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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGGTTAGGTCTCCGAGCCTCCGACCTTCCGATTCCTCTCCGCCGGCAGCCATGTCAGGTCGCGAGGTCCGCGAGTACACGAATCTCAGCGACCCCAAAGgtttgcgattccggcgcatccttccttcttcccggtttattattctcccccattgatgttctgtgcgctttcggttgttcaatattgattttgggttctgcag

Basic information

species Oryza sativa
transcript LOC_Os02g42540.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g42540.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G146786_T01 (Zea mays), 5'ss of exon 1
-----AGGGTTAGGTCTCCGAGCCTCCGACCTTCCGATTCCTCTCCGCCGGCAGCCATGTCAGGTCGCGAGGTCCGCGAGTACACGAATCTCAGCGACCCCAAAGgtttgcgattccggcgcatccttccttcttcccggtttattattctcccccattgatgttctgtgcgctttcggttgttcaatattgattttgggt-tctgcag
      |    |||  |  |      || ||| |||     ||  |  |  |||||||||| || |||||||||||||||||||| ||||||||||||||||||||| ||||  |||  |   |  ||  |   |     |    | || |||||  | |  |||||        |||  |   | |  |||  |  | |  | |||||
CGTTCGGAACCAGGGTTAGGGTTTCGCGTCCTCCCG-----TCGTCATCCTCAGCCATGTCCGGGCGCGAGGTCCGCGAGTACACCAATCTCAGCGACCCCAAAGgtgtgcgcctccttccactgatttatcgatttgcctaccctgttttccccgttgggcgttct------catcgaattcccgagtttggctccgtgcatgtgcag
















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|88338650|gb|CI644107.1|CI644107
EST:     CATGTCAGGTCGCGAGGTCCGCGAGTACACGAATCTCAGCGACCCCAAAG                         ATAGGAAGTGGGGGAAGGGGAAGGACAAGATTGATGATGAGGACATCACCT
genomic: CATGTCAGGTCGCGAGGTCCGCGAGTACACGAATCTCAGCGACCCCAAAGgtttgcgatt ... ggttctgcagATAGGAAGTGGGGGAAGGGGAAGGACAAGATTGATGATGAGGACATCACCT
EST: gi|88331773|gb|CI640804.1|CI640804
EST:     CATGTCAGGTCGCGAGGTCCGCGAGTACACGAATCTCAGCGACCCCAAAG                         ATAGGAAGTGGGGGAAGGGGAAGGACAAGATTGATGATGAGGACATCACCT
genomic: CATGTCAGGTCGCGAGGTCCGCGAGTACACGAATCTCAGCGACCCCAAAGgtttgcgatt ... ggttctgcagATAGGAAGTGGGGGAAGGGGAAGGACAAGATTGATGATGAGGACATCACCT
EST: gi|88331772|gb|CI640803.1|CI640803
EST:     CATGTCAGGTCGCGAGGTCCGCGAGTACACGAATCTCAGCGACCCCAAAG                         ATAGGAAGTGGGGGAAGGGGAAGGACAAGATTGATGATGAGGACATCACCT
genomic: CATGTCAGGTCGCGAGGTCCGCGAGTACACGAATCTCAGCGACCCCAAAGgtttgcgatt ... ggttctgcagATAGGAAGTGGGGGAAGGGGAAGGACAAGATTGATGATGAGGACATCACCT
EST: gi|88381604|gb|CI682270.1|CI682270
EST:     CATGTCAGGTCGCGAGGTCCGCGAGTACACGAATCTCAGCGACCCCAAAG                         ATAGGAAGTGGGGGAAGGGGAAGGACAAGATTGATGATGAGGACATCACCT
genomic: CATGTCAGGTCGCGAGGTCCGCGAGTACACGAATCTCAGCGACCCCAAAGgtttgcgatt ... ggttctgcagATAGGAAGTGGGGGAAGGGGAAGGACAAGATTGATGATGAGGACATCACCT
EST: gi|88330892|gb|CI638300.1|CI638300
EST:     CATGTCAGGTCGCGAGGTCCGCGAGTACACGAATCTCAGCGACCCCAAAG                         ATAGGAAGTGGGGGAAGGGGAAGGACAAGATTGATGATGAGGACATCACCT
genomic: CATGTCAGGTCGCGAGGTCCGCGAGTACACGAATCTCAGCGACCCCAAAGgtttgcgatt ... ggttctgcagATAGGAAGTGGGGGAAGGGGAAGGACAAGATTGATGATGAGGACATCACCT
EST: gi|88571094|gb|CI662467.1|CI662467
EST:     CATGTCAGGTCGCGAGGTCCGCGAGTACACGAATCTCAGCGACCCCAAAG                         ATAGGAAGTGGGGGAAGGGGAAGGACAAGATTGATGATGAGGACATCACCT
genomic: CATGTCAGGTCGCGAGGTCCGCGAGTACACGAATCTCAGCGACCCCAAAGgtttgcgatt ... ggttctgcagATAGGAAGTGGGGGAAGGGGAAGGACAAGATTGATGATGAGGACATCACCT
EST: gi|88453631|gb|CI682502.1|CI682502
EST:     CATGTCAGGTCGCGAGGTCCGCGAGTACACGAATCTCAGCGACCCCAAAG                         ATAGGAAGTGGGGGAAGGGGAAGGACAAGATTGATGATGAGGACATCACCT
genomic: CATGTCAGGTCGCGAGGTCCGCGAGTACACGAATCTCAGCGACCCCAAAGgtttgcgatt ... ggttctgcagATAGGAAGTGGGGGAAGGGGAAGGACAAGATTGATGATGAGGACATCACCT
EST: gi|88324974|gb|CI644986.1|CI644986
EST:     CATGTCAGGTCGCGAGGTCCGCGAGTACACGAATCTCAGCGACCCCAAAG                         ATAGGAAGTGGGGGAAGGGGAAGGACAAGATTGATGATGAGGACATCACCT
genomic: CATGTCAGGTCGCGAGGTCCGCGAGTACACGAATCTCAGCGACCCCAAAGgtttgcgatt ... ggttctgcagATAGGAAGTGGGGGAAGGGGAAGGACAAGATTGATGATGAGGACATCACCT
EST: gi|88576151|gb|CI670296.1|CI670296
EST:     CATGTCAGGTCGCGAGGTCCGCGAGTACACGAATCTCAGCGACCCCAAAG                         ATAGGAAGTGGGGGAAGGGGAAGGACAAGATTGATGATGAGGACATCACCT
genomic: CATGTCAGGTCGCGAGGTCCGCGAGTACACGAATCTCAGCGACCCCAAAGgtttgcgatt ... ggttctgcagATAGGAAGTGGGGGAAGGGGAAGGACAAGATTGATGATGAGGACATCACCT
EST: gi|27547521|gb|CA765797.2|CA765797
EST:     CATGTCAGGTCGCGAGGTCCGCGAGTACACGAATCTCAGCGACCCCAAAG                         ATAGGAAGTGGGGGAAGGGGAAGGACAAGATTGATGATGAGGACATCACCT
genomic: CATGTCAGGTCGCGAGGTCCGCGAGTACACGAATCTCAGCGACCCCAAAGgtttgcgatt ... ggttctgcagATAGGAAGTGGGGGAAGGGGAAGGACAAGATTGATGATGAGGACATCACCT
EST: gi|88501795|gb|CI695478.1|CI695478
EST:     CATGTCAGGTCGCGAGGTCCGCGAGTACACGAATCTCAGCGACCCCAAAG                         ATAGGAAGTGGGGGAAGGGGAAGGACAAGATTGATGATGAGGACATCACCT
genomic: CATGTCAGGTCGCGAGGTCCGCGAGTACACGAATCTCAGCGACCCCAAAGgtttgcgatt ... ggttctgcagATAGGAAGTGGGGGAAGGGGAAGGACAAGATTGATGATGAGGACATCACCT
EST: gi|88341833|gb|CI642977.1|CI642977
EST:     CATGTCAGGTCGCGAGGTCCGCGAGTACACGAATCTCAGCGACCCCAAAG                         ATAGGAAGTGGGGGAAGGGGAAGGACAAGATTGATGATGAGGACATCACCT
genomic: CATGTCAGGTCGCGAGGTCCGCGAGTACACGAATCTCAGCGACCCCAAAGgtttgcgatt ... ggttctgcagATAGGAAGTGGGGGAAGGGGAAGGACAAGATTGATGATGAGGACATCACCT
EST: gi|33810840|gb|CF331311.1|CF331311
EST:     CATGTCAGGTCGCGAGGTCCGCGAGTACACGAATCTCAGCGACCCCAAAG                         ATAGGAA--GGGGGAAGGGGAAGGACAAGATTGATGATGAGGACATCACCT
genomic: CATGTCAGGTCGCGAGGTCCGCGAGTACACGAATCTCAGCGACCCCAAAGgtttgcgatt ... ggttctgcagATAGGAAGTGGGGGAAGGGGAAGGACAAGATTGATGATGAGGACATCACCT
EST: gi|88320199|gb|CI672378.1|CI672378
EST:     CATGTCAGGTCGCGAGGTCCGCGAGTACACGAATCTCAGCGACCCCAAAG                         ATAGGAAGTGGGGGAAGGGGAAGGACAAGATTGATGATGAGGACATCACCT
genomic: CATGTCAGGTCGCGAGGTCCGCGAGTACACGAATCTCAGCGACCCCAAAGgtttgcgatt ... ggttctgcagATAGGAAGTGGGGGAAGGGGAAGGACAAGATTGATGATGAGGACATCACCT

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: 68 (upstream exon), 71 (downstream exon)
Score: 9

AGGGTTAGGTCTCCGAGCCTCCGACCTTCCGATTCCTCTCCGCCGGCAGCCATGTCAGGTCGCGAGGTCCGCGAGTACACGAATCTCAGCGACCCCAAAGgtttgcgatt ... ggttctgcagATAGGAAGTGGGGGAAGGGGAAGGACAAGATTGATGATGAGGACATCACCTTCCAGCGCATGGTCGCAAAG




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