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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccagtagtaaaatgggttgagaaacagaagtgttttgatttcttatcgacacccagggttgctaatgttctaacatttaacttttttaaatgtgctgaagATTAATAGGAGGATGGAGTTTGTGTTTGCAAGTCATACATTTGATGTTTGGGAGAGCTGGATGCTGGAGGGGTCCTTGTTGGAGGGTTGCAAACTTATCA

Basic information

species Oryza sativa
transcript LOC_Os03g03460.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g03460.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM5G841360_T01 (Zea mays), 3'ss of exon 5
----ccagtagtaaaatgggttgagaaacagaagtgttttgatttcttatcgacacccagggttgctaatgttctaacatttaacttttttaaatgtgctga-agATTAATAGGAGGATGGAGTTTGTGTTTGCAAGTCATACATTTGATGTTTGGGAGAGCTGGATGCTGGAGGGGTCCTTGTTGGAGGGTTGCAAACTTATCA
      |  |  ||||  | |||||||| ||| |  |  |    | || ||    |||| | |  || ||||||| | |    | || ||  | |    ||| |||||||||||| ||||||||||||||||||||| ||| | ||||||||||||||||||||||||||||| || |||||| |||||||| |||| |||||||
ttctgaacgaaaaaaaaagtttgagaaatagaggcatcat----ttttctcagtgcccatgatcactgatgttcttataaa-gatttgttgcactacattgacagATTAATAGGAAGATGGAGTTTGTGTTTGCAAGCCATTCTTTTGATGTTTGGGAGAGCTGGATGCTGGACGGTTCCTTGCTGGAGGGTAGCAAGCTTATCA

upper sequence: LOC_Os03g03460.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G476107_T02 (Zea mays), 3'ss of exon 5
----ccagtagtaaaatgggttgagaaacagaagtgttttgatttcttatcgacacccagggttgctaatgttctaacatttaacttttttaaatgtgctga-agATTAATAGGAGGATGGAGTTTGTGTTTGCAAGTCATACATTTGATGTTTGGGAGAGCTGGATGCTGGAGGGGTCCTTGTTGGAGGGTTGCAAACTTATCA
      |  |  ||||  | |||||||| ||| |  |  |    | || ||    |||| | |  || ||||||| | |    | || ||  | |    ||| |||||||||||| ||||||||||||||||||||| ||| | ||||||||||||||||||||||||||||| || |||||| ||||||               
ttctgaacgaaaaaaaaagtttgagaaatagaggcatcat----ttttctcagtgcccatgatcactgatgttcttataaa-gatttgttgcactacattgacagATTAATAGGAAGATGGAGTTTGTGTTTGCAAGCCATTCTTTTGATGTTTGGGAGAGCTGGATGCTGGACGGTTCCTTGCTGGAGG---------------

upper sequence: LOC_Os03g03460.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA09G39090.1 (Glycine max), 3'ss of exon 5
--ccagtagtaaaatgggttgagaaacagaagtgttttgatttcttatcgacacccagggttgctaatgttctaacatttaacttttttaaatgtgctgaagATTAATAGGAGGATGGAGTTTGTGTTTGCAAGTCATACATTTGATGTTTGGGAGAGCTGGATGCTGGAGGGGTCCTTGTTGGAGGGTTGCAAACTTATCA---
       ||| ||||   || ||| | |  | |   |  | |   |      |||| |       || |  || |  ||     |         |  || |||| ||||| || ||||||||||| ||||| |||||||  |||||||||||||||| |||||  || || || |||||   |||    |||| |||  | |   
caatgaaagttaaat--atttagatatatgactaactctactatgttatattaccctgcaaacacaaggcccttaatttggttataaactgtcattttgcagATCAATAGAAGAATGGAGTTTGTATTTGCTAGTCATAGTTTTGATGTTTGGGAGAACTGGACTCTAGAAGGTTCCTTACAGGAA---TGCAGACTGGTGAACT

upper sequence: LOC_Os03g03460.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA18G47240.1 (Glycine max), 3'ss of exon 5
-ccagtagtaaaatgggttgagaaacagaagtgttttgatttcttatcgacacccagggttgctaatgttctaacatttaacttttttaaatgtgctgaagATTAATAGGAGGATGGAGTTTGTGTTTGCAAGTCATACATTTGATGTTTGGGAGAGCTGGATGCTGGAGGGGTCCTTGTTGGAGGGTTGCAAACTTATCA----
      ||  ||||   || ||| | |    |   |  |     |      || | |      | |||  || |  ||     |         |  || |||| ||||| || ||||||||||| ||||| |||||||  |||||||||||||||| |||||  || || || |||||   |||    |||| |||  | |    
aatgaaagctaaat--atttagatatatggctaactctaccatgttatattacactgcaaacatgatgcccttaatttggttgtaaactgtcattttgcagaTCAATAGAAGAATGGAGTTTGTATTTGCTAGTCATAGTTTTGATGTTTGGGAGAACTGGACTCTAGAAGGTTCCTTACAGGAA---TGCAGACTGGTGAACTG

upper sequence: LOC_Os03g03460.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv15s0046g02250.t01 (Vitis vinifera), 3'ss of exon 5
-ccagtagtaaa-atgggttgagaaacagaagtgttttgatttcttatcgacacccagggttgctaatgttctaacatttaacttttttaaatgtgctgaagATTAATAGGAGGATGGAGTTTGTGTTTGCAAGTCATACATTTGATGTTTGGGAGAGCTGGATGCTGGAGGGGTCCTTGTTGGAGGGTTGCAAACTTATCA---
  || || |    ||  | ||    |   || |  | ||   || ||  ||     |   ||  | | |   ||   | ||| | | ||     || || |||| ||||| || ||||| ||||| ||||| ||||| |  ||||||||||||||||| |||||| |||| || || |||   ||||  || |   |  |||   
aacaataattttcataagatgctgcatgtaaattatatgtagtcatactgatgtttata-ttctttagggaatatagtataattatattttg-atgatgcagATAAATAGAAGAATGGAATTTGTATTTGCCAGTCACAGCTTTGATGTTTGGGAGAGTTGGATGTTGGAAGGTTCTTTG---GAGGAATGTAGGTTGGTCAACT

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|86251584|gb|CI016873.1|CI016873
EST:     GATACCATGGGATTACGTTCCTTCGTCGCTGGTGGTAAACTATTGCAG                         ATTAATAGGAGGATGGAGTTTGTGTTTGCAAGTCATACATTTGATGTTTGG
genomic: GATACCATGGGATTACGTTCCTTCGTCGCTGGTGGTAAACTATTGCAGgtatcatctc ... tgtgctgaagATTAATAGGAGGATGGAGTTTGTGTTTGCAAGTCATACATTTGATGTTTGG
EST: gi|88473977|gb|CI411248.1|CI411248
EST:     CTTCGTCGCTGGTGGTAAACTATTGCAG                         ATTAATAGGAGGATGGAGTTTGTGTTTGCAATTCATACATTTGATGTTTGG
genomic: CTTCGTCGCTGGTGGTAAACTATTGCAGgtatcatctc ... tgtgctgaagATTAATAGGAGGATGGAGTTTGTGTTTGCAAGTCATACATTTGATGTTTGG
EST: gi|86493313|gb|CI135946.1|CI135946
EST:     GATACCATGGGATTACGTTCCTTCGTCGCTGGTGGTAAACTATTGCAG                         ATTAATAGGAGGATGGAGTTTGTGTTTGCAAGTCATACATTTGATGTTTGG
genomic: GATACCATGGGATTACGTTCCTTCGTCGCTGGTGGTAAACTATTGCAGgtatcatctc ... tgtgctgaagATTAATAGGAGGATGGAGTTTGTGTTTGCAAGTCATACATTTGATGTTTGG
EST: gi|33804331|gb|CF328040.1|CF328040
EST:     GATACCATGGGATTACGTTCCTTCGTCGCTGGTGGTAAACTATTGCAG                         ATTAATAGGAGGATGGAGTTTGTGTTTGCAAGTCATACATTTGATGTTTGG
genomic: GATACCATGGGATTACGTTCCTTCGTCGCTGGTGGTAAACTATTGCAGgtatcatctc ... tgtgctgaagATTAATAGGAGGATGGAGTTTGTGTTTGCAAGTCATACATTTGATGTTTGG
EST: gi|87031789|gb|CI272490.1|CI272490
EST:     GATACCATGGGATTACGTTCCTTCGTCGCTGGTGGTAAACTATTGCAG                         ATTAATAGGAGGATGGAGTTTGTGTTTGCAAGTCATACATTTGATGTTTGG
genomic: GATACCATGGGATTACGTTCCTTCGTCGCTGGTGGTAAACTATTGCAGgtatcatctc ... tgtgctgaagATTAATAGGAGGATGGAGTTTGTGTTTGCAAGTCATACATTTGATGTTTGG
EST: gi|88417707|gb|CI535866.1|CI535866
EST:     AACTATTGCAG                         ATTAATAGGAGGATGGAGTTTGTGTTTGCAAGTCATACATTTGATGTTTGG
genomic: AACTATTGCAGgtatcatctc ... tgtgctgaagATTAATAGGAGGATGGAGTTTGTGTTTGCAAGTCATACATTTGATGTTTGG
EST: gi|88227952|gb|CI227432.1|CI227432
EST:     CATGGGATTACGTTCCTTCGTCGCTGGTGGTAAACTATTGCAG                         ATTAATAGGAGGATGGAGTTTGTGTTTGCAAGTCATACATTTGATGTTTGG
genomic: CATGGGATTACGTTCCTTCGTCGCTGGTGGTAAACTATTGCAGgtatcatctc ... tgtgctgaagATTAATAGGAGGATGGAGTTTGTGTTTGCAAGTCATACATTTGATGTTTGG
EST: gi|29661381|gb|CB657656.1|CB657656
EST:     GATACCATGGGATTACGTTCCTTCGTCGCTGGTGGTAAACTATTGCAG                         ATTAATAGGAGGATGGAGTTTGTGTTTGCAAGTCATACATTTGATGTTTGG
genomic: GATACCATGGGATTACGTTCCTTCGTCGCTGGTGGTAAACTATTGCAGgtatcatctc ... tgtgctgaagATTAATAGGAGGATGGAGTTTGTGTTTGCAAGTCATACATTTGATGTTTGG

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 1 RNA-Seqlibrary.


Block sizes: 74 (upstream exon), 66 (downstream exon)
Score: 22

GATACCATGGGATTACGTTCCTTCGTCGCTGGTGGTAAACTATTGCAGgtatcatctc ... tgtgctgaagATTAATAGGAGGATGGAGTTTGTGTTTGCAAGTCATACATTTGATGTTTGGGAGAGCTGGATGCTGGAGGGGTCCTTGTTGGAGGGTTGCAAACTTATCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgacacccagggttgctaatgttctaacatttaacttttttaaatgtgctgaagATTAATAGGAGGATGGAGTTTGTGTTTGCAAGTCATACATTTGATGTTTGGGAGAGCTGGATGCTGGAGGGGTCCTTGTTGGAGGGTTGCAAACTTATCA
                 taatgttctaacattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccagtagtaaaatgggttgagaaacagaagtgttttgatttcttatcgacacccagggttgctaatgttctaacatttaacttttttaaatgtgctgaagATTAATAGGAGGATGGAGTTTGTGTTTGCAAGTCATACATTTGATGTTTGGGAGAGCTGGATGCTGGAGGGGTCCTTGTTGGAGGGTTGCAAACTTATCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - -agtaaaa
- - - - - - - - - -agaaaca
- - - - - - - - - - - - - - - tgttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ggttgct