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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTGCTCCTTCGACGTTGTCTGGACAGCAAGGAGGGTCTTGAGACATACCCTGATATTGGTCATGCCGCCTTTGGCACCACTGGACGTATAGCAATCTCGgtaaaatctcttgtagatgatgatatttcaactgtatgcttcaggttatgcaaaaatgactgctcttgtgctaaccctttttccttgtatgtggctccactatctacag

Basic information

species Oryza sativa
transcript LOC_Os02g01100.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g01100.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G105192_T03 (Zea mays), 5'ss of exon 3
AGTGCTCCTTCGACGTTGTCTGGACAGCAAGGAGGGTCTTGAGACATACCCTGATATTGGTCATGCCGCCTTTGGCACCACTGGACGTATAGCAATCTCGgta------aaatc-----tcttgtagatgatgatat---ttcaa---ctgtatgcttcaggt----tatgcaaaaatgactgctcttgtgctaac---cctttttccttgtatgtggctccactatctacag
 |||||||| || || || ||||||||||||||||| |||||||||||||| |||||||||||||||||||||||  |||| || |||||||| ||||| |||      |||||     || | || || |  |      |||||   ||| |   ||    |    | || |   | || |||| |||| |||||   ||||||||||||| ||||| | | || | | |||
TGTGCTCCTGCGCCGCTGCCTGGACAGCAAGGAGGGCCTTGAGACATACCCAGATATTGGTCATGCCGCCTTTGGAGCCACCGGCCGTATAGCCATCTCAgtatggttcaaatcattaatcctataaataacaactgccattcaatttctgcacattttcaatatgatgtgaatggaggaatgcttttgtactaacttacctttttccttgtttgtggtttccctgt-tgcag

upper sequence: LOC_Os02g01100.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G134888_T01 (Zea mays), 5'ss of exon 3
AGTGCTCCTTCGACGTTGTCTGGACAGCAAGGAGGGTCTTGAGACATACCCTGATATTGGTCATGCCGCCTTTGGCACCACTGGACGTATAGCAATCTCGgtaaaatctcttgtagatgatgatat----ttcaactgtatgcttcaggttatgcaaaaatgactgctcttgtgctaac--cctttttccttgtatgtggctccactatctacag
 |||||||| || | ||| ||||||||||||||||| ||  |||||||||| |||||||| ||||| |||||||||| ||| || || ||||  ||||||||||| |||  |  |||| ||||||     || ||| ||  | ||    || |||  |         || |||||| ||  |  | |||||||| ||||||| | || |  |   
TGTGCTCCTGCGCCATTGCCTGGACAGCAAGGAGGGCCTCAAGACATACCCAGATATTGGCCATGCAGCCTTTGGCAGCACAGGCCGCATAGTTATCTCGgtaaa-tctgcttcagattatgatagcgaatttaaccgtgcgttttgttttctgcgca---------tcatgtgctgactactctgttccttgtttgtggcttcgctgttgaag-

upper sequence: LOC_Os02g01100.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA10G15130.1 (Glycine max), 5'ss of exon 1
AGTGCTCCTTCGACGTTGTCTGGACAGCAAGGAGGGTCTTGAGACATACCCTGATATTGGTCATGCCGCCTTTGGCACCACTGGACGTATAGCAATCTCGgtaa----------aatctc-----ttgtagatgatgatatttcaactgta--tgcttca--ggttatgcaaaaatgactgctcttgtgctaaccctttttccttgtatgtggctccactatctacag
  ||||| | ||    ||  |||| ||      ||||||||||||||||||||| ||||| || || || ||||| || ||||||||| |    ||||||||||          ||| ||     || |   |||  ||  || || | |   | |||||  |||||     |||  | |  |||    ||     | |||     | |     |    |   | |||
GTTGCTCTTGCGTTACTGCTTGGATAGTGCACCGGGTCTTGAGACATACCCTGACATTGGCCAAGCAGCTTTTGGTACTACTGGACGTGTCATCATCTCGgtaattcttgctcaaatatccttaattttgtttgaatatgctttaatttttctttcttcaacggttaatttcaaagcattagtctctaactggtattgtttttcaattttctctttttgtggatgcag

upper sequence: LOC_Os02g01100.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA20G32260.1 (Glycine max), 5'ss of exon 4
AGTGCTCCTTCGACGTTGTCTGGACAGCAAGGAGGGTCTTGAGACATACCCTGATATTGGTCATGCCGCCTTTGGCACCACTGGACGTATAGCAATCTCGgtaaaatctcttgtagatgatgatatttcaactgtatgcttcaggt--tatgcaaaaatgac-tgctcttgtgctaaccctttttccttgtatgtggctccactatctacag
  ||||  | ||    ||  |||||||  |    |  ||||||||||||||||||||||| || || || ||||| || ||||||||||| || || || ||||    || ||  |||    |  | | |  || |   | || ||  ||| |     | || ||   |  ||  || |   | |  |   || |  |              
GCTGCTTTTGCGTTCCTGCTTGGACAGTGAACCTGAGCTTGAGACATACCCTGATATTGGCCAAGCTGCTTTTGGTACTACTGGACGTATTGCCATTTCAgtaagtcatcatgctgatctctac-tcttatttgaagtgtccatgtcctatccgtttctcacatgtattcatgtcaaacacatgtattaaaatatcacaat-----------

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|88574161|gb|CI665930.1|CI665930
EST:     CTGATATTGGTCATGCCGCCTTTGGCACCACTGGACGTATAGCAATCTCG                         ATAATCCTGTACATCGAACTGTAT
genomic: CTGATATTGGTCATGCCGCCTTTGGCACCACTGGACGTATAGCAATCTCGgtaaaatctc ... ctatctacagATAATCCTGTACATCGAACTGTAT
EST: gi|88327908|gb|CI648307.1|CI648307
EST:     CTGATATTGGTCATGCCGCCTTTGGCACCACTGGACGTATAGCAATCTCG                         ATAATCCTGTACATCGAACTGTAT
genomic: CTGATATTGGTCATGCCGCCTTTGGCACCACTGGACGTATAGCAATCTCGgtaaaatctc ... ctatctacagATAATCCTGTACATCGAACTGTAT

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: 48 (upstream exon), 28 (downstream exon)
Score: 1

AGTGCTCCTTCGACGTTGTCTGGACAGCAAGGAGGGTCTTGAGACATACCCTGATATTGGTCATGCCGCCTTTGGCACCACTGGACGTATAGCAATCTCGgtaaaatctc ... ctatctacagATAATCCTGTACATCGAACTGTAT




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