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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccttttaatcatgtgattgtacagccatggtacttggatcagtagcatgggaatatagtcagattctccgtactgtactgaaatgactgacgtgtggcagGGAACAAGTAGGCCCGCTCACTACCATGTCCTCTGGGATGAGAACAATTTCACAGCAGACGAAATGCAAACACTGACAAACAACCTTTGCTACAC

Basic information

species Zea mays
transcript AC189879.3_FGT003
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC189879.3_FGT003 (Zea mays), 3'ss of exon 18
lower sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 19
ccttttaatcatgtgattgtacagccatggtacttggatcagtagcatgggaatatagtc-----agattctccgtactgtactgaaatgactgacgtgtgg--------cagGGAACAAGTAGGCCCGCTCACTACCATGTCCTCTGGGATGAGAACAATTTCACAGCAGACGAAATGCAAACACTGACAAACAACCTTTGCTACAC
          |  ||  |   ||   ||  |   ||    ||||||   |||||||| |      || || |||    ||||||||||||||||| |||||         ||||||||||||||||| ||||||||||| ||||| |||||||||||||||||||| |||||||||||||| ||| ||||||||||||||||||||||
----------acttggatcagcaaatattctgtctg---tagtagcgctggaatataattccccaagtttgtcctccatgtactgaaatgactgatgtgtgtgagttttccagGGAACAAGTAGGCCAGCTCACTACCACGTCCTTTGGGATGAGAACAATTTCACTGCAGACGAAATGCAGACATTGACAAACAACCTTTGCTACAC

upper sequence: AC189879.3_FGT003 (Zea mays), 3'ss of exon 18
lower sequence: GLYMA06G23920.1 (Glycine max), 3'ss of exon 19
ccttttaatcatgtgattgtacagccatggtacttgga--tcagtagcatgggaatatagtcagattctccgtactgtactgaaatgactgacgtgtggcagGGAACAAGTAGGCCCGCTCACTACCATGTCCTCTGGGATGAGAACAATTTCACAGCAGACGAAATGCAAACACTGACAAACAACCTTTGCTACAC
|  ||    ||      |    |    ||  ||||| |   || |   ||| | |    ||   |   |||    |    ||   ||  || | | |  ||||| |||||||| || || ||||| || ||||||||||| |||||||||||||| ||||| || || ||  | || || |||||  | ||||||||
caattgctgcaatcagcttcctattgttgaaacttgaaaaccattcaaatgtgtagcatgtagtagcatccaatttacgttgg--tgtttggcattttacagGGTACAAGTAGACCAGCACACTATCACGTCCTCTGGGACGAGAACAATTTCACTGCAGATGAGATTCAGTCTCTAACCAACAATTTGTGCTACAC

upper sequence: AC189879.3_FGT003 (Zea mays), 3'ss of exon 18
lower sequence: GLYMA05G08170.1 (Glycine max), 3'ss of exon 15
-ccttttaatcatgtgattgtacagccatggtacttggatcagtagcatgggaatatagtcagattctccgtactgtactgaaatgactgacgtgtggcagGGAACAAGTAGGCCCGCTCACTACCATGTCCTCTGGGATGAGAACAATTTCACAGCAGACGAAATGCAAACACTGACAAACAACCTTTGCTACAC----
 || |  ||  | |  ||||   |     | ||    |   || |  | |    || |   | | | |  |||    | | | || | ||   | |  ||||| |||||||| || ||||| || ||||| || ||||| |||||||||||||| || || || || ||| | ||||| |||||| | ||||||||    
accatacaaatagggtattggtgacttgggatagggtgtaaagaactaagatgttaaaagaataatttttgtatcagatttacattaatgctattta-cagGGTACAAGTAGACCAGCTCATTATCATGTTCTGTGGGACGAGAACAATTTCACTGCTGATGAGATCCAATCTCTGACCAACAACTTGTGCTACACGTAA

upper sequence: AC189879.3_FGT003 (Zea mays), 3'ss of exon 18
lower sequence: GLYMA20G28970.1 (Glycine max), 3'ss of exon 20
ccttttaatcatgtgattgtacagccatggtacttggatcagtagcatgggaatatagtcagattctccgta-ctgtactgaaatgactgacgt-gtgg--cagGGAACAAGTAGGCCCGCTCACTACCATGTCCTCTGGGATGAGAACAATTTCACAGCAGACGAAATGCAAACACTGACAAACAACCTTTGCTACAC-----
       |   |   ||| || | |     |||| | |||      |     | |   |    || ||| || || | |  |  |   | |  |  |    ||||| || ||| |||| ||||| || |||||||| |||||||| ||||| ||||||||||| | ||| ||  | ||||||||||| ||||| || ||     
----cccagagtaaaattctagatctgctttactagtatcttagaaaaatctaaacctttgatttttccttaactatgcatactttttttatattatcattcagGGTACTAGTCGGCCAGCTCATTATCATGTCCTGTGGGATGAAAACAACTTCACAGCAGATGGAATTCAGTCTCTGACAAACAATCTTTGTTATACATATG

upper sequence: AC189879.3_FGT003 (Zea mays), 3'ss of exon 18
lower sequence: GLYMA17G12850.1 (Glycine max), 3'ss of exon 19
--ccttttaatcatgtgattg---tacagccatggtacttggatcagtagcatgggaatatagtcagattctccgtactgtactgaaatgactgacgtgtggcagGGAACAAGTAGGCCCGCTCACTACCATGTCCTCTGGGATGAGAACAATTTCACAGCAGACGAAATGCAAACACTGACAAACAACCTTTGCTACAC
   ||  ||| |||   | |    ||  |   | |    |  |  | |  ||||  || | | | | |||    |||  | | | | || | || |   |  ||||| |||||||| || ||||| || ||||| || ||||| |||||||||||||| || || || || ||| | ||||| |||||| | ||||||||
cttctcataaccatacaaataggatattggggtagggtgtaaagaaatgacatgttaa-agaataatattt---gtatcggatttacattaatg-caatttacagGGTACAAGTAGACCAGCTCATTATCATGTTCTGTGGGACGAGAACAATTTCACTGCTGATGAGATCCAATCTCTGACCAACAACTTGTGCTACAC

upper sequence: AC189879.3_FGT003 (Zea mays), 3'ss of exon 18
lower sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 19
ccttttaatcatgtgattgtacagccatggtacttggatcagtagcatgggaatatagtcagattctccgtactgtactgaaatgactgacgtgtggcagGGAACAAGTAGGCCCGCTCACTACCATGTCCTCTGGGATGAGAACAATTTCACAGCAGACGAAATGCAAACACTGACAAACAACCTTTGCTACAC-----
  |   || ||  |      | | || |  || |  || |  |  | |    ||| ||  | | |      |||||  ||   |   ||   ||    |||||||||| ||||| || || |||||||| || ||||| |||||||||||||||||||| |  || ||| | ||||| ||||| || || || ||     
-gtacgaaacaactatcgaaatatccgt--taatatgaccttttccgtaactatacagataaaatg---acactgt-ttgtgtttgttg-tatgatctagGGAACAAGCAGGCCTGCACATTACCATGTTCTTTGGGACGAGAACAATTTCACAGCAGATGGTATTCAATCTCTGACTAACAATCTCTGTTATACCTATG

upper sequence: AC189879.3_FGT003 (Zea mays), 3'ss of exon 18
lower sequence: Vv05s0020g04190.t01 (Vitis vinifera), 3'ss of exon 17
ccttttaatcatgtgattgtacagccatggtacttggatcagtagcatgggaatatagtcagattctccgtactgtac------tgaaatgactgacgtgtggcagGGAACAAGTAGGCCCGCTCACTACCATGTCCTCTGGGATGAGAACAATTTCACAGCAGACGAAATGCAAACACTGACAAACAACCTTTGCTACAC-----
      ||   |    ||     ||  |  |   |   |   || |       |    |||||   |  | | || |       | |  |   |    |||||||||| ||||||||||| ||||| ||||||||  | |||||||||||||||||||||||||| | ||| ||| |  |||| ||||| |||||||||||     
------aacactcactttaggaggctctcatttgtcagtttctaactaacatgtgctttcagaacttttggaatggatgagtcattattttctttctttgtggcagGGGACAAGTAGGCCTGCTCATTACCATGTTTTATGGGATGAGAACAATTTCACAGCAGATGGAATTCAATCCTTGACGAACAATCTTTGCTACACATATG

upper sequence: AC189879.3_FGT003 (Zea mays), 3'ss of exon 18
lower sequence: Vv11s0016g04620.t01 (Vitis vinifera), 3'ss of exon 19
---------------------------------------------------------------------------------------ccttttaatcatgtgattgtacagccatggtacttggatcagtagcatgggaatatagtcagattctccgtactgtactgaaatgactgacgtgtggcagGGAACAAGTAGGCCCGCTCACTACCATGTCCTCTGGGATGAGAACAATTTCACAGCAGACGAAATGCAAACACTGACAAACAACCTTTGCTACAC
                                                                                        |||| ||    ||| | | |  |||| | |  ||   |     | |  | | || |     |   |  ||  |||||||||||   |||| | |||||||| || ||  | |||||||| || ||||| ||||||||||||||||| || |||||||| || || ||| |  |||| |||||||| || |||||
gtaccttgttgaactcattaaatattgcaaggcctgaaatttataatagataagaaaaacacagaagttctcaatttctgcaagagaactttcaagttggtgttggcat-gccaggatggtt---ttgaatgtaaagtactacatgtcaagaatttgt-ttgtactgaaat---tgacatttggcagGGGACCAGCCGACCCGCTCATTATCATGTTCTCTGGGATGAGAACAACTTTACAGCAGATGAGATCCAATCTTTGACGAACAACCTCTGTTACAC

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|19351412|gb|BM895959.1|BM895959
EST:     GCCACCCAACAGAGTTTGATTTCTNCCTCTGTAGTCATGCTGGAATCCAG                         GGAACAAGTAGGCCCGCTCACTACCATGTCCTCTGGGATGAGAACAATTTC
genomic: GCCACCCAACAGAGTTTGATTTCTACCTCTGTAGTCATGCTGGAATCCAGgtaagagtga ... cgtgtggcagGGAACAAGTAGGCCCGCTCACTACCATGTCCTCTGGGATGAGAACAATTTC




















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: 374

GAACTGTTGTTGATTCTAAGATATGCCACCCAACAGAGTTTGATTTCTACCTCTGTAGTCATGCTGGAATCCAGgtaagagtga ... cgtgtggcagGGAACAAGTAGGCCCGCTCACTACCATGTCCTCTGGGATGAGAACAATTTCACAGCAGACGAAATGCAAACACTGACAAACAACCTTTGCTACAC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 109

GAACTGTTGTTGATTCTAAGATATGCCACCCAACAGAGTTTGATTTCTACCTCTGTAGTCATGCTGGAATCCAGgtaagagtga ... cgtgtggcagGGAACAAGTAGGCCCGCTCACTACCATGTCCTCTGGGATGAGAACAATTTCACAGCAGACGAAATGCAAACACTGACAAACAACCTTTGCTACAC


Block sizes: 43 (upstream exon), 46 (downstream exon)
Score: 53

GAACTGTTGTTGATTCTAAGATATGCCACCCAACAGAGTTTGATTTCTACCTCTGTAGTCATGCTGGAATCCAGgtaagagtga ... cgtgtggcagGGAACAAGTAGGCCCGCTCACTACCATGTCCTCTGGGATGAGAACAATTTCACAGCAGACGAAATGCAAACACTGACAAACAACCTTTGCTACAC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 87

GAACTGTTGTTGATTCTAAGATATGCCACCCAACAGAGTTTGATTTCTACCTCTGTAGTCATGCTGGAATCCAGgtaagagtga ... cgtgtggcagGGAACAAGTAGGCCCGCTCACTACCATGTCCTCTGGGATGAGAACAATTTCACAGCAGACGAAATGCAAACACTGACAAACAACCTTTGCTACAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgggaatatagtcagattctccgtactgtactgaaatgactgacgtgtggcagGGAACAAGTAGGCCCGCTCACTACCATGTCCTCTGGGATGAGAACAATTTCACAGCAGACGAAATGCAAACACTGACAAACAACCTTTGCTACAC
                                       gactgac  putative branch site (score: 87)
      aatatagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccttttaatcatgtgattgtacagccatggtacttggatcagtagcatgggaatatagtcagattctccgtactgtactgaaatgactgacgtgtggcagGGAACAAGTAGGCCCGCTCACTACCATGTCCTCTGGGATGAGAACAATTTCACAGCAGACGAAATGCAAACACTGACAAACAACCTTTGCTACAC

- - - - - -tgtgatt
- - - - - - - - - - - -gccatgg
- - - - - - - - - - - - - - - - - - - -cagtagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atgactg