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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_Os10g40555.1
intron # 4
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

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|58607388|gb|CK035421.1|CK035421
EST:     CTGATTCGAGTGGTCAGCATGTGGAATGTATCAGGTCCACTGATTCAGAG                         GGTAAAGAGGTCAACCTCTTCCAACCTGCAAGTGAGTTTTTACCTATGATC
genomic: CTGATTCGAGTGGTCAGCATGTGGAATGTATCAGGTCCACTGATTCAGAGgtgcaacagc ... tggctcatagGGTAAAGAGGTCAACCTCTTCCAACCTGCAAGTGAGTTTTTACCTATGATT