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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGGAGGAGAACAGCCGCCTCAAGGACGAGCTCATGCTCAAGACGCGAGAGCTTGACAGATTCgtaagcggctccccgatctgcccttttcctctccgtctcttcttctccacccgaatctcaccttacaataatatggagtacatccgcatcgcacaactaactaactaactaactagtactgcaacactcgtcggaggtactagtattgatttgcattcatctgctgctctgccag

Basic information

species Oryza sativa
transcript LOC_Os05g01060.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g01060.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G104377_T02 (Zea mays), 5'ss of exon 2
CTGGAGGAGAACAGCCGCCTCAAGGACGAGCTCATGCTCAAGACGCGAGAGCTTGACAGATTCgtaagcggctccccgatctgcccttttcctctccgtctcttcttctccacccgaatctcaccttacaataatatggagtacatccgcatcgcacaactaactaactaactaactagtactgcaacactcgtcgg-aggtactagtattgatttgcat-tcatctgctgctctgccag
|||||||||||||||||  | ||||||||||| |||||||||||||| |||||  ||||| | ||||||   | |  ||| |   |    | || |  ||          ||  | ||||  |   |   |     || || ||| |  || | ||  | |  ||   |     |  | | |     || | | |   ||  |||| | | | | | | | |||||| |  |    ||||
CTGGAGGAGAACAGCCGGTTGAAGGACGAGCTGATGCTCAAGACGCGGGAGCTCCACAGAATTgtaagcacattc--gatttcgacgccccttcccgatc----------caaacaaatcatatactcttaactagtgcagcacagc-acaactcatcatttcctttttgctctatca-tgccattccatttgcctatagaaactaatgt-gctgtacgtctcatctccgacctaaccag
















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|88302566|gb|CI668412.1|CI668412
EST:     GCCGCCTCAAGGACGAGCTCATGCTCAAGACGCGAGAGCTTGACAGATTC                         AGGTCAGAGGCTACCAAGCCCACTTCTCTTGCCGACACCTTTTCAACTTCT
genomic: GCCGCCTCAAGGACGAGCTCATGCTCAAGACGCGAGAGCTTGACAGATTCgtaagcggct ... gctctgccagAGGTCAGAGGCTACCAAGCCCACTTCTCTTGCCGACACCTTTTCAACTTCT
EST: gi|88393943|gb|CI684210.1|CI684210
EST:     GCCGCCTCAAGGACGAGCTCATGCTCAAGACGCGAGAGCTTGACAGATTC                         AGGTCAGAGGCTACCAAGCCCAC
genomic: GCCGCCTCAAGGACGAGCTCATGCTCAAGACGCGAGAGCTTGACAGATTCgtaagcggct ... gctctgccagAGGTCAGAGGCTACCAAGCCCAC
EST: gi|88372382|gb|CI619712.1|CI619712
EST:     GCCGCCTCAAGGACGAGCTCATGCTCAAGACGCGAGAGCTTGACAGATTC                         AGGTCAGAGGCTACCAAGCCCACTTCTCTTGCCGACAC
genomic: GCCGCCTCAAGGACGAGCTCATGCTCAAGACGCGAGAGCTTGACAGATTCgtaagcggct ... gctctgccagAGGTCAGAGGCTACCAAGCCCACTTCTCTTGCCGACAC
EST: gi|88409673|gb|CI568963.1|CI568963
EST:     GCCGCCTCAAGGACGAGCTCATGCTCAAGACGCGAGAGCTTGACAGATTC                         AGGTCAGAGGCTACCAAGCCCACTTCTCTTGCCGACACCTTTTCAACTTCT
genomic: GCCGCCTCAAGGACGAGCTCATGCTCAAGACGCGAGAGCTTGACAGATTCgtaagcggct ... gctctgccagAGGTCAGAGGCTACCAAGCCCACTTCTCTTGCCGACACCTTTTCAACTTCT
EST: gi|88349232|gb|CI678207.1|CI678207
EST:     GCCGCCTCAAGGACGAGCTCATGCTCAAGACGCGAGAGCTTGACAGATTC                         AGGTCAGAGGCTAC
genomic: GCCGCCTCAAGGACGAGCTCATGCTCAAGACGCGAGAGCTTGACAGATTCgtaagcggct ... gctctgccagAGGTCAGAGGCTAC
EST: gi|88358406|gb|CI606915.1|CI606915
EST:     GACGCCTCAAGGACGAGCTCATGCTCAAGACGCGAGAGCTTGACAGATTC                         AGGTCAGAGGCTACCAAGCC-ACTTCTCTTGCGGACACCTTTTCAACTTCT
genomic: GCCGCCTCAAGGACGAGCTCATGCTCAAGACGCGAGAGCTTGACAGATTCgtaagcggct ... gctctgccagAGGTCAGAGGCTACCAAGCCCACTTCTCTTGCCGACACCTTTTCAACTTCT
EST: gi|88333795|gb|CI643827.1|CI643827
EST:     GCCGCCTCAAGGACGAGCTCATGCTCAAGACGCGAGAGCTTGACAGATTC                         AGGTCAGAGGCTACCAAGCCC
genomic: GCCGCCTCAAGGACGAGCTCATGCTCAAGACGCGAGAGCTTGACAGATTCgtaagcggct ... gctctgccagAGGTCAGAGGCTACCAAGCCC
EST: gi|88310594|gb|CI672453.1|CI672453
EST:     GCCGCCTCAAGGACGAGCTCATGCTCAAGACGCGAGAGCTTGACAGATTC                         AGGTCAGAGGCTACCAAGC
genomic: GCCGCCTCAAGGACGAGCTCATGCTCAAGACGCGAGAGCTTGACAGATTCgtaagcggct ... gctctgccagAGGTCAGAGGCTACCAAGC

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: 66 (upstream exon), 39 (downstream exon)
Score: 9

CTGGAGGAGAACAGCCGCCTCAAGGACGAGCTCATGCTCAAGACGCGAGAGCTTGACAGATTCgtaagcggct ... gctctgccagAGGTCAGAGGCTACCAAGCCCACTTCTCTTGCCGACACCTTTTCAACTTCTCCCCATGGGACCTCAACATGCTTCGGTACCACTTCCTCGTCGCTCAATT




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGGAGGAGAACAGCCGCCTCAAGGACGAGCTCATGCTCAAGACGCGAGAGCTTGACAGATTCgtaagcggctccccgatctgcccttttcctctccgtctcttcttctccacccgaatctcaccttacaataatatggagtacatccgcatcgcacaactaactaactaactaactagtactgcaacactcgtcggaggtactagtattgatttgcattcatctgctgctctgccag

- - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - GAGCTT