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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctctgtcatttgcaatcacacattcactcatcaattcttattactttcttctgatgtcacaacaccgatctgaactattgaattccccaacagCAGGTCAGATTTTTAGACATATGGGAACCAGCTGTTCTAGCAATAAAGAGGGAAGGTTACAGCATTAAATGTAATGGGCAGCGTGGTGTTCTAATCACAG

Basic information

species Zea mays
transcript GRMZM2G036206_T01
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G036206_T01 (Zea mays), 3'ss of exon 17
lower sequence: LOC_Os01g01800.1 (Oryza sativa), 3'ss of exon 17
--gtatgctctgtcatttgcaatcacacattcactcatcaattcttattactttcttctgatgtcacaacaccgatctgaactattgaattccccaacagCAGGTCAGATTTTTAGACATATGGGAACCAGCTGTTCTAGCAATAAAGAGGGAAGGTTACAGCATTAAATGTAATGGGCAGCGTGGTGTTCTAATCACAG
   | | |||| | | ||| ||| |   ||  |   |   ||||| | || |||||| |||| |||   ||   || | || | || |||   |  | ||||||| | ||||||||| || |||||||||||| || | ||||||||||||||||| ||||| |||||||||| ||| |||||||||||| |  ||||||
gtatgttctctattacttggaattatctatcaa---aagcattctcactaatttcttatgatttcatg-caattatttcaaatgttaaatcttcttatagCAGGTGAAATTTTTAGATATGTGGGAACCAGCTATTTTGGCAATAAAGAGGGAAGGCTACAGTATTAAATGTACTGGTCAGCGTGGTGTTGTTCTCACAG

upper sequence: GRMZM2G036206_T01 (Zea mays), 3'ss of exon 17
lower sequence: LOC_Os01g01800.2 (Oryza sativa), 3'ss of exon 17
--gtatgctctgtcatttgcaatcacacattcactcatcaattcttattactttcttctgatgtcacaacaccgatctgaactattgaattccccaacagCAGGTCAGATTTTTAGACATATGGGAACCAGCTGTTCTAGCAATAAAGAGGGAAGGTTACAGCATTAAATGTAATGGGCAGCGTGGTGTTCTAATCACAG---
   | | |||| | | ||| ||| |   ||  |   |   ||||| | || |||||| |||| |||   ||   || | || | || |||   |  | ||||||| | ||||||||| || |||||||||||| || | ||||||||||||||||| ||||| |||||||||| ||| |||||||||||| |  ||||||   
gtatgttctctattacttggaattatctatcaa---aagcattctcactaatttcttatgatttcatg-caattatttcaaatgttaaatcttcttatagcagGTGAAATTTTTAGATATGTGGGAACCAGCTATTTTGGCAATAAAGAGGGAAGGCTACAGTATTAAATGTACTGGTCAGCGTGGTGTTGTTCTCACAGAGA
















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|78180678|gb|DV551006.1|DV551006
EST:     GAACCCTTGACATTGGGCATGTGACCTATGAAGTCCAAGTCCAACTGCCT                         CAGGTCAGATTTTTAGACATATGGGAACCAGCTGTTCTAGCAATAAAGAGG
genomic: GAACCCTTGACATTGGGCATGTGACCTATGAAGTCCAAGTCCAACTGCCTgtatgctctg ... tccccaacagCAGGTCAGATTTTTAGACATATGGGAACCAGCTGTTCTAGCAATAAAGAGG
EST: gi|7844204|gb|AW787426.1|AW787426
EST:     GAACCCTTGACATTGGGCATGTGACCTATGAAGTCCAAGTCCAACTGCCT                         CAGGTCAGATTTTTAGACATATGGGAACCAGCTGTTCTAGCAATAAAGAGG
genomic: GAACCCTTGACATTGGGCATGTGACCTATGAAGTCCAAGTCCAACTGCCTgtatgctctg ... tccccaacagCAGGTCAGATTTTTAGACATATGGGAACCAGCTGTTCTAGCAATAAAGAGG
EST: gi|211089151|gb|FL459717.1|FL459717
EST:     GAACCCTTGACATTGGGCATGTGACCTATGAAGTCCAAGTCCAACTGCCT                         CAGGTCAGATTTTTAGACATATGGGAACCAGCTGTTCTAGCAATAAAGAGG
genomic: GAACCCTTGACATTGGGCATGTGACCTATGAAGTCCAAGTCCAACTGCCTgtatgctctg ... tccccaacagCAGGTCAGATTTTTAGACATATGGGAACCAGCTGTTCTAGCAATAAAGAGG
EST: gi|7844203|gb|AW787425.1|AW787425
EST:     GAACCCTTGACATTGGGCATGTGACCTATGAAGTCCAAGTCCAACTGCCT                         CAGGTCAGATTTTTAGACATATGGGAACCAGCTGTTCTAGCAATAAAGAGG
genomic: GAACCCTTGACATTGGGCATGTGACCTATGAAGTCCAAGTCCAACTGCCTgtatgctctg ... tccccaacagCAGGTCAGATTTTTAGACATATGGGAACCAGCTGTTCTAGCAATAAAGAGG
EST: gi|6020818|gb|AW065746.1|AW065746
EST:     GAACCCTTGACATTGGGCATGTGACCTATGAAGTCCAAGTCCAACTGCCT                         CAGGTCAGATTTT-AGACATATGGGAACCAGCTGTTCTAGCAATAAAGAGG
genomic: GAACCCTTGACATTGGGCATGTGACCTATGAAGTCCAAGTCCAACTGCCTgtatgctctg ... tccccaacagCAGGTCAGATTTTTAGACATATGGGAACCAGCTGTTCTAGCAATAAAGAGG
EST: gi|5762226|gb|AI967274.1|AI967274
EST:     GAACCCTTGACATTGGGCATGTGACCTATGAAGTCCAAGTCCAACTGCCT                         CAGGTCAGATTTTTAGACATATGGGAACCAGCTGTTCTAGCAATAAAGAGG
genomic: GAACCCTTGACATTGGGCATGTGACCTATGAAGTCCAAGTCCAACTGCCTgtatgctctg ... tccccaacagCAGGTCAGATTTTTAGACATATGGGAACCAGCTGTTCTAGCAATAAAGAGG
EST: gi|71772016|gb|DR969953.1|DR969953
EST:     GAACCCTTGACATTGGGCATGTGACCTATGAAGTCCAAGTCCAACTGCCT                         CAGGTCAGATTTTTAGACATATGGGAACCAGCTGTTCTAGCAATAAAGAGG
genomic: GAACCCTTGACATTGGGCATGTGACCTATGAAGTCCAAGTCCAACTGCCTgtatgctctg ... tccccaacagCAGGTCAGATTTTTAGACATATGGGAACCAGCTGTTCTAGCAATAAAGAGG
EST: gi|5871151|gb|AW017592.1|AW017592
EST:     TTGGGCATGTGACCTATGAAGTCCAAGTCCAACTGCCT                         CAGGTCAGATTTTTAGACATATGGGAACCAGCTGTTCTAGCAATAAAGAGG
genomic: TTGGGCATGTGACCTATGAAGTCCAAGTCCAACTGCCTgtatgctctg ... tccccaacagCAGGTCAGATTTTTAGACATATGGGAACCAGCTGTTCTAGCAATAAAGAGG
EST: gi|6020497|gb|AW065425.1|AW065425
EST:     CATGTGACCTATGAAGTCCAAGTCCAACTGCCT                         CAGGTCAGATTTTTAGACATATGGGAACCAGCTGTTCTAGCAATAAAGAGG
genomic: CATGTGACCTATGAAGTCCAAGTCCAACTGCCTgtatgctctg ... tccccaacagCAGGTCAGATTTTTAGACATATGGGAACCAGCTGTTCTAGCAATAAAGAGG
EST: gi|7844205|gb|AW787427.1|AW787427
EST:     GAACCCTTGACATTGGGCATGTGACCTATGAAGTCCAAGTCCAACTGCCT                         CAGGTCAGATTTTTAGACATATGGGAACCAGCTGTTCTAGCAATAAAGAGG
genomic: GAACCCTTGACATTGGGCATGTGACCTATGAAGTCCAAGTCCAACTGCCTgtatgctctg ... tccccaacagCAGGTCAGATTTTTAGACATATGGGAACCAGCTGTTCTAGCAATAAAGAGG

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: 43 (upstream exon), 48 (downstream exon)
Score: 43

ATCCTGAAACAAAGGAGCTTATTAAGAGAACCCTTGACATTGGGCATGTGACCTATGAAGTCCAAGTCCAACTGCCTgtatgctctg ... tccccaacagCAGGTCAGATTTTTAGACATATGGGAACCAGCTGTTCTAGCAATAAAGAGGGAAGGTTACAGCATTAAATGTAATGGGCAGCGTGGTGTTCTAATCACAG


Block sizes: 47 (upstream exon), 28 (downstream exon)
Score: 41

ATCCTGAAACAAAGGAGCTTATTAAGAGAACCCTTGACATTGGGCATGTGACCTATGAAGTCCAAGTCCAACTGCCTgtatgctctg ... tccccaacagCAGGTCAGATTTTTAGACATATGGGAACCAGCTGTTCTAGCAATAAAGAGGGAAGGTTACAGCATTAAATGTAATGGGCAGCGTGGTGTTCTAATCACAG


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 39

ATCCTGAAACAAAGGAGCTTATTAAGAGAACCCTTGACATTGGGCATGTGACCTATGAAGTCCAAGTCCAACTGCCTgtatgctctg ... tccccaacagCAGGTCAGATTTTTAGACATATGGGAACCAGCTGTTCTAGCAATAAAGAGGGAAGGTTACAGCATTAAATGTAATGGGCAGCGTGGTGTTCTAATCACAG


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 42

ATCCTGAAACAAAGGAGCTTATTAAGAGAACCCTTGACATTGGGCATGTGACCTATGAAGTCCAAGTCCAACTGCCTgtatgctctg ... tccccaacagCAGGTCAGATTTTTAGACATATGGGAACCAGCTGTTCTAGCAATAAAGAGGGAAGGTTACAGCATTAAATGTAATGGGCAGCGTGGTGTTCTAATCACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattactttcttctgatgtcacaacaccgatctgaactattgaattccccaacagCAGGTCAGATTTTTAGACATATGGGAACCAGCTGTTCTAGCAATAAAGAGGGAAGGTTACAGCATTAAATGTAATGGGCAGCGTGGTGTTCTAATCACAG
          ttctgat  putative branch site (score: 42)
                                            ttcccc  putative PPT
                                     tattgaatt  TA-rich tract