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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggcgaaagatccatattttcctacaattctcgtcttcaaattgttaaagcttcatataatgctgtttttgcttattaagcatgtactgttctgatcacagGACAGGGATCGTAAACTGAGGATATTTTCTGGAAATGAGCACCCATTCCATGATCGCCCTCTTGAACCTTTTATGATGCCACGACGCCAAGTGCGCGAGA

Basic information

species Oryza sativa
transcript LOC_Os05g15370.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g15370.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G163473_T01 (Zea mays), 3'ss of exon 4
-ggcgaaagatccatattttcctacaattctcgtcttcaaattgttaaagcttcatataatgctgtttttgcttattaagcatgtactgttctgatca--cagGACAGGGATCGTAAACTGAGGATATTTTCTGGAAATGAGCACCCATTCCATGATCGCCCTCTTGAACCTTTTATGATGCCACGACGCCAAGTGCGCGAGA
   ||   |    | ||||   |  ||||  | | ||  |||  ||      |||    |   |||  |||    || | ||| ||||| |||| ||   ||||| |||||||| || ||| ||||||||||||||| |||||| ||||||||||| |||||||||||| ||||| ||||||||| ||| ||||| || ||||
ttacgcgtggctgagatttatat-taatttgcattttgcaatattttgtttgtcacgcta-aatgtgcttgacctttga-catatactgctctggtcttccagGATAGGGATCGCAAGCTGCGGATATTTTCTGGAATTGAGCATCCATTCCATGACCGCCCTCTTGAAGCTTTTGTGATGCCACCACGGCAAGTACGGGAGA

upper sequence: LOC_Os05g15370.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G044584_T02 (Zea mays), 3'ss of exon 5
-ggcgaaagatccatattttcctacaattctcgtcttcaaattgttaaagcttcatataatgctgtttttgcttattaagcatgtactgttctgatca--cagGACAGGGATCGTAAACTGAGGATATTTTCTGGAAATGAGCACCCATTCCATGATCGCCCTCTTGAACCTTTTATGATGCCACGACGCCAAGTGCGCGAGA
   |  || |||  |||| |   |   | |  |   |||     ||      |||  | |   |||  ||| |  ||   ||| ||||| |||| ||   ||||| |||||||| || |||||||||||||||||||| || || ||||||||||| |||||||| ||||||||| ||||||| | ||| ||||| |||||||
tttcataacatct-tattgtatcatggt-cgaggaatcatgccttttgctggtcacgttaaaatgtgcttggt-gtttgacatatactgctctggtcctccagGATAGGGATCGCAAGCTGAGGATATTTTCTGGAAACGAACATCCATTCCATGACCGCCCTCTGGAACCTTTTGTGATGCCGCCACGGCAAGTACGCGAGA

upper sequence: LOC_Os05g15370.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA19G22420.1 (Glycine max), 3'ss of exon 5
ggcgaaagatccata--ttttcctacaattctcgt-cttcaaattgttaaagcttcatataatgctgtttttgcttattaagcatgtactgttc-tgatcacagGACAGGGATCGTAAACTGAGGATATTTTCTGGAAATGAGCACCCATTCCATGATCGCCCTCTTGAACCTTTTATGATGCCACGACGCCAAGTGCGCGAGA--
  |    | |    |  |||||  | | || | || | | | | | || ||    |  ||| ||    || |  ||| |  |||| || ||||  ||   | ||||||||||||| ||| | ||||| ||| |||| | ||||||||| ||   ||||||||| |||||||||| | ||||||| |  |   |||||  |||||  
-tcatttggttagaactttttctgatattttttgttccttataatattgaa-taactgatattgtaagttgtatttactt-gcat-tattgttaatggatatagGACAGGGATCGAAAATTAAGGATCTTTCCTGGCAGTGAGCACCCGTTTGTTGATCGCCCACTTGAACCTTATGTGATGCCTC--CTAGAAGTGTACGAGAAA

upper sequence: LOC_Os05g15370.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv14s0171g00250.t01 (Vitis vinifera), 3'ss of exon 4
-----ggcgaaagatccatattttcctacaattctcgtcttcaaattgttaaagcttcatataatgctgtttttgcttattaagcatgtactgttctgatcacagGACAGGGATCGTAAACTGAGGATATTTTCTGGAAATGAGCACCCATTCCATGATCGCCCTCTTGAACCTTTTATGATGCCACGACGCCAAGTGCGCGAGA
     | |   | ||  ||  | || |   |   | |  || | ||  || ||  |   |    || || |||   |||  | ||      | |  |  | |||||| || ||||| ||||| ||||||||| ||||  |||||||||| ||| ||||  | ||||||||||||| | ||||||| |  || ||||| || || |
ttttagtcattatatgaatgatgtcttgttaactttg--tttagatgattcaatgtgtttgct-tgttggtttacattacaacgc-cactttatgtttgt-acagGATAGAGATCGAAAACTAAGGATATTTGCTGGTGATGAGCACCCTTTCAATGACAGGCCTCTTGAACCTTATGTGATGCCGCCTCGGCAAGTACGAGAAA

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|88479736|gb|CI417007.1|CI417007
EST:     CGCAATAGATTGCGTGAT                         GACAGGGATCGTAAACTGAGGATATTTTCTGGAAATGAGCACCCATTCCAT
genomic: CGCAATAGATTGCGTGATgtaagtgaaa ... ctgatcacagGACAGGGATCGTAAACTGAGGATATTTTCTGGAAATGAGCACCCATTCCAT
EST: gi|286421|gb|D15229.1|D15229
EST:     CAATTCGCAAAGCTGTCATGCGCATGCTTCCTCGCAATAGATTGCGTGAT                         GACAGGGATCGTAAACTGAGGATATT
genomic: CAATTCGCAAAGCTGTCATGCGCATGCTTCCTCGCAATAGATTGCGTGATgtaagtgaaa ... ctgatcacagGACAGGGATCGTAAACTGAGGATATT
EST: gi|86523302|gb|CI163508.1|CI163508
EST:     CAATTCGCAAAGCTGTCATGCGCATGCTTCCTCGCAATAGATTGCGTGAT                         GACAGGGATCGTAAACTGAGGATATTTTCTGGAAATGAGCACCCATTCCAT
genomic: CAATTCGCAAAGCTGTCATGCGCATGCTTCCTCGCAATAGATTGCGTGATgtaagtgaaa ... ctgatcacagGACAGGGATCGTAAACTGAGGATATTTTCTGGAAATGAGCACCCATTCCAT
EST: gi|88731413|gb|CI755026.1|CI755026
EST:     CAATTCGCAAAGCTGTCATGCGCATGCTTCCTCGCAATAGATTGCGTGAT                         GACAGGGATCGTAAACTGAGGATATTTTCTGGAA
genomic: CAATTCGCAAAGCTGTCATGCGCATGCTTCCTCGCAATAGATTGCGTGATgtaagtgaaa ... ctgatcacagGACAGGGATCGTAAACTGAGGATATTTTCTGGAA
EST: gi|218498131|gb|FG955911.1|FG955911
EST:     TAATTCGCAAAGCTGTCATGCGCATGCTTCCTCGCAATAGATTGCGTGAT                         GACAGGGATCGTAAACTGAGGATATTTTCTGGAAATGAGCACCCATTCCAT
genomic: CAATTCGCAAAGCTGTCATGCGCATGCTTCCTCGCAATAGATTGCGTGATgtaagtgaaa ... ctgatcacagGACAGGGATCGTAAACTGAGGATATTTTCTGGAAATGAGCACCCATTCCAT
EST: gi|88427554|gb|CI548807.1|CI548807
EST:     TGTCATGCGCATGCTTCCTCGCAATAGATTGCGTGAT                         GACAGGGATCGTAAACTGAGGATATTTTCTGGAAATGAGCACCCATTCCAT
genomic: TGTCATGCGCATGCTTCCTCGCAATAGATTGCGTGATgtaagtgaaa ... ctgatcacagGACAGGGATCGTAAACTGAGGATATTTTCTGGAAATGAGCACCCATTCCAT
EST: gi|88291404|gb|CI529994.1|CI529994
EST:     TTCCTCCCAATAGATTGCGTGAT                         GACAGGGATCGTAAACTGAGGATATTTTCTGGAAATGAGCACCCATTCCAT
genomic: TTCCTCGCAATAGATTGCGTGATgtaagtgaaa ... ctgatcacagGACAGGGATCGTAAACTGAGGATATTTTCTGGAAATGAGCACCCATTCCAT
EST: gi|8860173|gb|AU097491.1|AU097491
EST:     CAATTCGCAAAGCTGTCATGCGCATGCTTC-TCGCAATAGATTGCGTGAT                         GACAGGGATCGTAA
genomic: CAATTCGCAAAGCTGTCATGCGCATGCTTCCTCGCAATAGATTGCGTGATgtaagtgaaa ... ctgatcacagGACAGGGATCGTAA
EST: gi|33655563|gb|CF278177.1|CF278177
EST:     CAATTCGCAAAGCTGTCATGCGCATGCTTCCTCGCAATAGATTGCGTGAT                         GACAGGGATCGTAAACTGAGGATATTTTCTGGAAATGAGCACCCATTCCAT
genomic: CAATTCGCAAAGCTGTCATGCGCATGCTTCCTCGCAATAGATTGCGTGATgtaagtgaaa ... ctgatcacagGACAGGGATCGTAAACTGAGGATATTTTCTGGAAATGAGCACCCATTCCAT
EST: gi|33693481|gb|CF321720.1|CF321720
EST:     GCTTCCTCGCAATAGATTGCGTGAT                         GACAGGGATCGTAAACTGAGGATATTTTCTGGAAATGAGCACCCATTCCAT
genomic: GCTTCCTCGCAATAGATTGCGTGATgtaagtgaaa ... ctgatcacagGACAGGGATCGTAAACTGAGGATATTTTCTGGAAATGAGCACCCATTCCAT
EST: gi|87006904|gb|CI275212.1|CI275212
EST:     CAATTCGCAAAGCTGTCATGCGCATGCTTCCTCGCAATAGATTGCGTGAT                         GACAGGGATCGTAAACTGAGGATATTTTCTGGAAATGAGCACCCATTCCAT
genomic: CAATTCGCAAAGCTGTCATGCGCATGCTTCCTCGCAATAGATTGCGTGATgtaagtgaaa ... ctgatcacagGACAGGGATCGTAAACTGAGGATATTTTCTGGAAATGAGCACCCATTCCAT

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: 72 (upstream exon), 45 (downstream exon)
Score: 42

TTTGAAGGAAAGAAGACTCAAGGACCAGATGGAAAAAGACCCAACTGAAGCAATTCGCAAAGCTGTCATGCGCATGCTTCCTCGCAATAGATTGCGTGATgtaagtgaaa ... ctgatcacagGACAGGGATCGTAAACTGAGGATATTTTCTGGAAATGAGCACCCATTCCATGATCGCCCTCTTGAACCTTTTATGATGCCACGACGCCAAGTGCGCGAGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaagcttcatataatgctgtttttgcttattaagcatgtactgttctgatcacagGACAGGGATCGTAAACTGAGGATATTTTCTGGAAATGAGCACCCATTCCATGATCGCCCTCTTGAACCTTTTATGATGCCACGACGCCAAGTGCGCGAGA
                                           ttctgat  putative branch site (score: 42)
                                        ctgttct  CT-rich tract
                   tttttgcttattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggcgaaagatccatattttcctacaattctcgtcttcaaattgttaaagcttcatataatgctgtttttgcttattaagcatgtactgttctgatcacagGACAGGGATCGTAAACTGAGGATATTTTCTGGAAATGAGCACCCATTCCATGATCGCCCTCTTGAACCTTTTATGATGCCACGACGCCAAGTGCGCGAGA

- - - - - - - - - tcctaca
- - - - - - - - - - - - - - - - - - - - - - - - gcttcat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcatgta