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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagattcctttattctcagtactgcagtttactagggtaatacttgacttttattcttgatctcttgtcttctggaacttatattttctcatcttcagCATACACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAATGCCGGTTGATGTGAATGATC

Basic information

species Zea mays
transcript GRMZM2G175510_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G175510_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os06g34690.1 (Oryza sativa), 3'ss of exon 6
gtaagattcctttattctcagtactgcagtttactagggtaatacttgacttttattcttgatctcttgtcttctggaac--ttatattttctcatcttcagCATACACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAATGCCGGTTGATGTGAATGATC
            ||||    | |     || |   | |||  || ||  | ||| ||  |  | |  | | ||||| |||  |||   | |||||| |||||||||||||||||| ||||| |||||| | ||||| |||||||||||||||||||  ||||| |||||||| |
-----------gtattgcttg-atcattgtatcagatggtgttattt--cctttgttgattttttagtctgttctgaaacatttagtgtctctcattttcagCATACACCAAAGCTCTTGAGGATGCTTTAGCTGTCCTTGACAAAATTGCAATGCATGTTGACGTGAATGACC

upper sequence: GRMZM2G175510_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA20G35760.1 (Glycine max), 3'ss of exon 4
gtaagattcctttattctcagtactgcagtttactagggtaatacttgacttttattcttgatctcttgtcttctggaacttatattttctcatcttcagCATACACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAATGCCGGTTGATGTGAATGATC
||||  |  || ||         |    |||   |    |  ||   |  | | |   |  ||    || ||| |  || | || ||     |||| |||| ||   ||||||  | || ||||| |||||||| |||||||||||||| ||||| |||||||  |||||||
gtaatctgtctataagtattaatcaatggttcttttcttttctaaaaggatatcagattgtatacgatgacttttataa-taatgtt-----atctgcagCTTATGACAAAGCTTTGGAGGATGCCATTGCTGTCCTTGACAAAATTGCTATGCCCGTTGATGCCAATGATC

upper sequence: GRMZM2G175510_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA16G33380.1 (Glycine max), 3'ss of exon 7
gtaagattcctttattctcagtactg-cagtttactagggtaatacttgacttttattcttgatctcttgtcttctggaa--cttatattttctcatcttcagCATACACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAATGCCGGTTGATGTGAATGATC
      |  ||| ||    |||  |  | ||| |  ||  |    ||      |  |     ||   || | ||   |||  ||   ||||| | || | |||||||  |||||||  | || |||||||||||||| ||||||||||||||||||||  |  |||   | ||||
-----gtaacttaat----agtgttaactgttaatcagtatttctctcctacatggtataaaattgtttatattaatgaatgctacaattttgtaatatgcagCATATGCCAAAGCTTTGGAGGATGCTATTGCTGTTCTTGACAAAATTGCAATGCCTATCAATGCTCAGGATC

upper sequence: GRMZM2G175510_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA09G28650.1 (Glycine max), 3'ss of exon 7
gtaagattcctttattctcagtactgcagtttactagggtaatacttgacttttattcttgatctcttgtcttctggaa--cttatattttctcatcttcagCATACACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAATGCCGGTTGATGTGAATGATC
      |  ||| ||    |||  | | ||| |  || ||    ||         |     ||   || | ||   |||  ||   ||||| | |||| ||||||| | ||||||  | || |||||||||||||| ||||||||||||||||||||  ||||||   | ||||
-----gtaacttaat----agtgttactgttaatcagtgtttctctcctacaaggtataaaattgtttatattaatgaatgctacaattttgtaatctgcagCATATAACAAAGCTTTGGAGGATGCTATTGCTGTCCTTGACAAAATTGCAATGCCTATTGATGCTCAGGATC

upper sequence: GRMZM2G175510_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv07s0130g00410.t01 (Vitis vinifera), 3'ss of exon 6
gtaagattcctttattctcagtactgcagtttactagggtaatacttgacttttattcttgatctcttgtcttctggaacttatattttctcatcttcagCATACACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAATGCCGGTTGATGTGAATGATC
            ||||||    | || | | |   | |    | ||    | |||   |  |  |||  | |  |       |  || | |  | |  ||||||||  ||||| || || |||||||||||||| |||||||||||||||||| |  | |||||||| || |
-----------gtattctagaaattg-attgtgacacgactct-ctaagttgttaaattaaacttctcttttgattatggaaactttatttgttgtgtagCATACAATAAAGCTCTGGAGGATGCTATTGCTGTGCTTGACAAAATTGCAATGTCCATAGATGTGAAGGACC

upper sequence: GRMZM2G175510_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv17s0000g08170.t01 (Vitis vinifera), 3'ss of exon 6
gtaagattcctttattctc---agtactgcagtttactagggtaatacttgacttttattcttgatctcttgtcttctggaacttatattttctcatcttcagCATACACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAATGCCGGTTGATGTGAATGATC
|||| |   |  | |  |    ||||||    |||| | | |    | || | ||||||| ||||||  ||      |  || | |  |  |    ||| |||| || |  ||||| ||||| ||||||||||| || |||||||| ||||||   || |||||||||||||| |
gtaacacctcaatgtgttgtaaagtactcatatttattggtg----atttaaattttatt-ttgatcaatt------taaaattgaggtact----tctgcagCTTATAATAAAGCTCTTGAGGATGCTATTGCGGTGCTTGACAAGATTGCAGCCCCTGTTGATGTGAATGACC

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|71438455|gb|DR819505.1|DR819505
EST:     TGCACAGGCATTCATTGACAAGAACTACCATCCTACTGTTATTTGTCGAG                         CATACACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAA
genomic: TGCACAGGCATTCATTGACAAGAACTACCATCCTACTGTTATTTGTCGAGgtaagattcc ... tcatcttcagCATACACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAA
EST: gi|211175329|gb|FL101110.1|FL101110
EST:     TGCACAGGCATTCATTGACAAGAACTACCATCCTACTGTTATTTGTCGAG                         CATACACCAAAGCACTTGATGATGCTATTGCTGTACTTGACAAAATTGCAA
genomic: TGCACAGGCATTCATTGACAAGAACTACCATCCTACTGTTATTTGTCGAGgtaagattcc ... tcatcttcagCATACACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAA
EST: gi|211175332|gb|FL101113.1|FL101113
EST:     TGCACAGGCATTCATTGACAAGAACTACCATCCTACTGTTATTTGTCGAG                         CATACACCAGAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAA
genomic: TGCACAGGCATTCATTGACAAGAACTACCATCCTACTGTTATTTGTCGAGgtaagattcc ... tcatcttcagCATACACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAA
EST: gi|211175327|gb|FL101108.1|FL101108
EST:     TGCACAGGCATTCATTGACAAGAACTACCATCCTACTGTTATTTGTCGAG                         CATACACCAAAGCACTTGATGATGCTATTGCTGTACTTGACAAAATTGCAA
genomic: TGCACAGGCATTCATTGACAAGAACTACCATCCTACTGTTATTTGTCGAGgtaagattcc ... tcatcttcagCATACACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAA
EST: gi|71332448|gb|DR803183.1|DR803183
EST:     TGCACAGGCATTCATTGACAAGAACTACCATCCTACTGTTATTTGTCGAG                         CATACACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAA
genomic: TGCACAGGCATTCATTGACAAGAACTACCATCCTACTGTTATTTGTCGAGgtaagattcc ... tcatcttcagCATACACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAA
EST: gi|31354620|gb|CD438977.1|CD438977
EST:     TGCACAGGCATTCATTGACAAGAACTACCATCCTACTGTTATTTGTCGAG                         CATACACCAAAGCACTTGATGATGCTATTGCTGTACTTGACAAAATTGCAA
genomic: TGCACAGGCATTCATTGACAAGAACTACCATCCTACTGTTATTTGTCGAGgtaagattcc ... tcatcttcagCATACACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAA
EST: gi|211175325|gb|FL101106.1|FL101106
EST:     TGCACAGGCATTCATTGACAAGAACTACCATCCTACTGTTATTTGTCGAG                         CATACACCAAAGCACTTGATGATGCTATTGCTGTACTTGACAAAATTGCAA
genomic: TGCACAGGCATTCATTGACAAGAACTACCATCCTACTGTTATTTGTCGAGgtaagattcc ... tcatcttcagCATACACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAA
EST: gi|211175333|gb|FL101114.1|FL101114
EST:     TGCACAGGCATTCATTGACAAGAACTACCATCCTACTGTTATTTGTCGAG                         CATACACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACNAAATTGCAA
genomic: TGCACAGGCATTCATTGACAAGAACTACCATCCTACTGTTATTTGTCGAGgtaagattcc ... tcatcttcagCATACACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAA
EST: gi|71428865|gb|DR809915.1|DR809915
EST:     TGCACAGGCATTCATTGACAAGAACTACCATCCTACTGTTATTTGTCGAG                         CATACACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAA
genomic: TGCACAGGCATTCATTGACAAGAACTACCATCCTACTGTTATTTGTCGAGgtaagattcc ... tcatcttcagCATACACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAA
EST: gi|94478012|gb|EB706970.1|EB706970
EST:     TGCACAGGCATTCATTGACAAGAACTACCATCCTACTGTTATTTGTCGAG                         CATACACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAA
genomic: TGCACAGGCATTCATTGACAAGAACTACCATCCTACTGTTATTTGTCGAGgtaagattcc ... tcatcttcagCATACACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAA
EST: gi|71448421|gb|DR829471.1|DR829471
EST:     TGCACAGGCATTCATTGACAAGAACTACCATCCTACTGTTATTTGTCGAG                         CATACACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAA
genomic: TGCACAGGCATTCATTGACAAGAACTACCATCCTACTGTTATTTGTCGAGgtaagattcc ... tcatcttcagCATACACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAA
EST: gi|211175328|gb|FL101109.1|FL101109
EST:     TGCACAGGCATTCATTGACAAGAACTACCATCCTACTGTTATTTGTCGAG                         CATACACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAA
genomic: TGCACAGGCATTCATTGACAAGAACTACCATCCTACTGTTATTTGTCGAGgtaagattcc ... tcatcttcagCATACACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAA
EST: gi|30306946|gb|CD001619.1|CD001619
EST:     TGCACAGGCATTCATTGACAAGAACTACCATCCTACTGTTATTTGTCGAG                         CATACACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAA
genomic: TGCACAGGCATTCATTGACAAGAACTACCATCCTACTGTTATTTGTCGAGgtaagattcc ... tcatcttcagCATACACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAA
EST: gi|74244741|gb|DT652655.1|DT652655
EST:     TGCACAGGCATTCATTGACAAGAACTACCATCCTACTGTTATTTGTCGAG                         CATACACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAA
genomic: TGCACAGGCATTCATTGACAAGAACTACCATCCTACTGTTATTTGTCGAGgtaagattcc ... tcatcttcagCATACACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAA

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: 204

CTGGAGAGATGCTACACGTTGCACAGGCATTCATTGACAAGAACTACCATCCTACTGTTATTTGTCGAGgtaagattcc ... tcatcttcagCATACACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAATGCCGGTTGATGTGAATGATC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 76

CTGGAGAGATGCTACACGTTGCACAGGCATTCATTGACAAGAACTACCATCCTACTGTTATTTGTCGAGgtaagattcc ... tcatcttcagCATACACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAATGCCGGTTGATGTGAATGATC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 84

CTGGAGAGATGCTACACGTTGCACAGGCATTCATTGACAAGAACTACCATCCTACTGTTATTTGTCGAGgtaagattcc ... tcatcttcagCATACACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAATGCCGGTTGATGTGAATGATC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 107

CTGGAGAGATGCTACACGTTGCACAGGCATTCATTGACAAGAACTACCATCCTACTGTTATTTGTCGAGgtaagattcc ... tcatcttcagCATACACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAATGCCGGTTGATGTGAATGATC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgacttttattcttgatctcttgtcttctggaacttatattttctcatcttcagCATACACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAATGCCGGTTGATGTGAATGATC
           tcttgat  putative branch site (score: 107)
                                      tattttctcatcttc  putative PPT
                                aacttatattttct  TA-rich tract