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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acgaattacttggattcaagttatattatttatgtgcgaatcaaacaagattttttacattttttttccaaatgtgttaattttctgatgcctaatgcagATACTTCTCATACGAGCACTTTTATGTGATATACTGCAAATTTTGGGAGTTGGACACAGATCATGATTTTTTGATTGATAAAGAGAACCTTATCAGATAT

Basic information

species Oryza sativa
transcript LOC_Os10g33680.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g33680.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G148323_T01 (Zea mays), 3'ss of exon 7
acgaattacttggattcaagttatatt-attta-tgtgcgaatcaaacaagattttttacattttttttccaaatgtgttaattttctgatgcc-taatgcagATACTTCTCATACGAGCACTTTTATGTGATATACTGCAAATTTTGGGAGTTGGACACAGATCATGATTTTTTGATTGATAAAGAGAACCTTATCAGATAT
 | | ||  || | |     ||| |||  || | |||     | | | |   ||   |   | |    |  |  || ||||||  |||     | |  |||||||| |||||||| || |||||||||||||| ||||||||||| |||||| ||||  |||| || ||||||||||||||||| || || || |||| ||||
-ccatttgttttg-tgtggattacatttgttcactgttttctttatatagtcttaactgtgtataacgtttac-tgagttaataatcttggatcatggtgcagATATTTCTCATATGAACACTTTTATGTGATCTACTGCAAATTCTGGGAGCTGGATGCAGACCACGATTTTTTGATTGATAAGGAAAATCTCATCAAATAT

upper sequence: LOC_Os10g33680.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA20G36530.1 (Glycine max), 3'ss of exon 7
------acgaattacttggattcaagttatattatttatgtgcgaatcaaacaagattt-tttacattttttttccaaatgtgttaatttt--ctgatgcctaa-tgcagATACTTCTCATACGAGCACTTTTATGTGATATACTGCAAATTTTGGGAGTTGGACACAGATCATGATTTTTTGATTGATAAAGAGAACCTTATCAGATAT
      |     || |   ||| || | | |  ||   | ||    |||  ||| || | || | |      | |    ||| || | ||   || ||   |   || || |||||||| || ||||| |||||||| ||||||||||||||||||||| |||| |||||||| ||||| || || || |||||||| ||||||||||||
gtagatatactatattatcattaaattcacacaatgactctgtttttcagccaaaatatattcataacaaaatgcattgtgtttttacttcacctaataattgtctgtagGTACTTCTCTTATGAGCATTTTTATGTTATATACTGCAAATTTTGGGAGCTGGATACAGATCACGATTTCTTTATAGACAAAGAGAATCTTATCAGATAT

upper sequence: LOC_Os10g33680.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA03G41180.1 (Glycine max), 3'ss of exon 7
---------------------------acgaattacttggattcaagttatattatttatgtg--cgaatcaaacaagattttttacattttttttccaaatgtgttaattttctgatgcctaat--gcagATACTTCTCATACGAGCACTTTTATGTGATATACTGCAAATTTTGGGAGTTGGACACAGATCATGATTTTTTGATTGATAAAGAGAACCTTATCAGATAT
                           |  || | |    | | |  ||   ||  ||||     ||||  ||| |  |||| |   ||  |   |  |  | | |||  ||||  |    | ||  |||| |||||||| |||||||| |||||||| ||||||||||| ||||||||| |||| |||||||||||||| ||||| || |||||||| || |||||||||
gtagatataattgaaaatttcatttcaattaacttcagaaaatgaccttggtttcattattcaaacgaactaaatat-atttgtattatgatgccttaatcttttttacctttcctaaatattatctgcagGTACTTCTCTTACGAGCATTTTTATGTTATATACTGCAAGTTTTGGGAGCTGGATACAGATCATGATTTCTTGATAGACAAAGAGAATCTCATCAGATAT

upper sequence: LOC_Os10g33680.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA10G32500.1 (Glycine max), 3'ss of exon 7
------acgaattacttggattca-agttatattatttatgtgcgaatcaaacaagattttttacattttttttccaaatgtgttaattttctgatgcctaatgcagATACTTCTCATACGAGCACTTTTATGTGATATACTGCAAATTTTGGGAGTTGGACACAGATCATGATTTTTTGATTGATAAAGAGAACCTTATCAGATAT
      | || | ||||  |||   | ||   || | | |||  ||||  ||    ||||| |   | ||| |      |   |||||| ||| | |   | | ||| ||||||||||| ||||| |||||||| || |||||||||||||||||| | |||||||||||||| ||||| ||||||| |||||||||||| | ||||
aaatccatgattgactttcattttcaatttagttctctctgta-gaattgaa----attttct-tgtctttgtatttgcttcattaattatcttacgaa-atttcagGTACTTCTCATATGAGCATTTTTATGTCATTTACTGCAAATTTTGGGAGCTCGACACAGATCATGACTTTTTCATTGATAGAGAGAACCTTATTAAATAT

upper sequence: LOC_Os10g33680.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA19G43790.1 (Glycine max), 3'ss of exon 7
------------------------acgaattactt-ggattcaagttatattatttatgtgcgaatcaaacaagattttttacattttttttccaaa---tgtgttaattttc--tgatgcctaatgcagATACTTCTCATACGAGCACTTTTATGTGATATACTGCAAATTTTGGGAGTTGGACACAGATCATGATTTTTTGATTGATAAAGAGAACCTTATCAGATAT
                         | | | ||||  ||         |  | |   | | | ||| ||  ||   | |||  ||| |  | ||  |   | | |||  ||||  | |||     ||||| |||||||| || ||||| |||||||| ||||||||||| ||||||||| |||| |||||||||||||| ||||| || |||||||| || |||||||||
gtagatataattgaaaatgtcatttcaattaacttcagaaaatgaccttggtgtcattattcaaatgaactaaatatatttgtattatgatgccttaatcttttttacctttccttaatgttatctgcagGTACTTCTCTTATGAGCATTTTTATGTTATATACTGCAAGTTTTGGGAGCTGGATACAGATCATGATTTCTTGATAGACAAAGAGAATCTCATCAGATAT

upper sequence: LOC_Os10g33680.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA10G30930.1 (Glycine max), 3'ss of exon 7
--------acgaattacttggattcaagttatattatttatgtgcgaatcaaacaagatttttt---acattttttttccaaatgtgttaatttt--ctgatgcctaa-tgcagATACTTCTCATACGAGCACTTTTATGTGATATACTGCAAATTTTGGGAGTTGGACACAGATCATGATTTTTTGATTGATAAAGAGAACCTTATCAGATAT
        || | | | |   ||| || | | |  ||   | ||    |||  ||| || | ||   ||     |      | ||| || | |||  || ||   |   || || |||||||| || ||||| |||||||| ||||||||||||||||||||| |||| |||||||| ||||| || || || |||||||| ||||||||||||
gtagatatacta-tcattatcattaaattcacacaatgactctgtttttcagccaaaatatattgataccagaatgcattgagtgtttttactttacctaataattgtctgtagGTACTTCTCTTATGAGCATTTTTATGTTATATACTGCAAATTTTGGGAGCTGGATACAGATCACGATTTCTTAATAGACAAAGAGAATCTTATCAGATAT

upper sequence: LOC_Os10g33680.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA20G35090.1 (Glycine max), 3'ss of exon 7
------acgaattacttggattca-agttatattatttatgtgcgaatcaaacaagattttttacattttttttccaaatgtgttaattttctgatgcctaatgcagATACTTCTCATACGAGCACTTTTATGTGATATACTGCAAATTTTGGGAGTTGGACACAGATCATGATTTTTTGATTGATAAAGAGAACCTTATCAGATAT
      | || | ||||  |||   | ||   || | | |||  ||||  ||    ||||| |   | |||||      |   |||||| ||| | |   | | ||| ||||||||||| ||||| |||||||| || |||||||||||||||||| | |||||||||||||| ||||| ||||||| |||||||||||| | ||||
aaattcatgattgactttcattttcaatttagttctctctgta-gaattgaa----attttct-tgtctttttatttgcttcattaattatcttacgga-atttcagGTACTTCTCATATGAGCATTTTTATGTCATTTACTGCAAATTTTGGGAGCTCGACACAGATCATGACTTTTTCATTGATAGAGAGAACCTTATTAAATAT

upper sequence: LOC_Os10g33680.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT1G03960.1 (Arabidopsis thaliana), 3'ss of exon 7
acgaattacttggat-tcaagttatattatttatgtgcgaatcaaacaagattttttacattttttttccaaatgtgttaattttctgatgcctaatg--cagATACTTCTCATACGAGCACTTTTATGTGATATACTGCAAATTTTGGGAGTTGGACACAGATCATGATTTTTTGATTGATAAAGAGAACCTTATCAGATAT
  ||  ||  ||  | |    |||||   |     |||   |  ||||  | || |  | |  |||| |||  ||   | || |  |      ||||   ||| |||||||| || |||||||| || |||||||||||||||||||||||  | ||    || ||||||| ||| |||||||| || || || |||| ||||
--gagctatatgagtattggcttataccttcatattgcttctgtaacagaacttat-gcctgattttaccatttgcaatcatgtcgtttcttttaattttcagGTACTTCTCCTATGAGCACTTCTACGTGATATACTGCAAATTTTGGGAACTTGATGGTGACCATGATTGTTTTATTGATAAGGACAATCTCATCAAATAT

upper sequence: LOC_Os10g33680.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT5G28850.1 (Arabidopsis thaliana), 3'ss of exon 6
acgaattacttggattcaagttatattatttatgtgcgaatcaaacaagattttttacattttttttccaaatgtgttaattttctgatgcctaatgcagATACTTCTCATACGAGCACTTTTATGTGATATACTGCAAATTTTGGGAGTTGGACACAGATCATGATTTTTTGATTGATAAAGAGAACCTTATCAGATAT
  | | |      |   || || |  ||||  |||       | |    ||| |||    |  |||  ||    | ||    ||    || | |||  |||||||||||||| ||||| || ||||| ||||||||||| || |||||| |||| || ||||| |||||  ||||||| ||||| || ||||| ||||||
--gtactgacaaaaacaaatttgtgctattgttgtat-----atatggtattgtttctgctcatttaacatgacttttctacttactttggcaaat--agATACTTCTCATATGAGCATTTCTATGTCATATACTGCAAGTTCTGGGAGCTGGATACGGATCACGATTTCCTGATTGACAAAGAAAATCTTATGAGATAT

upper sequence: LOC_Os10g33680.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT1G54450.1 (Arabidopsis thaliana), 3'ss of exon 7
acgaattacttggattcaagttatattatttatgtgcga-atcaaacaagattttttacattttttttccaaatgtgttaattttctgatgcctaatgcagATACTTCTCATACGAGCACTTTTATGTGATATACTGCAAATTTTGGGAGTTGGACACAGATCATGATTTTTTGATTGATAAAGAGAACCTTATCAGATAT
              ||   ||  ||  ||| ||  |  | || |||   |   || |  |    ||||   ||       | | |||  ||  || |  || |||||||| || || || || ||||| ||||||||||| || ||||||||||| |||||||||||||| || || || |||||||| || ||| |||||
-------------gttggtgtcttaagattaattagtaatatgaaattggtgcttattaacggcttttattaa------gactctctactgtttatt--agGTACTTCTCGTATGAACATTTCTATGTCATATACTGCAAGTTCTGGGAGTTGGATACAGATCATGATTTCTTAATCGACAAAGAGAATCTCATCCGATAT

upper sequence: LOC_Os10g33680.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT5G28900.1 (Arabidopsis thaliana), 3'ss of exon 7
acgaattacttggattcaagttatattatttatgtgcgaatcaaacaagattttttacattttttttccaaatgtg---ttaattttctgatgcctaatgca----gATACTTCTCATACGAGCACTTTTATGTGATATACTGCAAATTTTGGGAGTTGGACACAGATCATGATTTTTTGATTGATAAAGAGAACCTTATCAGATAT
              | |     | | |||||  |||| | |        |||| |   ||| ||||| |  || |    | | ||||||  |  ||   |||    |||||||||| || ||||| || ||||| ||||||||||| || |||||| |||| || ||||| |||||  ||||||| ||||| || |||||  |||||
-------------gtactgacaaaaatatttgcgtgctatt---gttgtatttatagtattgtttttgctcatttaacatcacttttctattcactttggcaattagATACTTCTCGTATGAGCATTTCTATGTCATATACTGCAAGTTCTGGGAGCTGGATACGGATCACGATTTCCTGATTGACAAAGAAAATCTTATGCGATAT

upper sequence: LOC_Os10g33680.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv07s0005g03730.t01 (Vitis vinifera), 3'ss of exon 8
acgaattacttggattcaagttatattatttatgtgcgaatcaaacaag---attttttacattttttttccaaatgtgttaattttctgatgcctaatgcagATACTTCTCATACGAGCACTTTTATGTGATATACTGCAAATTTTGGGAGTTGGACACAGATCATGATTTTTTGATTGATAAAGAGAACCTTATCAGATAT
   ||  ||   ||  ||  |     ||||| | |    || | |  |     || ||||   |  |         |     || |  | |   | | ||||| ||||| || || || ||||| ||||| ||||||||||| || |||||| ||||||||||||||||||| |||||||| |||||||| || |||||||||
---aacaacagagagacacatgcatatatttgttttattattagattaactagttatttatgatgatgaattgctaggccccatgtcttcacttcaactgcagGTACTTTTCTTATGAACACTTCTATGTTATATACTGCAAGTTCTGGGAGCTGGACACAGATCATGATTTCTTGATTGACAAAGAGAATCTCATCAGATAT

upper sequence: LOC_Os10g33680.1 (Oryza sativa), 3'ss of exon 7
lower sequence: PP1S7_163V6.1 (Physcomitrella patens), 3'ss of exon 7
--acgaattacttggattcaagttatattatttatgtgcgaatcaaacaagattttttacattttttttccaaatgtgttaattttctga-tgcctaatgcagATACTTCTCATACGAGCACTTTTATGTGATATACTGCAAATTTTGGGAGTTGGACACAGATCATGATTTTTTGATTGATAAAGAGAACCTTATCAGATAT
   |   || |    |   ||  || |||||       |||    | |   | ||| |  ||  | |  ||  | |  | ||| || | |  || |  ||||| ||||||||||| || || |||||||| ||||| ||||| || |||||| ||||  ||||||| |||||||| || || |||||  | ||  |  |||||
tatcagtttgccctcacgaaaagta-attatgataccacgacgtgagcttaagtttctg-atcatgtgcccttaggc-taaatattgtaagcgcttcgtgcagTTACTTCTCATATGAACATTTTTATGTCATATATTGCAAGTTCTGGGAGCTGGATTCAGATCACGATTTTTTAATAGACAAAGATGATCTCCTTCGATAT

upper sequence: LOC_Os10g33680.1 (Oryza sativa), 3'ss of exon 7
lower sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 7
---acgaattacttggattcaagttatattatt-tatgtgcgaatcaaacaagattttttacattttttttccaaatgtgttaattttctgatgcctaatgcagATACTTCTCATACGAGCACTTTTATGTGATATACTGCAAATTTTGGGAGTTGGACACAGATCATGATTTTTTGATTGATAAAGAGAACCTTATCAGATAT
     | ||  | |  ||  |||  | | |||  ||  |     | ||   || ||| |     | | | |  |      |  |  |  |   || |  ||||| ||||||||||| || || |||||||| ||||| |||||||| |||||| ||||  ||||||| || |||||||| || |||||  ||||| |  |||||
tattggcatgccctcaatagaag--acagtatggtacattgatgtgaatttaggtttctacttgtgtatctgtaggctcatccacgtaat--cgcttcgtgcagGTACTTCTCATATGAACATTTTTATGTCATATATTGCAAATTCTGGGAGCTGGATTCAGATCACGACTTTTTGATAGACAAAGATGACCTTCTTCGATAT

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: 56 (upstream exon), 61 (downstream exon)
Score: 19

CTGGAAATGGCCATCTTACCCTCAGAGAGCTAAAACGTGGGAATTTAATTGCTGCGATGCAGCAGCTGGATGAGGAAGAGGATATCAATAAAGTGTTGAGgtaattaaca ... cctaatgcagATACTTCTCATACGAGCACTTTTATGTGATATACTGCAAATTTTGGGAGTTGGACACAGATCATGATTTTTTGATTGATAAAGAGAACCTTATCAGATAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caagattttttacattttttttccaaatgtgttaattttctgatgcctaatgcagATACTTCTCATACGAGCACTTTTATGTGATATACTGCAAATTTTGGGAGTTGGACACAGATCATGATTTTTTGATTGATAAAGAGAACCTTATCAGATAT
                                            gcctaat  putative branch site (score: 19)
     ttttttacattttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acgaattacttggattcaagttatattatttatgtgcgaatcaaacaagattttttacattttttttccaaatgtgttaattttctgatgcctaatgcagATACTTCTCATACGAGCACTTTTATGTGATATACTGCAAATTTTGGGAGTTGGACACAGATCATGATTTTTTGATTGATAAAGAGAACCTTATCAGATAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - tatgtgc
- - - - - - - - - - - - - - - - - - - - - -aacaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtgtta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tctgatg