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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgaatctggtaggctcattttcctataattattacaagtcttattgctattcttgctttgcgtatgcacttcctgatttgctcacattcatatttcagAGGTGATTACATGTGCGGAGTTCCATCCATCCCATTGTAATACACTGGCCTATAGTAGTTCAAAGGGTTCTATCCGACTTATTGATCTGCGTCAATCAGC

Basic information

species Zea mays
transcript GRMZM2G165418_T04
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os06g36770.1 (Oryza sativa), 3'ss of exon 7
--tttgaatctggtaggctcattttcctataattattacaagtcttattgctattcttgctttgc--gtatgcacttcctgatttgctcacattcatatttcagAGGTGATTACATGTGCGGAGTTCCATCCATCCCATTGTAATACACTGGCCTATAGTAGTTCAAAGGGTTCTATCCGACTTATTGATCTGCGTCAATCAGC
  | |  || |   ||      |    | | ||  |||||   |||| ||  |||| ||   ||    ||||   | | |||| |  |    || ||||||||||||| |||||||||||||||||||| ||| | ||||||||||||||||||||||| ||||||||||||||||||||||| ||||||||||| ||||||||
attattgatgtttaagatgacctggaatctgatctttaca---cttactgtaattcatgtcctggtaatatgttgtgcatgatgtaatt-tgttgatatttcagAGGTCATTACATGTGCGGAGTTCCACCCAACTCATTGTAATACACTGGCCTATAGCAGTTCAAAGGGTTCTATCCGACTCATTGATCTGCGACAATCAGC

upper sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA08G20830.2 (Glycine max), 3'ss of exon 7
--tttgaatctggtaggctcattttcctataattattacaagtcttattgctattcttgctttgcgtatgcacttcctgatttgctc---acattcatatttcagAGGTGATTACATGTGCGGAGTTCCATCCATCCCATTGTAATACACTGGCCTATAGTAGTTCAAAGGGTTCTATCCGACTTATTGATCTGCGTCAATCAGC
  | | | ||| || |      | || || ||||     ||   || |   |||  ||  ||||    | || ||     ||  | |   | |||  |||| ||||||| || ||||  || || || || ||  | |||||||||||| |||| ||||| |||||||||||||| || || ||| ||||  |||| || |||||
gctgttagtcttgtggatcaggtatcata-aattg----aacctttttaaatatattttttttgtagcttcagttgagctttgaccctatatattattattgcagAGGTTATAACATCAGCAGAATTTCACCCTACACATTGTAATACATTGGCATATAGCAGTTCAAAGGGTTCAATTCGTCTTGTTGACTTGCGGCAGTCAGC

upper sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA13G42800.2 (Glycine max), 3'ss of exon 7
--tttgaatctggtaggctcattttcctataattattacaagtcttattgctattcttgctttgcgtatgcacttcctgatttgctcacattcatatttcagAGGTGATTACATGTGCGGAGTTCCATCCATCCCATTGTAATACACTGGCCTATAGTAGTTCAAAGGGTTCTATCCGACTTATTGATCTGCGTCAATCAGC
    ||||    | |   ||   ||||| |  |  ||      || | | | ||| |     |   |       || |||       | |||  |||| ||||||| || ||||  || || || || ||  | |||||||||||| |||| ||||| |||||||||||||| ||||| ||| ||||  |||| ||||||||
aaagtgaaggaagaataatctgcttccttttttgttttgcccactcagttccattttaaaagtat-tggttgaatcttgaccc-taaatattattattgcagAGGTTATAACATCAGCAGAATTTCACCCTACACATTGTAATACATTGGCATATAGCAGTTCAAAGGGTTCAATCCGTCTTGTTGACTTGCGGCAATCAGC

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|31352864|gb|CD437221.1|CD437221
EST:     GAGCTTTAACATTGTTGATGTGAAGCCTACAAACATGGAAGATCTAACAG                         AGGTGATTACATGTGCGGAGTTCCATCCATCCCATTGTAATACACTGGCCT
genomic: GAGCTTTAACATTGTTGATGTGAAGCCTACAAACATGGAAGATCTAACAGgtaattccac ... catatttcagAGGTGATTACATGTGCGGAGTTCCATCCATCCCATTGTAATACACTGGCCT
EST: gi|211384024|gb|FL015619.1|FL015619
EST:     GAGNTTTAACATTGTTGATGTGAAGCCTACAAACATGGAAGATCTAACAG                         AGGTGATTACNTGNGCGGAGTTCCATCCATCCCATTGNAATACACTGGCCT
genomic: GAGCTTTAACATTGTTGATGTGAAGCCTACAAACATGGAAGATCTAACAGgtaattccac ... catatttcagAGGTGATTACATGTGCGGAGTTCCATCCATCCCATTGTAATACACTGGCCT
EST: gi|24934206|gb|CA452424.1|CA452424
EST:     GAGCTTTAACATTGTTGATGTGAAGCCTACAAACATGGAAGATCTAACAG                         AGGTGATTACATGTGCGGAGTTCCATCCATCCCATTGTAATACACTGGCCT
genomic: GAGCTTTAACATTGTTGATGTGAAGCCTACAAACATGGAAGATCTAACAGgtaattccac ... catatttcagAGGTGATTACATGTGCGGAGTTCCATCCATCCCATTGTAATACACTGGCCT
EST: gi|211386654|gb|FL015627.1|FL015627
EST:     GAGCTTTAACATTGTTGATGTGAAGCCTACAAACATGGAAGATCTAACAG                         AGGTGATTACATGTGCGGAGTTCCATCCATCCCATTGTAATACACTGGCCT
genomic: GAGCTTTAACATTGTTGATGTGAAGCCTACAAACATGGAAGATCTAACAGgtaattccac ... catatttcagAGGTGATTACATGTGCGGAGTTCCATCCATCCCATTGTAATACACTGGCCT
EST: gi|211386649|gb|FL015622.1|FL015622
EST:     GAGCTTTAACATTGTTGATGTGAAGCCTACAAACATGGAAGATCTAACAG                         AGGTGATTACATGTGCGGAGTTCCATCCATCCCATTGTAATACNCTGGCCT
genomic: GAGCTTTAACATTGTTGATGTGAAGCCTACAAACATGGAAGATCTAACAGgtaattccac ... catatttcagAGGTGATTACATGTGCGGAGTTCCATCCATCCCATTGTAATACACTGGCCT
EST: gi|67025874|gb|CO454623.1|CO454623
EST:     GAGCTTTAACATTGTTGATGTGAAGCCTACAAACATGGAAGATCTAACAG                         AGGTGATTACATGTGCGGAGTTCCATCCATCCCATTGTAATACACTGGCCT
genomic: GAGCTTTAACATTGTTGATGTGAAGCCTACAAACATGGAAGATCTAACAGgtaattccac ... catatttcagAGGTGATTACATGTGCGGAGTTCCATCCATCCCATTGTAATACACTGGCCT

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: 48 (upstream exon), 49 (downstream exon)
Score: 123

TCAGCAGATGATCTCCGAATAAATTTATGGAACTTGGAAATAAACAGCCAGAGCTTTAACATTGTTGATGTGAAGCCTACAAACATGGAAGATCTAACAGgtaattccac ... catatttcagAGGTGATTACATGTGCGGAGTTCCATCCATCCCATTGTAATACACTGGCCTATAGTAGTTCAAAGGGTTCTATCCGACTTATTGATCTGCGTCAATCAGC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 143

TCAGCAGATGATCTCCGAATAAATTTATGGAACTTGGAAATAAACAGCCAGAGCTTTAACATTGTTGATGTGAAGCCTACAAACATGGAAGATCTAACAGgtaattccac ... catatttcagAGGTGATTACATGTGCGGAGTTCCATCCATCCCATTGTAATACACTGGCCTATAGTAGTTCAAAGGGTTCTATCCGACTTATTGATCTGCGTCAATCAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 156

TCAGCAGATGATCTCCGAATAAATTTATGGAACTTGGAAATAAACAGCCAGAGCTTTAACATTGTTGATGTGAAGCCTACAAACATGGAAGATCTAACAGgtaattccac ... catatttcagAGGTGATTACATGTGCGGAGTTCCATCCATCCCATTGTAATACACTGGCCTATAGTAGTTCAAAGGGTTCTATCCGACTTATTGATCTGCGTCAATCAGC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 130

TCAGCAGATGATCTCCGAATAAATTTATGGAACTTGGAAATAAACAGCCAGAGCTTTAACATTGTTGATGTGAAGCCTACAAACATGGAAGATCTAACAGgtaattccac ... catatttcagAGGTGATTACATGTGCGGAGTTCCATCCATCCCATTGTAATACACTGGCCTATAGTAGTTCAAAGGGTTCTATCCGACTTATTGATCTGCGTCAATCAGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgctattcttgctttgcgtatgcacttcctgatttgctcacattcatatttcagAGGTGATTACATGTGCGGAGTTCCATCCATCCCATTGTAATACACTGGCCTATAGTAGTTCAAAGGGTTCTATCCGACTTATTGATCTGCGTCAATCAGC
                                   tgctcac  putative branch site (score: 130)
                                          attcatattt  TA-rich tract