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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgactagcaatttaaattcatctgaatattacagacctgagataaatgctactatttgttttaagtattgaacagttgattaactgcaattctttctagGGACATACATTGACAAGAAGTGCCCATTCACTGGAACTGTTTCTATCAGAGGCAGAATCATTGCTGGAACATGCCACAGTGCCAAGATGAACAGAACTAT

Basic information

species Oryza sativa
transcript LOC_Os07g37780.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g37780.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G044800_T02 (Zea mays), 3'ss of exon 3
ttgactagcaatttaaattcatctgaatattacagacctgagataaatgctactatttgttttaagtattgaacagttgattaactgcaattctttc-tagGGACATACATTGACAAGAAGTGCCCATTCACTGGAACTGTTTCTATCAGAGGCAGAATCATTGCTGGAACATGCCACAGTGCCAAGATGAACAGAACTAT
  |  ||  |    || | |    | | || | |    ||   | | |  |  ||||| ||  | || |||| ||| | |||||      ||    |  |||||| |||||||||||||| |||||||||||||||||||||||||||||||||||||| |||||||| |||||||||||||| |||||||||||||||||
gaggatatgatcccaagtactatggcacatgaaaacattgcatttattagtgatatttcttgcatgtgttga-cagatcattaatatttgtttgcccacagGGACCTACATTGACAAGAAATGCCCATTCACTGGAACTGTTTCTATCAGAGGCAGAATTATTGCTGGGACATGCCACAGTGCTAAGATGAACAGAACTAT

upper sequence: LOC_Os07g37780.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G019325_T01 (Zea mays), 3'ss of exon 3
ttgactagcaatttaaattcatctgaatattacag-acctgagataaatgctactatttgttttaagtattgaaca-gttgattaactgcaattctttct--------agGGACATACATTGACAAGAAGTGCCCATTCACTGGAACTGTTTCTATCAGAGGCAGAATCATTGCTGGAACATGCCACAGTGCCAAGATGAACAGAACTAT
         |    ||||||  |  | || ||  | ||||||    |||||  ||||| ||  |   | ||| |   ||| |  ||    || | | | |        |||||| |||||||||||||| || |||||||||||||| |||||||||||||||||||| ||||||||||||||||||||||| |||||||||||||| ||
--------gaccccaaattc--ccaagtactatggcacctgaaggcaatgcatctattagtgatgtttcttgcatgtgttaacaaatattaaatgtctgtttgcgtacagGGACCTACATTGACAAGAAATGTCCATTCACTGGAACCGTTTCTATCAGAGGCAGAATTATTGCTGGAACATGCCACAGTGCTAAGATGAACAGAACCAT

upper sequence: LOC_Os07g37780.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA17G11430.1 (Glycine max), 3'ss of exon 3
ttgactagcaatttaaattcatctgaatattacagacctgagataaatgctactatttgttttaagtattgaacagttgattaactgcaattctttc---tagGGACATACATTGACAAGAAGTGCCCATTCACTGGAACTGTTTCTATCAGAGGCAGAATCATTGCTGGAACATGCCACAGTGCCAAGATGAACAGAACTAT
 | | |    || |||| |   ||   || |            || ||| |  | | |||||  |     |  |  |||||| | |    || |||     ||| || |||||||||||||||||||| |||||||| | |||||| ||| | ||| | ||| | ||||||||||| |||||||| ||||||||||| |||||
-tcatt--tcatataaaatgtcctagctaatctctcttatgtgtatatggtcgtttctgtttctaaatcaggtcttttgatttattattcttttttaatacagGAACCTACATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATCCGTGGCCGTATCTTGGCTGGAACATGTCACAGTGCTAAGATGAACAGGACTAT

upper sequence: LOC_Os07g37780.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA13G23400.2 (Glycine max), 3'ss of exon 3
ttgactagcaatttaaattcatctgaatattacagacctgagataaatgctactattt--gttttaagtattgaacagttgattaactgcaattctt---tctagGGACATACATTGACAAGAAGTGCCCATTCACTGGAACTGTTTCTATCAGAGGCAGAATCATTGCTGGAACATGCCACAGTGCCAAGATGAACAGAACTAT
   |||    || | || | | ||   |||| |   |   |  |  |||     ||||  | ||| |     |     |||||| | |     | ||   |  ||| || || ||||||||||||||||| |||||||| | |||||| ||| | ||| | ||| | ||||||||||| |||||||| ||||||||||| |||||
---act--tcatatcaaatgacctagttatttctctctgtacctgtatgtggtcatttctgcttttaaaccagttgttttgatttattattccttttgaatacagGAACCTATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATCCGTGGCCGTATCTTGGCTGGAACATGTCACAGTGCTAAGATGAACAGGACTAT

upper sequence: LOC_Os07g37780.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA09G12420.1 (Glycine max), 3'ss of exon 3
ttgactagcaatttaaat---tcatctgaatattacagacctgagataaatgctactatttgttttaagtattgaacagttgattaactgcaattctttctagGGACATACATTGACAAGAAGTGCCCATTCACTGGAACTGTTTCTATCAGAGGCAGAATCATTGCTGGAACATGCCACAGTGCCAAGATGAACAGAACTAT
 | ||   ||  || | |    ||| ||   |||            ||  || |    | |||||  |  ||        || ||   | |    |  |  ||| ||||| ||||||||||||||||| |||||||| | |||||| ||  | ||  | ||| | || || || || |||||||| |||||||  || || ||
gtaaccttcaccttcactattccatttgggcattttc--ttctgtctatttggtgacttctgtttccaa-atcatggtcctgctttttttcccccccatacagGAACATATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATTCGGGGTCGTATCCTAGCCGGTACTTGTCACAGTGCTAAGATGACAAGGACCAT

upper sequence: LOC_Os07g37780.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT5G23740.1 (Arabidopsis thaliana), 3'ss of exon 3
ttgactagcaatttaaattcatctgaatattacagacctgagataaatgctactatttgttttaagtattg-aacagttgat-taactgcaattctttctagGGACATACATTGACAAGAAGTGCCCATTCACTGGAACTGTTTCTATCAGAGGCAGAATCATTGCTGGAACATGCCACAGTGCCAAGATGAACAGAACTAT
 ||| || ||  | |      | ||  |     ||   |||   |||  | |  |||||    | || ||| ||   ||||| |   |    |       |||  | ||||||||||  || || |||||||||||||| ||||||||||||||  | ||| | ||||| || |||||||||||||||||| | ||||| ||
-tgaatatca-ctgagtgctgtttgctttgattaggtttgaagcaaaaccgaaaatttgagagatgttttgtaatctttgatatgtttattgtgtggaacagGAGCTTACATTGACAGTAAATGTCCATTCACTGGAACCGTTTCTATCAGAGGACGTATCTTAGCTGGTACTTGCCACAGTGCCAAGATGCAGAGAACCAT

upper sequence: LOC_Os07g37780.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT3G48930.1 (Arabidopsis thaliana), 3'ss of exon 3
ttgactagcaatttaaattcat--ctgaatattacagacctgagataaatgctactatttgttttaagtattgaacagttgattaac-tgcaattctttc---tagGGACATACATTGACAAGAAGTGCCCATTCACTGGAACTGTTTCTATCAGAGGCAGAATCATTGCTGGAACATGCCACAGTGCCAAGATGAACAGAACTAT
      |   |||| |||   |     |   | | |||     |    || || |||| |   || |     ||      | |||   || | || | |     |||  | ||| |||||||||| ||||| ||||||||||||||||| || |||||  | ||| | ||||| || ||||||||||| || ||| | || || ||
-----cactgatttgaatatgtgatcaagcttcatagaaacctgcatcattct-ctatatacctttaagtcagattctcaggttattgtgtatttgtgtggaacagGAGCTTACGTTGACAAGAAATGCCCCTTCACTGGAACTGTTTCCATTAGAGGTCGTATCTTAGCTGGTACTTGCCACAGTGCGAAAATGCAGAGGACCAT

upper sequence: LOC_Os07g37780.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv11s0118g00680.t01 (Vitis vinifera), 3'ss of exon 3
-ttgactagcaatttaaattcatctgaatattacagacctgagataaatgctactatttgttttaagtattgaacagttga-ttaactgcaattctttc-tagGGACATACATTGACAAGAAGTGCCCATTCACTGGAACTGTTTCTATCAGAGGCAGAATCATTGCTGGAACATGCCACAGTGCCAAGATGAACAGAACTAT
 ||||| | ||||| | |    | |    |||    | || || |  |  || |  ||  |      |  |||   |||   ||   ||   ||   |   ||| || || ||||| ||||| ||||| |||||||| ||||||||||| || ||| | ||| | ||||| || ||||| |||||||||||||  || || ||
gttgac-accaattcagaaaagtattctaattggctagctaagcttta-actgcc-ttcatgagcgatgctgacttgttcccttcgttgttgtttggtaacagGTACTTATATTGATAAGAAATGCCCCTTCACTGGCACTGTTTCTATTAGGGGCCGCATCTTAGCTGGCACTTGCCATAGTGCCAAGATGATGAGGACCAT

upper sequence: LOC_Os07g37780.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv04s0008g06220.t01 (Vitis vinifera), 3'ss of exon 3
-ttgactagcaatttaaattcatctgaatattacagacctgagataaatgctactatttgttttaagtattg-aacagttgattaactgcaattctttctagGGACATACATTGACAAGAAGTGCCCATTCACTGGAACTGTTTCTATCAGAGGCAGAATCATTGCTGGAACATGCCACAGTGCCAAGATGAACAGAACTAT
    | |||  ||||  |   |||  |||   |  | ||  |  | | |     |  ||||  |   |||   ||      | |||||     | ||   ||| ||||||||||||||||| || || |||||||||  |||||||||||| ||| | ||  ||||||| || ||||||||||| |||||||  || || ||
gcaaagtag--attttgagaaatcacaatgcaagcgcccaaatctgactctgtatgcttgtcatgtttataacaatgaactaataacttttgctattggcagGAACATACATTGACAAGAAATGTCCGTTCACTGGAGGTGTTTCTATCAGGGGCCGTATTCTTGCTGGTACTTGCCACAGTGCGAAGATGATGAGGACCAT

upper sequence: LOC_Os07g37780.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S30_89V6.1 (Physcomitrella patens), 3'ss of exon 3
ttgactagcaatttaaattcatctgaatattacagacctgagataaatg--ctactatttgttttaagtattgaacagttgattaactgcaattctttc-tagGGACATACATTGACAAGAAGTGCCCATTCACTGGAACTGTTTCTATCAGAGGCAGAATCATTGCTGGAACATGCCACAGTGCCAAGATGAACAGAACTAT
 | |  | ||      |  ||  ||          |||   | ||  ||   || ||||     | | || | |    |   | |||| |   |||     ||| || |||||||||||||||||||||||||| |||  ||| || ||  | ||| | ||  |  | |||||     || |  | || ||||   | |||||
-ttatgaacagagcgcaggcaggtgttcgggttcaacccaggctatgtgacttaatattctccatcattacttat--atctgtgaactactcctctcctgcagGCACCTACATTGACAAGAAGTGCCCATTCACCGGAGATGTGTCCATTCGCGGCCGCATTCTCACCGGAACCGTGAACTGCACAAAAATGACTCGCACTAT

upper sequence: LOC_Os07g37780.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S21_269V6.1 (Physcomitrella patens), 3'ss of exon 3
---ttgactagcaatttaaattcatctgaatattacagacctgagataaatgctactattt-gttttaagtattgaacagttgattaactgcaattctttctagGGACATACATTGACAAGAAGTGCCCATTCACTGGAACTGTTTCTATCAGAGGCAGAATCATTGCTGGAACATGCCACAGTGCCAAGATGAACAGAACTAT
    ||  ||| |  | ||||  |||  ||  || ||     | | |  |||  | | ||  ||  |  ||  |||    | |      | | |  ||||| ||| || |||||||||||||||||||||||||| |||  ||| || ||  ||||| | ||| |  |||||||     || |  |||||||||   | || ||
ttcatgcttag-acgtaaaataaatcccaaggttgca--ttagggtttgatgtgaatgttgagtgatctgtgctgagatctcgggagtgttctaaactttc-agGCACCTACATTGACAAGAAGTGCCCATTCACCGGAGATGTCTCCATTCGAGGCCGCATCCTAACTGGAACTGTGAACTGCACCAAGATGACTCGCACCAT

upper sequence: LOC_Os07g37780.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S51_307V6.1 (Physcomitrella patens), 3'ss of exon 3
ttgactagcaatttaaattcat---ctgaatattacagacctgagataaatgctactatttgttttaagtattgaacagttgattaactgcaattct--ttctagGGACATACATTGACAAGAAGTGCCCATTCACTGGAACTGTTTCTATCAGAGGCAGAATCATTGCTGGAACATGCCACAGTGCCAAGATGAACAGAACTAT
   | |||| ||  |  ||| |   ||     ||  |   ||  || |       ||| ||   | |     | |    ||||  ||  |||   ||  |  |||| |||||||| |||||||||||||| |||||||||  |||||||||| ||||  | ||| || | |||||   | || |  | || |||| | | || ||
--tagtagccatcgagtttcgtgacctagggtttggatttctttgaaacggatgtctagtttcctcactccctaa---tttgaggaagggcacccctgctattagGTACATACATCGACAAGAAGTGCCCCTTCACTGGAGATGTTTCTATCCGAGGGCGCATCCTTACCGGAACTGTCAACTGCACTAAAATGACCCGTACGAT

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: 75 (upstream exon), 75 (downstream exon)
Score: 237

TCAAAGAAGTCTGGCAAGGGTAAGAAGCCAGGCAAGGGTGGCAACCGCTTCTGGAAGAGCATTGGCCTTGGCTTCAAGACCCCCAGGGAAGCAATTGAAGgtacaatagg ... ttctttctagGGACATACATTGACAAGAAGTGCCCATTCACTGGAACTGTTTCTATCAGAGGCAGAATCATTGCTGGAACATGCCACAGTGCCAAGATGAACAGAACTAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgctactatttgttttaagtattgaacagttgattaactgcaattctttctagGGACATACATTGACAAGAAGTGCCCATTCACTGGAACTGTTTCTATCAGAGGCAGAATCATTGCTGGAACATGCCACAGTGCCAAGATGAACAGAACTAT
                                 gattaac  putative branch site (score: 237)
                                             ttctttct  putative PPT
        tatttgttttaagtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgactagcaatttaaattcatctgaatattacagacctgagataaatgctactatttgttttaagtattgaacagttgattaactgcaattctttctagGGACATACATTGACAAGAAGTGCCCATTCACTGGAACTGTTTCTATCAGAGGCAGAATCATTGCTGGAACATGCCACAGTGCCAAGATGAACAGAACTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG