic: CAGATAAGAACGCCGTCTTCCGCAAGCTTCGCGCCAAATCGGACAACAAGgtactgtgga ... aagcgtgcagATGTGCTTCGATTGCAACGCCAAGAACCCGACGTGGGCGTCCGTCACCTAC
EST: gi|211005951|gb|FL284224.1|FL284224
EST:     CAGATAAGAACGCCGTCTTCCGCAAGCTTCGCGCCAAATCGGACAACAAG                         ATGTGCTTCGATTGCAACGCCAAGAACCCGACGTGGGCGTCCGTCACCTAC
genomic: CAGATAAGAACGCCGTCTTCCGCAAGCTTCGCGCCAAATCGGACAACAAGgtactgtgga ... aagcgtgcagATGTGCTTCGATTGCAACGCCAAGAACCCGACGTGGGCGTCCGTCACCTAC
EST: gi|211008718|gb|FL284230.1|FL284230
EST:     CAGATAAGAACGCCGTCTTCCGCAAGCTTCGCGCCAAATCGGACAACAAG                         ATGTGCTTCGATTGCAACGCCAAGAACCCGACGTGGGCGTCCGTCACCTAC
genomic: CAGATAAGAACGCCGTCTTCCGCAAGCTTCGCGCCAAATCGGACAACAAGgtactgtgga ... aagcgtgcagATGTGCTTCGATTGCAACGCCAAGAACCCGACGTGGGCGTCCGTCACCTAC

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: 47 (upstream exon), 43 (downstream exon)
Score: 35

GGGTTCGTTGCCCGTGTGGGTGGGCGCTATGGCGGCGATGGATGCCTCGGCAGATAAGAACGCCGTCTTCCGCAAGCTTCGCGCCAAATCGGACAACAAGgtactgtgga ... aagcgtgcagATGTGCTTCGATTGCAACGCCAAGAACCCGACGTGGGCGTCCGTCACCTACGGCGTCTTCCTCTGCATCGACTGCTCGGCGGCGCACCGCAGCCTCGGCG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 127

GGGTTCGTTGCCCGTGTGGGTGGGCGCTATGGCGGCGATGGATGCCTCGGCAGATAAGAACGCCGTCTTCCGCAAGCTTCGCGCCAAATCGGACAACAAGgtactgtgga ... aagcgtgcagATGTGCTTCGATTGCAACGCCAAGAACCCGACGTGGGCGTCCGTCACCTACGGCGTCTTCCTCTGCATCGACTGCTCGGCGGCGCACCGCAGCCTCGGCG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 139

GGGTTCGTTGCCCGTGTGGGTGGGCGCTATGGCGGCGATGGATGCCTCGGCAGATAAGAACGCCGTCTTCCGCAAGCTTCGCGCCAAATCGGACAACAAGgtactgtgga ... aagcgtgcagATGTGCTTCGATTGCAACGCCAAGAACCCGACGTGGGCGTCCGTCACCTACGGCGTCTTCCTCTGCATCGACTGCTCGGCGGCGCACCGCAGCCTCGGCG


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

GGGTTCGTTGCCCGTGTGGGTGGGCGCTATGGCGGCGATGGATGCCTCGGCAGATAAGAACGCCGTCTTCCGCAAGCTTCGCGCCAAATCGGACAACAAGgtactgtgga ... aagcgtgcagATGTGCTTCGATTGCAACGCCAAGAACCCGACGTGGGCGTCCGTCACCTACGGCGTCTTCCTCTGCATCGACTGCTCGGCGGCGCACCGCAGCCTCGGCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caatattttttgtgtgtgtgcgaattccgtttctgatggcggtgcaagcgtgcagATGTGCTTCGATTGCAACGCCAAGAACCCGACGTGGGCGTCCGTCACCTACGGCGTCTTCCTCTGCATCGACTGCTCGGCGGCGCACCGCAGCCTCGGCG
                              ttctgat  putative branch site (score: 94)
     ttttttgt  TA-rich tract