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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactactgcacatggttatcttgtgacatcatttcggttaagctctgctccgctgcaagtgccttttatgtgatctgtcaacttgtccatgctcttgaacccctgatttcagCTTGTAAAGAGGCACGCAGCAGAGATTTTCACATCAATTGCCATTGCGTCGACATTCTCTCTGTACTCAACCGCTGTCATAGGGCGCCTGATTGGGCTGG

Basic information

species Zea mays
transcript GRMZM2G478212_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G478212_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os10g42780.1 (Oryza sativa), 3'ss of exon 5
-----------------------------------------------------------------------------gtactactgcacatggttatcttgtgacatcatttcggttaagctctgctccgctg--caa--gtgccttttat------gtgatctgtcaacttgtccatgctcttgaacccctgatttcagCTTGTAAAGAGGCACGCAGCAGAGATTTTCACATCAATTGCCATTGCGTCGACATTCTCTCTGTACTCAACCGCTGTCATAGGGCGCCTGATTGGGCTGG
                                                                             | |   ||     |  || | ||| || |  | |  |  ||     ||    |||    ||   ||| |   |       || ||   | ||  | |   || |    ||      |||||||||||||| |||||| ||||| || |||||||||||||| ||  | || || ||||||||  | || ||||| ||  || |||| ||  || | | ||| |
gtaggtacccttctctcagttagtagtattactagtagttagcatatggttatatatgttgtgacatgatcatattcgaagctctctgtttaatt-tgttgcgagacgagtgtgcctagctgttggctagctaattaaccatgcatccaaccaaggagtaattaattaatgtttttgtgttggataatataatatttcagCTTGTAAGGAGGCATGCAGCGGAAATTTTCACATCAATCGCTGTGGCATCAACATTCTCGTTATATTCAACTGCCATCCTAGGACGAGTGGTAGAGCTAG

upper sequence: GRMZM2G478212_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA01G01340.1 (Glycine max), 3'ss of exon 4
gtactactgcacatggttatcttgtgacatcatttcggttaagctctgctccgctgcaagtgccttttatgtgatctgtcaacttgtccatgctcttgaacccctgatttcagCTTGTAAAGAGGCACGCAGCAGAGATTTTCACATCAATTGCCATTGCGTCGACATTCTCTCTGTACTCAACCGCTGTCATAGGGCGCCTGATTGGGCTGG
  | ||    |||||      |||| || |  | |   | |   | |  ||  |    | || ||         ||  |  |  | |  |||   || | |  ||| |||||||||||||| ||||| ||||| ||||||||||| ||  |    ||| |  |   ||||||  |||||||||| ||| |  | || || ||  |||   | |
-caatatgaaacatg----ctttgttac-ttgtctttctcatcttttaatcaacatttaatggct-----aaattccatttaagtattaatga--ttcatctactgttttcagCTTGTAAAAAGGCATGCAGCTGAGATTTTCACCTCTGTCATAATTTCTACCTTATTCTCATTGTACTCAACTGCTCTTGTTGGACGTCTAGTTGCTTTAG

upper sequence: GRMZM2G478212_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv08s0056g01690.t01 (Vitis vinifera), 3'ss of exon 5
gtactactgcacatggttatcttgtgacatcatttcggttaagctctgctccgctgcaagtgccttttatgtgatct-gtcaact-tgtccatgctcttgaacccctgattt--cagCTTGTAAAGAGGCACGCAGCAGAGATTTTCACATCAATTGCCATTGCGTCGACATTCTCTCTGTACTCAACCGCTGTCATAGGGCGCCTGATTGGGCTGG
             |    | | | |  |||||     |  | |  || | ||   |   | ||   |  ||  |||  || |||| | ||  | ||  |    |  ||||||  ||||||||||||||||| ||||| |||||||||||||| ||    ||  |  | | ||||||  |||| ||||| ||| | || || ||| |  | ||| | |
-----------tgtaaagagcatttatcatca----agagatgtccttcaccatagt--gcgctagtcttgcaatcgagtaaactctctctttcctactttctctatgatttttcagCTTGTAAAGAGGCATGCAGCTGAGATTTTCACATCTATCATTATCTCAACAATATTCTCCTTGTATTCAACTGCTTTTATTGGACGCATTCTGGGGTTAG

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 2 RNA-Seq libraries.


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 34

CACAAAGGCGCCCTCTAATCCTGGAGCTGGTGACGTACTAATGGGTTTCCTTGGGTCTGTGATCATATCATTTGCATTCTCAATGTTCAAACAGAGAAAGgtactactgc ... ctgatttcagCTTGTAAAGAGGCACGCAGCAGAGATTTTCACATCAATTGCCATTGCGTCGACATTCTCTCTGTACTCAACCGCTGTCATAGGGCGCCTGATTGGGCTGG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 30

CACAAAGGCGCCCTCTAATCCTGGAGCTGGTGACGTACTAATGGGTTTCCTTGGGTCTGTGATCATATCATTTGCATTCTCAATGTTCAAACAGAGAAAGgtactactgc ... ctgatttcagCTTGTAAAGAGGCACGCAGCAGAGATTTTCACATCAATTGCCATTGCGTCGACATTCTCTCTGTACTCAACCGCTGTCATAGGGCGCCTGATTGGGCTGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtgccttttatgtgatctgtcaacttgtccatgctcttgaacccctgatttcagCTTGTAAAGAGGCACGCAGCAGAGATTTTCACATCAATTGCCATTGCGTCGACATTCTCTCTGTACTCAACCGCTGTCATAGGGCGCCTGATTGGGCTGG
                                           ccctgat  putative branch site (score: 30)
                                          cccct  CT-rich tract
      ttttatgt  TA-rich tract