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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTTCTGTCTACACGTGCTGGTGGGCTTGGTATTAATCTTGCAACAGCAGATACCGTGATCATTTTTGATTCAGACTGGAATCCGCAAAATGATTTACAGgttcccctctctctctctctctctcatatatgggttttcaatttttgtcttgaaagagtttctcatatttcgggtttttgaatgtgtgatgtcatgctag

Basic information

species Oryza sativa
transcript LOC_Os07g46590.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g46590.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G010342_T01 (Zea mays), 5'ss of exon 18
TCTTCTGTCTACACGTGCTGGTGGGCTTGGTATTAATCTTGCAACAGCAGATACCGTGATCATTTTTGATTCAGACTGGAATCCGCAAAATGATTTACAGgttcc-cctctctctctctctctctcatatatgggttttcaatttttgtcttgaaagagtttctcatatttcgggtttttgaatgtgtgatgtcatgctag-----------------------------------
                              ||||||||||||||| |||||||| ||||| |||||||||||||| |||||||| ||||||||| | |||||||  ||||||  |||||  |||    |  || || |  || ||        ||||| ||  | || |||    | |||  |||  | |  |  ||||||                                   
------------------------------TATTAATCTTGCAACTGCAGATACAGTGATAATTTTTGATTCAGATTGGAATCCACAAAATGATCTGCAGGTTCTTCCTCTCATTCTCTTCCTCCTGCAAgtgtgtgtctaactt------aaaaagatttatttatctttattatgtttttatggttcaatttttgctaggccatgagtagggcacataggattggccaacagga

upper sequence: LOC_Os07g46590.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G141258_T01 (Zea mays), 5'ss of exon 22
TCTTCTGTCTACACGTGCTGGTGGGCTTGGTATTAATCTTGCAACAGCAGATACCGTGATCATTTTTGATTCAGACTGGAATCCGCAAAATGATTTACAGgttcccctctctctctctctct---ctcatatatgggttttcaatttttgtcttgaaagagtttctcatatttcgggtttttgaatgtgtgatgtcatgctag
|||| | || |||||||| || || |||||||||||||| ||||| |||||||| ||||| |||||||||||||| |||||||| ||||||||||| ||||||| | ||||||||| || |    ||| |  | | |  ||    |||    |   |||| || || || ||||   | |||     | ||   ||||     
TCTTTTATCCACACGTGCCGGAGGACTTGGTATTAATCTAGCAACTGCAGATACAGTGATAATTTTTGATTCAGATTGGAATCCACAAAATGATTTGCAGgttctcttctctctctttcccctcgctcctggaagtgagtttgtgtttaacttgtgaagatttccttatctttcctatgtttcttaatatggc-tcatttc--

upper sequence: LOC_Os07g46590.1 (Oryza sativa), 5'ss of exon 8
lower sequence: Vv06s0009g03750.t01 (Vitis vinifera), 5'ss of exon 19
TCTTCTGTCTACACGTGCTGGTGGGCTTGGTATTAATCTTGCAACAGCAGATACCGTGATCATTTTTGATTCAGACTGGAATCCGCAAAATGATTTACAGgttccc-ctctctctctctctctctcatatatgggttttcaatttttgtcttgaaagagtttctcatatttcgggtttttgaatgtgtgatgtcatgctag
 || || || || ||||||||||| || || ||||| |||||||| ||||| || || || || |||||||| ||||||||||| |||||||| |||||||||    ||   | || ||   | |  |      |||    || ||| |||      | ||   | ||||   | ||| || |   |              
CCTCCTTTCAACCCGTGCTGGTGGCCTGGGCATTAACCTTGCAACTGCAGACACAGTTATTATATTTGATTCTGACTGGAATCCCCAAAATGACTTACAGgttttgactggatgtcccttagtttggtcatgtagttggttatatttttctc-----aattatacttattatagctttatgcactag--------------

upper sequence: LOC_Os07g46590.1 (Oryza sativa), 5'ss of exon 8
lower sequence: PP1S93_123V6.1 (Physcomitrella patens), 5'ss of exon 20
TCTTCTGTCTACACGTGCTGGTGGGCTTGGTATTAATCTTGCAACAGCAGATACCGTGATCATTTTTGATTCAGACTGGAATCCGCAAAATGATTTACAGgttcccctctc-----tctctctctctctcatatatgg-gttttcaat---ttttgt-----cttgaaagagtttctcatat-----ttcgggtttttgaat-gtgtgatgtcatgctag---------------------------------------------
  |  |||| ||||| ||||||||  | || ||||||||||| || |||||||| || || || || ||||| || |||||||| || |||||| |||||||   | ||       | |  |   ||   ||| |||  || ||  ||    | |||     ||| |   |  |  | | ||      | | ||| || ||  || || | | |   |                                               
CTTATTGTCAACACGAGCTGGTGGTTTAGGCATTAATCTTGCCACTGCAGATACTGTCATTATATTCGATTCGGATTGGAATCCTCAGAATGATCTACAGgtctgcttcctgaaggttttacctgcttaaatagatgaagtgttgtatgcgctatgtaaaaacttaatgaatctgtttaaatggatgctagagttcttcaaccgtctgctttaacatttctttggagtaataactgcatttttctgaaaagcttgtttcctgcag

upper sequence: LOC_Os07g46590.1 (Oryza sativa), 5'ss of exon 8
lower sequence: PP1S317_10V6.1 (Physcomitrella patens), 5'ss of exon 20
TCTTCTGTCTACACGTGCTGGTGGGCTTGGTATTAATCTTGCAACAGCAGATACCGTGATCATTTTTGATTCAGACTGGAATCCGCAAAATGATTTACAGgttcccctctct----ctctctctctctcatatatgggttttcaatttt--tgtcttgaaagagtttctcatatttcgggtt--tttgaatgtgtgatgtcatgctag----------------------------------------------------------------------
  | || ||||| |||||||||||  | || ||||||||||| || ||||| || || || || ||||| || || |||||||| || |||||||||||||||  || |  |       |  ||  || |  || |    |  | | ||  | |  || | | |||    | || | |||    |||   ||     |||  |   ||                                                                      
CTTACTATCTACCCGTGCTGGTGGTTTGGGAATTAATCTTGCTACCGCAGACACTGTCATTATATTTGACTCGGATTGGAATCCCCAGAATGATTTACAGgtttgcccccttaaaatgttaccttcctaagttaagtacatgaagtattgatatactgtatgcgttaagtagatgttgggagaattttgttgcaaactgttgttgcagctcttttgccgcgggcttgaacgttttgttacgaaacaagtgcatgtgctgagaggtttgtttcctgcag

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|58694189|gb|CK082876.1|CK082876
EST:     ATACCGTGATCATTTTTGATTCAGACTGGAATCCGCAAAATGATTTACAG                         GCAATGAGTAGGGCACACAGGATTGGGCAACAAGAAACTGTTAACATATAT
genomic: ATACCGTGATCATTTTTGATTCAGACTGGAATCCGCAAAATGATTTACAGgttcccctct ... gtcatgctagGCAATGAGTAGGGCACACAGGATTGGGCAACAAGAAACTGTTAACATATAT
EST: gi|88453014|gb|CI574561.1|CI574561
EST:     ATACCGTGATCATTTTTGATTCAGACTGGAATCCGCAAAATGATTTACAG                         GCAATGAGTAGGGCACACAGGATTGGGCAACAAGAAACTGTTAACATATAT
genomic: ATACCGTGATCATTTTTGATTCAGACTGGAATCCGCAAAATGATTTACAGgttcccctct ... gtcatgctagGCAATGAGTAGGGCACACAGGATTGGGCAACAAGAAACTGTTAACATATAT
EST: gi|88412791|gb|CI576055.1|CI576055
EST:     ATACCGTGATCATTTTTGATTCAGACTGGAATCCGCAAAATGATTTACAG                         GCAATGAGTAGGGCACACAGGATTGGGCAACAAGAAACTGTTAACATATAT
genomic: ATACCGTGATCATTTTTGATTCAGACTGGAATCCGCAAAATGATTTACAGgttcccctct ... gtcatgctagGCAATGAGTAGGGCACACAGGATTGGGCAACAAGAAACTGTTAACATATAT

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: 58 (upstream exon), 74 (downstream exon)
Score: 31

TCTTCTGTCTACACGTGCTGGTGGGCTTGGTATTAATCTTGCAACAGCAGATACCGTGATCATTTTTGATTCAGACTGGAATCCGCAAAATGATTTACAGgttcccctct ... gtcatgctagGCAATGAGTAGGGCACACAGGATTGGGCAACAAGAAACTGTTAACATATATCGTTTCGTGACATGCAAAAGTGTTGAAGAGGATATATTGGAACGTGCAA




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