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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catctgaaccgccccagagaggagtgacccggggtagagaatatgtgctgttagcaaaaagtactgctgtctgatatctgtattgttttgctacatacagGATGGGGCTGGGCGTGTTGGAAAGATGTTTTTTGCCCGCCAAGGGAAGAAATTTGATTATGACCTGAAGCAG

Basic information

species Zea mays
transcript AC218035.3_FGT004
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC218035.3_FGT004 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g34650.1 (Oryza sativa), 3'ss of exon 3
-catctg-aaccgccccagagaggagtgacccggggtagagaatatgtgc-tgttagcaaaaagtactgctgtctgatatctgtattgttttgctacatacagGATGGGGCTGGGCGTGTTGGAAAGATGTTTTTTGCCCGCCAAGGGAAGAAATTTGATTATGACCTGAAGCAG
  | | |  |||  | |||   |   |           |   || ||| | | ||| |     ||  |  || ||  | |||| || ||||   | | |||||||||| ||||| || |||||||| ||| |||||||||||||||||||||||||||| || ||||| ||||||
ataccagtgacctactcagtatgatttagtttctaagtgctgatgtgttcatattaaccttttgtgattgtg-ctattctctg-atagtttcattcc-tacagGATGGAGCTGGCCGAGTTGGAAAAATGCTTTTTGCCCGCCAAGGGAAGAAATTTGACTACGACCTAAAGCAG

upper sequence: AC218035.3_FGT004 (Zea mays), 3'ss of exon 3
lower sequence: AT5G49820.1 (Arabidopsis thaliana), 3'ss of exon 3
catctgaaccgccccagagaggagtgacccggggtaga-gaatatgtgctgttagcaaaaagtactgctgtctgatatctg--tattgttttgctacatacagGATGGGGCTGGGCGTGTTGGAAAGATGTTTTTTGCCCGCCAAGGGAAGAAATTTGATTATGACCTGAAGCAG
  | |      | |          | |  |    |  | | |||       ||   || | |   | ||  || ||   ||  |||   | |  | | |  ||||||| |||||||||||||| || ||| |||||||  | || || |||||||||||||||||  |||| |||
-gttttcctttctcgtatatcctttcatgcatcatgcatgtataacaatcctttaaaacatggcttactcactcattgttgaatatcaatgtaattcttgtagGATGGTGCTGGGCGTGTTGGGAAAATGCTTTTTGCGAGGCAGGGAAAGAAATTTGATTATGATTTGAAACAG

upper sequence: AC218035.3_FGT004 (Zea mays), 3'ss of exon 3
lower sequence: Vv12s0035g01870.t01 (Vitis vinifera), 3'ss of exon 3
----catctgaaccgccccagagaggagtgacccggggt--agagaatatgtgctgttagcaaaaagtactgctgtctgatatctgtattgttttgctacatacagGATGGGGCTGGGCGTGTTGGAAAGATGTTTTTTGCCCGCCAAGGGAAGAAATTTGATTATGACCTGAAGCAG
    | |     ||  |        |  |||     | |  |  |||||  |||  ||      || |  |  |   |||  |     ||   ||  ||  | |||||||| ||||| |||||||| || ||| ||||||| || ||||||||||| ||||||||||| || || |||
tttgctttatggccttcttttttcagtttgaatttagcttcatggaataattgcatttg-----aaatgatatttgttgaatttaaagttacatta-tatgtgcagGATGGTGCTGGTCGTGTTGGGAAAATGCTTTTTGCACGGCAAGGGAAGAAGTTTGATTATGATCTAAAACAG

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), 48 (downstream exon)
Score: 92

AGCAATGGGTGTGTTTACAACAAGAACCTTGCTCAATTCTGTTGGAGTCTCCCAAAGCAGGGCCGCATCTGGTGCTGTGGCTATCAACTGGATACTCAAGgtaaaaatac ... ctacatacagGATGGGGCTGGGCGTGTTGGAAAGATGTTTTTTGCCCGCCAAGGGAAGAAATTTGATTATGACCTGAAGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 129

AGCAATGGGTGTGTTTACAACAAGAACCTTGCTCAATTCTGTTGGAGTCTCCCAAAGCAGGGCCGCATCTGGTGCTGTGGCTATCAACTGGATACTCAAGgtaaaaatac ... ctacatacagGATGGGGCTGGGCGTGTTGGAAAGATGTTTTTTGCCCGCCAAGGGAAGAAATTTGATTATGACCTGAAGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 121

AGCAATGGGTGTGTTTACAACAAGAACCTTGCTCAATTCTGTTGGAGTCTCCCAAAGCAGGGCCGCATCTGGTGCTGTGGCTATCAACTGGATACTCAAGgtaaaaatac ... ctacatacagGATGGGGCTGGGCGTGTTGGAAAGATGTTTTTTGCCCGCCAAGGGAAGAAATTTGATTATGACCTGAAGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 282

AGCAATGGGTGTGTTTACAACAAGAACCTTGCTCAATTCTGTTGGAGTCTCCCAAAGCAGGGCCGCATCTGGTGCTGTGGCTATCAACTGGATACTCAAGgtaaaaatac ... ctacatacagGATGGGGCTGGGCGTGTTGGAAAGATGTTTTTTGCCCGCCAAGGGAAGAAATTTGATTATGACCTGAAGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctgttagcaaaaagtactgctgtctgatatctgtattgttttgctacatacagGATGGGGCTGGGCGTGTTGGAAAGATGTTTTTTGCCCGCCAAGGGAAGAAATTTGATTATGACCTGAAGCAG
                       gtctgat  putative branch site (score: 282)
                                        ttttgct  putative PPT
                                   tattgtttt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catctgaaccgccccagagaggagtgacccggggtagagaatatgtgctgttagcaaaaagtactgctgtctgatatctgtattgttttgctacatacagGATGGGGCTGGGCGTGTTGGAAAGATGTTTTTTGCCCGCCAAGGGAAGAAATTTGATTATGACCTGAAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- -ctgaacc
- - - - - gccccag
- - - - - - - - - - - - - - - - - - - - - - -tgctgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - agcaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - actgctg