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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagatatctgtgcttctcaatgacagatgccaatctgtactctgactcactcaaccacacatgcttaaaatgtttcgaaacttctgtcttctgcagTGGAAGAGCACTTCAAGGTCAGTCAACCCAATGTTTGTAGACCCTAACAACCCACAATGGGGATGGAGCTGGTTGGAACGCTGGATGGCAGCAAAGCCTT

Basic information

species Oryza sativa
transcript LOC_Os05g03190.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g03190.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G012584_T01 (Zea mays), 3'ss of exon 5
gtagatatctgtgcttctcaatgacagatgccaatctgtactctgactcactcaaccacac--atgcttaaaatgtttcgaaacttctgtcttctgcagTGGAAGAGCACTTCAAGGTCAGTCAACCCAATGTTTGTAGACCCTAACAACCCACAATGGGGATGGAGCTGGTTGGAACGCTGGATGGCAGCAAAGCCTT
||||  |    |||| ||||   |||  |    ||   |  ||   ||  ||| |  |     | ||||||||||| || |||  | |||  | | ||||||||||| || || || || ||||||||||||||||||||||| |||||||  || ||||| ||||||||| |||| ||||||||||||||||| || |
gtaggaactcttgct-ctcag-aacatctatatatacttgatcctccttgctctatgatggtaaagcttaaaatgtctcaaaa--tgtgttgtttacagTGGAAGAGTACATCGAGATCTGTCAACCCAATGTTTGTAGACCCAAACAACCTGCAGTGGGGCTGGAGCTGGCTGGAGCGCTGGATGGCAGCAAAACCAT

upper sequence: LOC_Os05g03190.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM5G826979_T03 (Zea mays), 3'ss of exon 5
---------gtagatatctgtgctt---ctcaatgacagatgccaatctgtactctgactcactcaaccaca-catgcttaaaatgtttcgaaacttctgtcttctgcagTGGAAGAGCACTTCAAGGTCAGTCAACCCAATGTTTGTAGACCCTAACAACCCACAATGGGGATGGAGCTGGTTGGAACGCTGGATGGCAGCAAAGCCTT
          | | | || |  | |   || |   | | ||||  |  | | ||     |  ||| |  ||   | ||||||||||| || |||  | |||  | | |||||||||||||| ||||| || |  |||||||||||||||||||| || |||   || ||||| |||||||||||||| ||||||||||||||||| ||||
gtttgagttcttgctctcagaacatacgctaatctatatatgcatacatatgcttcatttggctctatgacggtaagcttaaaatgtctcaaaa--tgtgttgtttacagTGGAAGAGCACATCAAGATCTGCGAACCCAATGTTTGTAGACCCAAATAACTTGCAGTGGGGCTGGAGCTGGTTGGAGCGCTGGATGGCAGCAAAACCTT

upper sequence: LOC_Os05g03190.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA03G33560.1 (Glycine max), 3'ss of exon 5
----------gtagatatctgtgcttctcaatgacagatgccaatctgtactctgactcactcaaccacacatgcttaa--aatgtttcgaaacttctgtcttctgcagTGGAAGAGCACTTCAAGGTCAGTCAACCCAATGTTTGTAGACCCTAACAACCCACAATGGGGATGGAGCTGGTTGGAACGCTGGATGGCAGCAAAGCCTT
           |  ||| |  |    ||     | |  |  ||| |   | | | | |  ||  |         |  ||  | |||||    || | || |  |   | ||||||| | | || || || || || ||||||||  | || || | ||| |||   ||||| ||||||||||||||||| |||||||||||        
catattttgaatgaatagcattctgcctatgatataattttcaaccataagtgtaagttccttgatgctttgaacaaaatcagtgttt---gacatttggcagCAAAATTGGAAGAACTCATCTAGATCTGTAAATCCAATGTTCATGGATCCAACCAATCCAAGCTGGGGTTGGAGCTGGTTGGAACGATGGATGGCAGCCC------

upper sequence: LOC_Os05g03190.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA19G36270.1 (Glycine max), 3'ss of exon 5
-----gtagatatc-tgtgcttctcaatgacagatgccaatctgtactctgactcactcaaccacacatgcttaaaatgtttcg-------aaacttctgtcttctgcagTGGAAGAGCACTTCAAGGTCAGTCAACCCAATGTTTGTAGACCCTAACAACCCACAATGGGGATGGAGCTGGTTGGAACGCTGGATGGCAGCAAAGCCTT
      |   |||  | || || ||||| | |  ||  | |     |  |||  |  ||||| |     |  |   || ||| |       |||  | || |  |   | ||||||| | | || || || || || ||||||||| | || || |  || ||    ||||| ||||||||||||||||| |||||||||||        
gcattctgcctatgatatgattttcaatcataagtgtaagtt----ccttgatgctgtcaacaaattcagtgtttgatatttgggggcaaaaaatatttggcagCAAAACTGGAAGAACTCGTCTAGATCTGTAAATCCAATGTTTATGGATCCAACTAATCCGAGCTGGGGTTGGAGCTGGTTGGAACGATGGATGGCAGCCC------

upper sequence: LOC_Os05g03190.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv08s0040g02360.t01 (Vitis vinifera), 3'ss of exon 5
------------------------------------------------------------------------gtagatatctgtgcttctcaatga---------cagatgccaatc-tgtactctgactcactca---------accacacatgcttaa--aatgtttcgaaacttctgtctt-ctgca---gTGGAAGAGCACTTCAAGGTCAGTCAACCCAATGTTTGTAGACCCTAACAACCCACAATGGGGATGGAGCTGGTTGGAACGCTGGATGGCAGCAAAGCCTT
                                                                          || ||||| || |    ||||          || || ||| |  || ||||      || ||         |   || || ||| |  |||   |       |  ||| | | |||   ||||||||   |||||| |||    |||| | ||||  | || || | |||||| || ||||| ||||||||||||||||| |||||||| ||        
gtatcctattcatcaatactgtttcctgcccattatccatttttaggatcaagaactcactggttggatcttccagttatct-tggtatgaaatggaaagaaaatcaaataccagtggtgcactcatgtagacacatgttttattattgcaaattcttgattaatccctgatggaattggtcctacagCAAGCGTGGAAGAATTCTTCAAAGTCCACAAACCTATTGTTCATGGATCCAAGCAACCCCCATTGGGGTTGGAGCTGGTTGGAACGATGGATGGCGGCCC------

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|25797630|gb|CA753591.1|CA753591
EST:     AGGCTGCAGTAAGAAGGGAGAGGGCGCTCGCATATGCATTTTCACATCAG                         TGGAAGAGCACTTCAAGGTCAGTCAACCCAATGTTTGTAGACCCTAACAAC
genomic: AGGCTGCAGTAAGAAGGGAGAGGGCGCTCGCATATGCATTTTCACATCAGgtagatatct ... tcttctgcagTGGAAGAGCACTTCAAGGTCAGTCAACCCAATGTTTGTAGACCCTAACAAC
EST: gi|58676494|gb|CK065181.1|CK065181
EST:     AGGCTGCAGTAAGAAGGGAGAGGGCGCTCGCATATGCATTTTCACATCAG                         TGGAAGAGCACTT
genomic: AGGCTGCAGTAAGAAGGGAGAGGGCGCTCGCATATGCATTTTCACATCAGgtagatatct ... tcttctgcagTGGAAGAGCACTT
EST: gi|571925|gb|D41436.1|D41436
EST:     AGGCTGCAGTAAGAAGGGAGAGGGCGCTCGCATATGCATTTTCACATCAG                         TGGAAGAGCACTTCAAGGTCAGTCAACCCAATGTTTGTAGACCCTAACAAC
genomic: AGGCTGCAGTAAGAAGGGAGAGGGCGCTCGCATATGCATTTTCACATCAGgtagatatct ... tcttctgcagTGGAAGAGCACTTCAAGGTCAGTCAACCCAATGTTTGTAGACCCTAACAAC
EST: gi|58678634|gb|CK067321.1|CK067321
EST:     GGGAGAGGGCGCTCGCATATGCATTTTCACATCAG                         TGGAAGAGCACTTCAAGGTCAGTCGACCCAATGTTTGTAGATCCTAACAAC
genomic: GGGAGAGGGCGCTCGCATATGCATTTTCACATCAGgtagatatct ... tcttctgcagTGGAAGAGCACTTCAAGGTCAGTCAACCCAATGTTTGTAGACCCTAACAAC
EST: gi|699976|gb|D46267.1|D46267
EST:     AGGCTNCAGTAAGAAGGGAGAAGGCGCTCGCATATGCATTTTCACATCAG                         TTGAAGAGCACTTCAAGGTCAGTCAACCCA
genomic: AGGCTGCAGTAAGAAGGGAGAGGGCGCTCGCATATGCATTTTCACATCAGgtagatatct ... tcttctgcagTGGAAGAGCACTTCAAGGTCAGTCAACCCA

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: 73 (upstream exon), 69 (downstream exon)
Score: 41

CAGCACTCAGTCTAAGGAACAAATTGAGGCGAGTCTTATAAGCAGGCAAGAGGCTGCAGTAAGAAGGGAGAGGGCGCTCGCATATGCATTTTCACATCAGgtagatatct ... tcttctgcagTGGAAGAGCACTTCAAGGTCAGTCAACCCAATGTTTGTAGACCCTAACAACCCACAATGGGGATGGAGCTGGTTGGAACGCTGGATGGCAGCAAAGCCTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgactcactcaaccacacatgcttaaaatgtttcgaaacttctgtcttctgcagTGGAAGAGCACTTCAAGGTCAGTCAACCCAATGTTTGTAGACCCTAACAACCCACAATGGGGATGGAGCTGGTTGGAACGCTGGATGGCAGCAAAGCCTT
  gactcac  putative branch site (score: 41)
                                       cttctgtcttctgc  putative PPT
                       ttaaaatgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagatatctgtgcttctcaatgacagatgccaatctgtactctgactcactcaaccacacatgcttaaaatgtttcgaaacttctgtcttctgcagTGGAAGAGCACTTCAAGGTCAGTCAACCCAATGTTTGTAGACCCTAACAACCCACAATGGGGATGGAGCTGGTTGGAACGCTGGATGGCAGCAAAGCCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG