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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATTACGCTGGAAGTCATGGAATGGATATCATGGGGCCTGTTAGGAAGTCTGATTCGAGTGGTCAGCATGTGGAATGTATCAGGTCCACTGATTCAGAGgtgcaacagctttgttgattttttccacagacaaatttctctcttgtgacaaaattctaattagttattgctttttggctcatag

Basic information

species Oryza sativa
transcript LOC_Os10g40550.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g40550.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G178546_T01 (Zea mays), 5'ss of exon 5
---GTATTACGCTGGAAGTCATGGAATGGATATCATGGGGCCTGTTAGGAAGTCT---GATTCGAGTGGTCAGCATGTGGAATGTATCAGGTCCACTGATTCAGAGgtgcaacagctttgttgattttttccacagac--aaatttctctcttgtgacaaaattctaattagttattgctt-tttggctcatag
   ||| ||||||||||| ||||||||||| || ||||| |||||||||||| ||   || || | |||       |||||||||||  |||| ||||||    | ||| |||  |||| | ||| ||| ||    |   |||| | |  ||||        |  || |  ||   | ||| |    ||| |||
ATTGTACTACGCTGGAAGCCATGGAATGGACATAATGGGCCCTGTTAGGAAGACTACTGACTCCAATGG------CGTGGAATGTATTCGGTCAACTGATGTGCATgtgaaactactttctagatctttaccctcaatttaaatgttttacttgctt-----tcttagtgtgtatcttcttatcctcctcgtag

upper sequence: LOC_Os10g40550.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA09G36570.1 (Glycine max), 5'ss of exon 5
---GTATTACGCTGGAAGTCATGGAATGGATATCATGGGGCCTGTTAGGAAGTCTGATTCGAGTGGTCAGCATGTGGAATGTATCAGGTCCACTGATTCAGAGgtgcaacagctttgttgattttttccacagac--------aaatttctctcttgtgacaaaattctaattagttattgctttt--tggctcatag--------------------
    ||||||||||| |||||||||||||| ||||| || ||||||||  | ||||  ||   || | | ||  |  | || || ||||| || ||     |||| ||     ||    | || | ||  ||  |         ||| |||||||          ||||  | | ||||| | ||   |||||  |                      
ACTTTATTACGCTGGTAGTCATGGAATGGACATCATTGGCCCTGTTAGACAATCTGTATC---TGATAATCACCTAAATTGCATTAGGTCTACAGACAAGCAGgtacagggagttgaaagtttctatctgcaatctgttttgtgaatatctctctcact-ttctgttctcttgaattatttcattaaatggcttctgttattatctttaaatttacag

upper sequence: LOC_Os10g40550.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA12G00790.1 (Glycine max), 5'ss of exon 5
---GTATTACGCTGGAAGTCATGGAATGGATATCATGGGGCCTGTTAGGAAGTCTGATTCGAGTGGTCAGCATGTGGAATGTATCAGGTCCACTGATTCAGAGgtgc---------aacagctttgt---tgattttttccacagacaaatttctctcttgtgacaaaattctaattagttattgctttt--tggctcatag--------------------
    ||||| ||||| |||||||||||||| ||||| |||||||||||  | ||||  ||   || | | ||     | || || ||||| || ||     |||| |         ||    | | |   |||| | ||  |   | |  | |||| |||          | |  | | |||||   ||   |||||  |                      
ACTCTATTATGCTGGTAGTCATGGAATGGACATCATTGGGCCTGTTAGACAATCTGTATC---TGATAATCACCCAAATTGCATTAGGTCTACAGACAAGCAGgtactgggagttgaaagtttctatctgtgatctgttttatgaatatctctctcactttctgttct-ctttcttgaattattttattaaatggcttctgttattatctttaaatttacag

upper sequence: LOC_Os10g40550.1 (Oryza sativa), 5'ss of exon 6
lower sequence: PP1S47_110V6.1 (Physcomitrella patens), 5'ss of exon 5
------GTATTACGCTGGAAGTCATGGAATGGATATCATGGGGCCTGTTAGGAAGTC---TGATTC--GAGTGGTCAGCATGTGGAATGTATCAGGTCCACTGATTCAGAGgtgcaacagctttgttgattttttc-cacagac--aaatttctctcttgtgacaaaattctaattagttattgc-----tttttggctcatag-----------------------------------------------
      ||| || ||||||||||||||||||||||| ||||| ||||  |  |  ||   || ||    |||   | | |   |   |  |          || ||   |  |   |    |||| | |||||  | || || |  || ||| | | ||||  |    |  |  | |  || ||      | | | |||  |||                                               
GGAGTTGTACTATGCTGGAAGTCATGGAATGGATATAATGGGTCCTGCAAAAAGTTCAAGTGGTTTTAAAGTCAACGGAACTCGAGTTAAAGACAAGAAGgtggtttttaattttcaagtttttgataattttaactcaaagtcttaattttttttattgtttctctctgtttgtaaactaatgaacatatatgtcgctagtaggttattcgaatcgtccgctccttctaacaatgattgttactgttcag

upper sequence: LOC_Os10g40550.1 (Oryza sativa), 5'ss of exon 6
lower sequence: PP1S46_31V6.1 (Physcomitrella patens), 5'ss of exon 5
------GTATTACGCTGGAAGTCATGGAATGGATATCATGGGGCCTGTTAGGAAGTCTGATTCGAGTGGTCAGCATGTGGAATGTATCAGGTCCACTGATTCAGAGgtgc-----aacagctttgttgattttttcc-----------acagacaaatttctctcttgtgacaaaattctaattagttattgctttttggctcatag-------------------------------
       |||||||||||||||||||| |||||||||||||| ||||  | ||       |||   |||  | |  ||| |  | || | ||| |  ||     ||||       |  || ||| |||   ||||             |  || || ||||| | ||       |        || | |  | | |||| ||  |||                               
AGAACTATATTACGCTGGAAGTCATGGCATGGATATCATGGGACCTGCAAAGAG------TTCAGATGGGTATCGAGTGAAGGGAATAAAGTCTAGAGACAAGAAGgtatcttttagaagtttttttggacttttatggttgagtgtaaatgataattttctttgttccatttgatcgaccgatattcagcgttgtttgccttctagtgtcttactgttactggtatttgttttgcag

upper sequence: LOC_Os10g40550.1 (Oryza sativa), 5'ss of exon 6
lower sequence: PP1S141_116V6.1 (Physcomitrella patens), 5'ss of exon 4
------GTATTACGCTGGAAGTCATGGAATGGATATCATGGGGCCTGTTAGGAAGTC---TGATTC--GAGTGGTCAGCATGTGGAATGTA----------TCAGGTCCAC----TGATTCAGAGgtgcaa---cagctttg---ttgattttttccacagacaaatttctctcttgtgacaaaattctaattagttattgctttttggctcatag---------------
      ||| ||||| |||||||||||||||||||| ||||| ||||  |  |  ||   || ||    |||   | | |   |   |  |          | || ||||     ||| | | |    |||   ||  | ||     |||   |  |||      || | ||  | || |    ||| |||||   || | ||  ||    || ||               
GGAATTGTACTACGCGGGAAGTCATGGAATGGATATAATGGGTCCTGCGAAAAGTTCAAGTGGTTTTAAAGTCAACGGAACTCGAGTTAAAGACAAGAAGgtgagttccatgacttgacttatactgccaagttcatatctgagaccgatacatgacacctgtgtatatgtccttcgtaagcttattttaattgtctactcctgctta---caaagattttctttgcacag

upper sequence: LOC_Os10g40550.1 (Oryza sativa), 5'ss of exon 6
lower sequence: PP1S333_42V6.1 (Physcomitrella patens), 5'ss of exon 4
------GTATTACGCTGGAAGTCATGGAATGGATATCATGGGGCCTGTTAGGAAGTCTGATTCGAGTGGTCAGCATGTGGAATGTATCAGGTCCACTGATTCAGAGgtgcaacagctttgttgattttttccacagacaaatttctctcttgtgacaaaattctaattagttattgctttttggctcatag-------------------------------------------------
       ||||||||||| |||||||| ||||| |||||||||||||  |       ||  ||   ||||   | |||| || | |||| | |||  |||    ||||   | |  | |  ||  | | | |  ||     |     |  |||     ||   |  ||  | |  | | |  |      ||                                                 
AGAATTATATTACGCTGGGAGTCATGGTATGGACATCATGGGGCCTGCGAA------TGGCTCCGATGGTTTTCGTGTGAAAGGAATCAAGGCCAGAGATAAGAAGgtattaaaattct--tgtatctgttcgtagttgtgtgagcatactgtacttgaagattttttgttcaaggatctgagatggtgagctggttatcctctttttgacatctaatcttcatccttttttgtctacag

upper sequence: LOC_Os10g40550.1 (Oryza sativa), 5'ss of exon 6
lower sequence: PP1S227_48V6.1 (Physcomitrella patens), 5'ss of exon 4
------GTATTACGCTGGAAGTCATGGAATGGATATCATGGGGCCTGTTAGGAAGTCTGAT-----TCGAGT---GGTCAGCATGTGGAATG-TATCAGGTCCACTGATTCAGA-Ggtgcaacagctttgttgatttt-----ttccacagacaaattt---ctctcttgtgacaaaattctaattagttattgctttttggctcatag-------------------
      |||||||||||| |||||||| |||||||||||||| |||| ||  |  || |||      |||||   ||  | || ||  |  | ||  |||    ||  |   ||     || || || | |  | |       ||| | | |  | | |    |    |   |   |  |  ||     | |  ||| |||||| ||                     
AGAACTGTATTACGCTGGGAGTCATGGCATGGATATCATGGGCCCTGCTAAAAGCTCGGATGGTTTCCGAGTTAAGGGTACCAAGTCTAGGGATAAAAGGgtatctattcttgataacccagcaactatttgaaatagcccaattcgataaaatagtatggatttctgtacaatcgatgttcaaccgtgtttgccttcttggctaatcttatttacttcaccttgcag

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: 57 (upstream exon), 60 (downstream exon)
Score: 12

GTATTACGCTGGAAGTCATGGAATGGATATCATGGGGCCTGTTAGGAAGTCTGATTCGAGTGGTCAGCATGTGGAATGTATCAGGTCCACTGATTCAGAGgtgcaacagc ... tggctcatagGGTAAAGAGGTCAACCTCTTCCAACCTGCAAGTGAGTTTTTACCTATGATTAGCGAG




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