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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATATATGgtaatatttatgattctgtgttggctatatgaccatcagttatggccaagcatgttctaaatctcttgtttcggttgcag

Basic information

species Zea mays
transcript GRMZM2G176546_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G176546_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os11g04980.1 (Oryza sativa), 5'ss of exon 19
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATATATGgtaatatttatgattctgtgttggctatatgaccatcagttatg-gccaagcatgttctaaatctcttgtttcggttgcag
||||||||||||||||||||||||||||||||||||||||| ||||||||||| ||||||||||| || |||||||| ||||| || || |||||||||||||||||| |||||  | | |||| ||| |    |  | ||||   ||| | || ||||||  |  ||| || |  |||||
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATATATGgtaatattcatgatcttatattggttat-tacgtactaattatttaccatgtatattctaagccg-ttgatttgaatgcag

upper sequence: GRMZM2G176546_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os12g04990.3 (Oryza sativa), 5'ss of exon 18
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATATATGgtaatatttatgattctgtgttggctatatgaccatcagttatg-gccaagcatgttctaaatctcttgtttcggttgcag
||||||||||||||||||||||||||||||||||||||||| ||||||||||| ||||||||||| || |||||||| ||||| || |  |||||||||||||||||| |||    | |  ||| ||||  || | || | ||  ||||   |||||||||  || ||| ||||| |||||
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTCCTTTATATATGgtaatattcatgtccttatactggttata--actaccaataatttgccatatatgttctaag-ctgttgattcggatgcag

upper sequence: GRMZM2G176546_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA20G28200.1 (Glycine max), 5'ss of exon 19
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATATATGgta---atatttatgattct---gtgttggctatatgaccatcagttatggccaagcatgttctaaatctcttgtttcggttgcag
||||| || || ||||| || ||||| || ||||| ||||| |||||||||||||| || |||||||||||||| ||  | || ||||| ||| |||||||||   | ||  || ||||       ||   | | ||    ||| || |   | ||| |||  | |  ||  | |||   ||| ||
AAGAATATCTTTAAGTTGGCACAAGGGGAGTACATTGCTCCTGAGAAGATTGAAAACGTATATGCCAAATGCAAATTTGTGGCGCAATGCTTTGTATATGgtatggaaataaatcattcccacaaattcagtgtgtg-tggtcatttgta--ctagcttgt--tgatgcttcttttttctttgtag

upper sequence: GRMZM2G176546_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA10G39540.1 (Glycine max), 5'ss of exon 19
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATATATGgtaat---atttatgattct---gtgttggctatatgaccatcagttatggccaagcatgttctaaatctcttgtttcggttgcag
||||| || || ||||| || ||||| || ||||| ||||| ||||||||||||||||| || ||||||||||| ||  | || || || ||| ||||||||||    ||  || ||||       || | | | ||   |||  || |   | ||| ||  || |  ||  | ||| | ||| ||
AAGAATATCTTTAAGTTGGCACAAGGCGAGTACATTGCTCCTGAGAAGATTGAAAATGTATACGCCAAATGCAAATTTGTGGCGCAGTGCTTTGTATATGgtaaggaaataaatcattcccacaaattcggtgtgtg-tgatcgtttgta--ctagcttg--ctgatgcttcttttttgtttgtag

upper sequence: GRMZM2G176546_T01 (Zea mays), 5'ss of exon 10
lower sequence: AT5G27600.1 (Arabidopsis thaliana), 5'ss of exon 19
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATATATGgtaatatttatgattctgtgttggctatatg-accatcagttatggccaagcatgttctaaatctct------tgtttcggttgcag
|||||||| || ||||| || ||||||||||| ||||| ||||||||||| |||||||| ||| ||||||| |  ||| || | || ||||| ||  | |||||     | || |||       |||||     | ||   |        ||   |||| || |         ||| ||  ||  ||
AAGAACATATTTAAGTTGGCGCAAGGAGAATATATAGCACCAGAGAAGATCGAAAATGTTTATACCAAATGTAGATTCGTTTCGCAGTGTTTCATTCACGgtaa--gcaaagactctactcacactatacatggcttcttcttcacttgtgctatttctcaaccgagccagaatgtctctattatag

upper sequence: GRMZM2G176546_T01 (Zea mays), 5'ss of exon 10
lower sequence: AT3G05970.1 (Arabidopsis thaliana), 5'ss of exon 19
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATATATGgtaatatttatgattctgtgttggctatatgac-catcagttatggccaagcatgttctaaatctcttgtttcgg--ttgcag
|||||||| ||||| || || || || || || |||||||||||||| |||||||| ||||||||||||||||| ||  | | ||| || || ||||||||||   |  |  ||| |  ||    | | |     | || ||      |  | |   | |  || | |||| |    || |||
AAGAACATCTTCAAATTGGCGCAGGGGGAGTATATAGCTCCAGAGAAAATTGAAAACGTCTATGCCAAATGCAAATTTGTGGGCCAGTGCTTCATATATGgtatagtaaacaattata-gtaaattgttttgtataacattttgctttatcctttccccatctcacctgttaccaattttcag

upper sequence: GRMZM2G176546_T01 (Zea mays), 5'ss of exon 10
lower sequence: Vv05s0020g03080.t01 (Vitis vinifera), 5'ss of exon 19
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATATATGgtaatatttatgattctgtgttggctatatgaccatcagttatggccaagcatgttctaaatctcttgtttcggttgcag
||||||||||| ||||| || |||||||| ||||||||||||||||| ||||| ||||| ||||| |||||||| ||  ||||||| || ||| |||||||||| |   ||||   | |              ||||  || || |     |     ||  |||||  |    |      
AAGAACATTTTTAAGTTGGCACAAGGAGAGTACATAGCTCCAGAGAAAATTGAGAATGTATATGCTAAATGCAAATTTGTTGCCCAGTGCTTTGTATATGgtaagaaaaatgagattttacaaatctctctttcatc--ttttgcctgctgactgcttatttctctgatgatag------

upper sequence: GRMZM2G176546_T01 (Zea mays), 5'ss of exon 10
lower sequence: Vv14s0128g00720.t01 (Vitis vinifera), 5'ss of exon 19
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATATATGgtaatatttatgattctgtgttggctatatgaccatcagttatggccaagcatgttcta--aatctcttgtttcggttgcag
|||||||| |||||| | || || || ||||| ||||| |||||||| ||||| ||||| |||||||| ||||| ||  || ||||||||||||| ||||||||     |||    |   |||   ||  | || ||       || |||     | |    |   |||  || | ||  ||
AAGAACATCTTCAAGCTGGCACAGGGTGAATATATAGCACCAGAGAAAATTGAGAATGTATATGCCAAGTGCAAATTTGTTTCCCAATGTTTTATCTATGgtaaggcagatggagtttacttgcagattgggccctc---cccagctaagttctctttgctgactgcttaatt-gattttag

upper sequence: GRMZM2G176546_T01 (Zea mays), 5'ss of exon 10
lower sequence: PP1S12_178V6.2 (Physcomitrella patens), 5'ss of exon 21
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATATATGgtaatatttatgattctgtgttggc------tatatgaccatcagttatggccaagcatgttctaaatctcttgtttcggttgcag---------------------------------------------------------------------------------
||||||||||||||||||||||||||||||||||| || || || |||||||| ||  | |||       |   ||| ||| | || |||||  ||||||||    |   | | ||   | | ||      |  ||||      ||||       |  ||    |||  | | |   | | ||                                                                                    
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATTGCACCGGAAAAGATTGAGAACATTTATCTTCGCAGTCGGTTTATTTCGCAGTGTTTCGTATATGgtgcgttcatttaatcgacggtcgcatctttttaatgattgcacgttactttttcgtgtgacggaaacgtgtagcaactggtgttacgtatactggaaaaactaccaactcattgaaatccaatcattcttaccaatcgtataattggttggtggtgaattgcacag

upper sequence: GRMZM2G176546_T01 (Zea mays), 5'ss of exon 10
lower sequence: EFJ33980 (Selaginella moellendorffii), 5'ss of exon 20
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATATATGgtaatatttatgattctgtgttggctatatgaccatcagttatggccaagcatgttctaaatctcttgtttcggttgcag
||||||||||| ||| | || || || ||||||||||| |||||||||||||| |||||||||   ||| |||||||| |||| || |||||  | || ||| | |   |  ||| ||| |||  | | |  | | | ||| || |  |  ||  |||   ||  ||||  | |      
AAGAACATTTTTAAGCTTGCACAGGGTGAATACATAGCGCCAGAGAAGATTGAGAATGTCTATCATAAAAGCAAGTTCGTTGCTCAGTGTTTCGTCTACGgtgaga---acaattttgttttg--tgtctagcgagcggttttgac--acaattctct---tcgattgtaacag------

upper sequence: GRMZM2G176546_T01 (Zea mays), 5'ss of exon 10
lower sequence: EFJ37488 (Selaginella moellendorffii), 5'ss of exon 20
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATATATGgtaatatttatg--attctgtgtt------ggctatatgacca-----tcagttatggccaagcatgttctaaatctcttgtttcggttgcag---------------------------------
||||||||||| ||| | || || || ||||||||||| |||||||||||||| |||||||||   ||| |||||||| |||| || |||||  | || ||| | |   ||    || |||||       | | |  || | |     || ||    |   ||||||    |  | |||   |  |  ||                                    
AAGAACATTTTTAAGCTTGCACAGGGTGAATACATAGCGCCAGAGAAGATTGAGAATGTCTATCAAAAAAGCAAGTTCGTTGCTCAGTGTTTCGTCTACGgtgagaacaattttgttttgtgtctagcgagtccacctggcgaaaggatcggtcgctgaatagcatggcaaagttttctccctatgtgtgactcggttttgacacaattctcttcgattgtaacag

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|6194573|gb|AW146677.1|AW146677
EST:     TGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATATATG                         GCGACAGTTTCAACTCTTCCTTAGTTGGTATTGTTGCAGTTGAACCAGAGG
genomic: TGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATATATGgtaatattta ... tcggttgcagGCGACAGTTTCAACTCTTCCTTAGTTGGTATTGTTGCAGTTGAACCAGAGG
EST: gi|67023162|gb|CO451911.1|CO451911
EST:     TGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATTTATG                         GCGACAGTTTCAACTCTTCCTTAGTTGGTATTGTTGCAGTTGAACCAAAGG
genomic: TGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATATATGgtaatattta ... tcggttgcagGCGACAGTTTCAACTCTTCCTTAGTTGGTATTGTTGCAGTTGAACCAGAGG
EST: gi|93281969|gb|EB674233.1|EB674233
EST:     TGAAAATGTTTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATATATG                         GCGACAGTTTCAACTCTTCCTTAGTTGGTATTGTTGCAGTTGAACCAGAGG
genomic: TGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATATATGgtaatattta ... tcggttgcagGCGACAGTTTCAACTCTTCCTTAGTTGGTATTGTTGCAGTTGAACCAGAGG
EST: gi|6194494|gb|AW146598.1|AW146598
EST:     TGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATATATG                         GCGACAGTTTCAACTCTTCCTTAGTTGGTATTGTTGCAGTTGAACCAGAGG
genomic: TGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATATATGgtaatattta ... tcggttgcagGCGACAGTTTCAACTCTTCCTTAGTTGGTATTGTTGCAGTTGAACCAGAGG
EST: gi|50335868|gb|CO530994.1|CO530994
EST:     TGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATATATG                         GCGACAGTTTCAACTCTTCCTTAGTTGGTATTGTTGCAGTTGAACCAGAGG
genomic: TGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATATATGgtaatattta ... tcggttgcagGCGACAGTTTCAACTCTTCCTTAGTTGGTATTGTTGCAGTTGAACCAGAGG

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), 49 (downstream exon)
Score: 45

AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATATATGgtaatattta ... tcggttgcagGCGACAGTTTCAACTCTTCCTTAGTTGGTATTGTTGCAGTTGAACCAGAGGTTATGAAGGCTTGGGCTGCATCTGAAGGGATCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 154

AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATATATGgtaatattta ... tcggttgcagGCGACAGTTTCAACTCTTCCTTAGTTGGTATTGTTGCAGTTGAACCAGAGGTTATGAAGGCTTGGGCTGCATCTGAAGGGATCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 128

AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATATATGgtaatattta ... tcggttgcagGCGACAGTTTCAACTCTTCCTTAGTTGGTATTGTTGCAGTTGAACCAGAGGTTATGAAGGCTTGGGCTGCATCTGAAGGGATCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 44

AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATATATGgtaatattta ... tcggttgcagGCGACAGTTTCAACTCTTCCTTAGTTGGTATTGTTGCAGTTGAACCAGAGGTTATGAAGGCTTGGGCTGCATCTGAAGGGATCCAG