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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtccattttctatatggattacagagattgtatttcttagctttcatgattgttggatagattgtgcatgtatagtacggccatttgcctaggaagcgaaattgaacttttcatgactctactaccctgtagGTTCTTTTACGAATGCTTCCAAACTATTATGATCATGTCCGTACCTATGAGAACACCCTCATAACTAAGTTTTTTGGCCTCCACAGGGTGAAACCTTCTA

Basic information

species Zea mays
transcript GRMZM2G050309_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G050309_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g57660.2 (Oryza sativa), 3'ss of exon 5
-gtccattttctatatggatta-cagagattgtatt----tcttag------ctttcat----gattgttggatagattgtgcatgtatagtacggccatttgcctaggaagcgaaatt---gaacttttcatgactctacta---ccctgtagGTTCTTTTACGAATGCTTCCAAACTATTATGATCATGTCCGTACCTATGAGAACACCCTCATAACTAAGTTTTTTGGCCTCCACAGGGTGAAACCTTCTA
  ||  |||| |   |  |||  |||||||  |||     |  |||      |||| ||    |||| || |||| ||| | |||    ||||   |||  | | ||| ||||| || |    ||| |||||||||||||      || || ||||||||||||||||||||||||| |||||  ||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||| |||||||
gttctgttttatgcttaaattttcagagatcatataagcgtgctagaaaattctttaatggtagattcttcgataaattatacattataagtaacaccacctacttagcaagcggaagttaaaaacatttcatgactctatatgatccttgcagGTTCTTTTACGAATGCTTCCAAAATATTACCATCATGTCCGTACTTATGAGAACACCCTCATAACTAAGTTTTTTGGCCTCCACAGGGTGAAGCCTTCTA

upper sequence: GRMZM2G050309_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT3G09920.1 (Arabidopsis thaliana), 3'ss of exon 3
gtccattttctatatggattacagagattgtatttcttagctttcatgattgttggatagattg-tgcatgtata-gtacggccatttgcctaggaagcgaaattgaacttttcatgactctactaccctgtagGTTCTTTTACGAATGCTTCCAAACTATTATGATCATGTCCGTACCTATGAGAACACCCTCATAACTAAGTTTTTTGGCCTCCACAGGGTGAAACCTTCTA
      ||| |  |    ||||| |      || |||  | |||||   |   |   ||| ||  | ||||| |  |    | |  ||     |   ||  | |||| |||        | ||||    ||||||||||| |  | ||||||||| | ||  || |||||||    || ||||||||||||||||| ||||| || |||||||| |||||  | ||||| || |
-----gtttgtg-actacttacatatccaccatctct--gttttcacattatcttcttagttttctccatgtctttgcgtagactctttgtccgtctgccca-ttgagcttcc---agatttactg---tgtagGTTCTTCTGAGGATGCTTCCAGATTACCATCATCATGTGAAGACATATGAGAACACCCTCATTACTAAATTCTTTGGCCTTCACAGAATCAAACCATCAA

upper sequence: GRMZM2G050309_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv08s0007g04700.t01 (Vitis vinifera), 3'ss of exon 3
gtccattttctatatggattacagagattgtatttcttagctttcatgattgttggatagattgtgcatgtatagtacggccatttgcctaggaagcgaaattgaacttttcat-gactctactaccctgtagGTTCTTTTACGAATGCTTCCAAACTATTATGATCATGTCCGTACCTATGAGAACACCCTCATAACTAAGTTTTTTGGCCTCCACAGGGTGAAACCTTCTA
                                |||  |||   | | | || |   ||   || |     | |  | |     || |  ||  |     || |   ||  |||| ||   |       | ||||||||||| |||||||||||||||||| || ||||||| ||  || |||||||||| |||||||| || |||||||| || |||||| | |||||||| |
--------------------------------tttactagaactgaagtttatctaattt-ttatttccttcttttcctttttttgggttaaaagattgaagttctctagtcatcgaagttgtgtttttatagGTTCTTTTGCGAATGCTTCCAAACTATCATCATCATGTGCGGTCCCATGAGAACACACTCATAACAAAATTTTTTGGTCTTCACAGGATCAAACCTTCAA

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: 45 (upstream exon), 49 (downstream exon)
Score: 45

TCTTAGGCAACTATCTTCCCCTGGAAAGAGTGGAAGTGTCTTTTTCCTGTCACAAGATGATAGATTCATGATTAAGACTCTCCGAAAATCTGAAGTGCAGgtccattttc ... taccctgtagGTTCTTTTACGAATGCTTCCAAACTATTATGATCATGTCCGTACCTATGAGAACACCCTCATAACTAAGTTTTTTGGCCTCCACAGGGTGAAACCTTCTA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 155

TCTTAGGCAACTATCTTCCCCTGGAAAGAGTGGAAGTGTCTTTTTCCTGTCACAAGATGATAGATTCATGATTAAGACTCTCCGAAAATCTGAAGTGCAGgtccattttc ... taccctgtagGTTCTTTTACGAATGCTTCCAAACTATTATGATCATGTCCGTACCTATGAGAACACCCTCATAACTAAGTTTTTTGGCCTCCACAGGGTGAAACCTTCTA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 130

TCTTAGGCAACTATCTTCCCCTGGAAAGAGTGGAAGTGTCTTTTTCCTGTCACAAGATGATAGATTCATGATTAAGACTCTCCGAAAATCTGAAGTGCAGgtccattttc ... taccctgtagGTTCTTTTACGAATGCTTCCAAACTATTATGATCATGTCCGTACCTATGAGAACACCCTCATAACTAAGTTTTTTGGCCTCCACAGGGTGAAACCTTCTA


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 37

TCTTAGGCAACTATCTTCCCCTGGAAAGAGTGGAAGTGTCTTTTTCCTGTCACAAGATGATAGATTCATGATTAAGACTCTCCGAAAATCTGAAGTGCAGgtccattttc ... taccctgtagGTTCTTTTACGAATGCTTCCAAACTATTATGATCATGTCCGTACCTATGAGAACACCCTCATAACTAAGTTTTTTGGCCTCCACAGGGTGAAACCTTCTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cggccatttgcctaggaagcgaaattgaacttttcatgactctactaccctgtagGTTCTTTTACGAATGCTTCCAAACTATTATGATCATGTCCGTACCTATGAGAACACCCTCATAACTAAGTTTTTTGGCCTCCACAGGGTGAAACCTTCTA
                                       ctctact  CT-rich tract
                     aaattgaa  TA-rich tract