Skip to another splice site:
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATTGTCCTGGAAACAGAAGGAAGTGTGATAGCTGAAAAGGTGTCAGCACATGGAATAGAAGGTGCTACTTCACTCGCTGAGCAGgtaagttttagccatgatcttactaaaggaagctgttcggtttaaccaaacataacgagttattgctctctgaatgcag

Basic information

species Oryza sativa
transcript LOC_Os05g38610.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g38610.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM5G883149_T03 (Zea mays), 5'ss of exon 5
GATTGTCCTGGAAACAGAAGGAAGTGTGATAGCTGAAAAGGTGTCAGCACATGGAATAGAAGGTGCTACTTCACTCGCTGAGCAGgtaagttttagccatgatct--------tactaaaggaagctgttcggtttaaccaaacataacgagttattgctctctgaatgcag
|||||| || |||||||||||||| | |||||||||||||||||| |  || |||   || ||||||   |||   |||||||||||| | |  || |   ||||        |  |||  ||||    | |||||     ||| || | || ||| | | | ||  |||||
GATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAAGGTGTCTGGTCACGGATCGGAGGGTGCT---TCATCGGCTGAGCAGgtaggctgcaggctgtatctatttcaaattttaactgaagaaact-ggtttcttttaactta-ctagctatcgttatttgcgtgcag

upper sequence: LOC_Os05g38610.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM5G883149_T02 (Zea mays), 5'ss of exon 3
------------------GATTGTCCTGGAAACAGAAGGAAGTGTGATAGCTGAAAAGGTGTCAGCACATGGAATAGAAGGTGCTACTTCACTCGCTGAGCAGgtaagttttagccatgatct--------tactaaaggaagctgttcggtttaaccaaacataacgagttattgctctctgaatgcag
                  |||||| || |||||||||||||| | |||||||||||||||||| |  || |||   || ||||||   |||   |||||||||||| | |  || |   ||||        |  |||  ||||    | |||||     ||| || | || ||| | | | ||  |||||
TTCTGAATGATTACACAGGATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAAGGTGTCTGGTCACGGATCGGAGGGTGCT---TCATCGGCTGAGCAGgtaggctgcaggctgtatctatttcaaattttaactgaagaaact-ggtttcttttaactta-ctagctatcgttatttgcgtgcag

upper sequence: LOC_Os05g38610.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G431350_T02 (Zea mays), 5'ss of exon 3
------------------GATTGTCCTGGAAACAGAAGGAAGTGTGATAGCTGAAAAGGTGTCAGCACATGGAATAGAAGGTGCTACTTCACTCGCTGAGCAGgtaagttttagccatgatct-------tactaaaggaagctgttcggtttaaccaaacataacgagttattgctctctgaatgcag
                  |||||| || |||||||||||||| | |||||||||||||||||| | ||||||| | || ||||||   |||   |||||||||||| | |  || |   ||||       |  | ||   |       |||||     ||| || | || ||| | | | ||  |||||
TCTTGAATGATTACACAGGATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAAGGTGTCTGGACATGGATTGGAGGGTGCT---TCATCAGCTGAGCAGgtaggctgcaggctgcatctattccaattttgaactgaagaaactggtttcttttaactta-ctagctatcgttatttgcttgcag

upper sequence: LOC_Os05g38610.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G431350_T03 (Zea mays), 5'ss of exon 4
GATTGTCCTGGAAACAGAAGGAAGTGTGATAGCTGAAAAGGTGTCAGCACATGGAATAGAAGGTGCTACTTCACTCGCTGAGCAGgtaagttttagccatgatct-------tactaaaggaagctgttcggtttaaccaaacataacgagttattgctctctgaatgcag
|||||| || |||||||||||||| | |||||||||||||||||| | ||||||| | || ||||||   |||   |||||||||||| | |  || |   ||||       |  | ||   |       |||||     ||| || | || ||| | | | ||  |||||
GATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAAGGTGTCTGGACATGGATTGGAGGGTGCT---TCATCAGCTGAGCAGgtaggctgcaggctgcatctattccaattttgaactgaagaaactggtttcttttaactta-ctagctatcgttatttgcttgcag

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|58696220|gb|CK084907.1|CK084907
EST:     AAAGGTGTCAGCACATGGGAATAGAAGGTGCTACTTCACTCGCTGAGCAG                         ACTATAGTTCAAGCCC
genomic: AAAGGTGTCAGCACATGG-AATAGAAGGTGCTACTTCACTCGCTGAGCAGgtaagtttta ... ctgaatgcagACTATAGTTCAAGCCC
EST: gi|88983146|gb|CI020710.1|CI020710
EST:     AAAAGGTGTCAGCACATGGAATAGAAGGTGCTACTTCACTCGCTGAGCAG                         ACTATAGTTCAAGCCCTAACAACAGCAAGAGAGCACTTGACCAAATCTCTT
genomic: AAAAGGTGTCAGCACATGGAATAGAAGGTGCTACTTCACTCGCTGAGCAGgtaagtttta ... ctgaatgcagACTATAGTTCAAGCCCTAACAACAGCAAGAGAGCACTTGACCAAATCTCTT
EST: gi|88528858|gb|CI457130.1|CI457130
EST:     CACTCGGTGAGCAG                         ACTATAGTTCAAGCCCTAACAACAGCAAGAGAGCACTTGACCAAATTTCTT
genomic: CACTCGCTGAGCAGgtaagtttta ... ctgaatgcagACTATAGTTCAAGCCCTAACAACAGCAAGAGAGCACTTGACCAAATCTCTT
EST: gi|88531910|gb|CI458431.1|CI458431
EST:     AAAAGGTGTCAGCACATGGAATAGAAGGTGCTACTTCACTCGCTGAGCAG                         ACTATAGTTCAAGCCCTAACAACAGCAAGAGAGCACTTGACCAAATCTCTT
genomic: AAAAGGTGTCAGCACATGGAATAGAAGGTGCTACTTCACTCGCTGAGCAGgtaagtttta ... ctgaatgcagACTATAGTTCAAGCCCTAACAACAGCAAGAGAGCACTTGACCAAATCTCTT
EST: gi|33692847|gb|CF321086.1|CF321086
EST:     AAAAGGTGTCAGCACATGGAATAGAAGGTGCTACTTCACTCGCTGAGCAG                         ACTATAGTTCAAGCCCTAACAACAGCAAGAGAGCACTTGACCAAATCTCTT
genomic: AAAAGGTGTCAGCACATGGAATAGAAGGTGCTACTTCACTCGCTGAGCAGgtaagtttta ... ctgaatgcagACTATAGTTCAAGCCCTAACAACAGCAAGAGAGCACTTGACCAAATCTCTT
EST: gi|396941400|gb|HO188609.1|HO188609
EST:     AAAAGGTGTCAGCACATGGAATAGAAGGTGCTACTTCACTCGCTGAGCAG                         ACTATAGTTCAAGCCCTAACAACAGCAAGAGAGCACTTGACCAAATCTCTT
genomic: AAAAGGTGTCAGCACATGGAATAGAAGGTGCTACTTCACTCGCTGAGCAGgtaagtttta ... ctgaatgcagACTATAGTTCAAGCCCTAACAACAGCAAGAGAGCACTTGACCAAATCTCTT
EST: gi|88531919|gb|CI458441.1|CI458441
EST:     AAAAGGTGTCAGCACATGGAATAGAAGGTGCTACTTCACTCGCTGAGCAG                         ACTATAGTTCAAGCCCTAACAACAGCAAGAGAGCACTTGACCAAATCTCTT
genomic: AAAAGGTGTCAGCACATGGAATAGAAGGTGCTACTTCACTCGCTGAGCAGgtaagtttta ... ctgaatgcagACTATAGTTCAAGCCCTAACAACAGCAAGAGAGCACTTGACCAAATCTCTT
EST: gi|33692848|gb|CF321087.1|CF321087
EST:     AAAAGGTGTCAGCACATGGAATAGAAGGTGCTACTTCACTCGCTGAGCAG                         ACTATAGTTCAAGCCCTAACAACAGCAAGAGAGCACTTGACCAAATCTCTT
genomic: AAAAGGTGTCAGCACATGGAATAGAAGGTGCTACTTCACTCGCTGAGCAGgtaagtttta ... ctgaatgcagACTATAGTTCAAGCCCTAACAACAGCAAGAGAGCACTTGACCAAATCTCTT
EST: gi|88839775|gb|CI015866.1|CI015866
EST:     AAAAGGTGTCAGCACATGGAATAGAAGGTGCTACTTCACTCGCTGAGCAG                         ACTATAGTTCAAGCCCTAACAACAGCAAGAGAGCACTTGACCAAATCTCTT
genomic: AAAAGGTGTCAGCACATGGAATAGAAGGTGCTACTTCACTCGCTGAGCAGgtaagtttta ... ctgaatgcagACTATAGTTCAAGCCCTAACAACAGCAAGAGAGCACTTGACCAAATCTCTT
EST: gi|8857691|gb|AU095009.1|AU095009
EST:     AAAAGGTGTCAGCACATGGAATAGAAGGTGCTACTTCACTCGCTGAGCAG                         ACTATAGTTCAAGCCCTAACAACAGCAAGAGAGCACTTGACCAAATCTCTT
genomic: AAAAGGTGTCAGCACATGGAATAGAAGGTGCTACTTCACTCGCTGAGCAGgtaagtttta ... ctgaatgcagACTATAGTTCAAGCCCTAACAACAGCAAGAGAGCACTTGACCAAATCTCTT
EST: gi|88480576|gb|CI417847.1|CI417847
EST:     AAAAGGTGTCAGCACATGGAATAGAAGGTGCTACTTCACTCGCTGAGCAG                         ACTATAGTTCAAGCCCTAACAACAGCAAGAGAGCACTTGACCAAATCTCTT
genomic: AAAAGGTGTCAGCACATGGAATAGAAGGTGCTACTTCACTCGCTGAGCAGgtaagtttta ... ctgaatgcagACTATAGTTCAAGCCCTAACAACAGCAAGAGAGCACTTGACCAAATCTCTT
EST: gi|86868980|gb|CI334352.1|CI334352
EST:     TGTCAGCACATGGAATAGAAGGTGCTACTTCACTCGCTGAGCAG                         AATATAGTTCAAGCCCTAACAACAGCAAGAGAGCACTTGACCAAATCTCTT
genomic: TGTCAGCACATGGAATAGAAGGTGCTACTTCACTCGCTGAGCAGgtaagtttta ... ctgaatgcagACTATAGTTCAAGCCCTAACAACAGCAAGAGAGCACTTGACCAAATCTCTT
EST: gi|88541797|gb|CI471090.1|CI471090
EST:     AAAAGGTGTCAGCACATGGAATAGAAGGTGCTACTTCACTCGCTGACCAG                         ACTATAGTTCAAGCCCTAACAACAGCAAGAGAGCACTTGACCAAATCTCTT
genomic: AAAAGGTGTCAGCACATGGAATAGAAGGTGCTACTTCACTCGCTGAGCAGgtaagtttta ... ctgaatgcagACTATAGTTCAAGCCCTAACAACAGCAAGAGAGCACTTGACCAAATCTCTT
EST: gi|29682909|gb|CB679184.1|CB679184
EST:     AAAAGGTGTCAGCACATGGAATAGAAGGTGCTACTTCACTCGCTGAGCAG                         ACTATAGTTCAAGCCCTAACAACAGCAAGAGAGCACTTGACCAAATCTCTT
genomic: AAAAGGTGTCAGCACATGGAATAGAAGGTGCTACTTCACTCGCTGAGCAGgtaagtttta ... ctgaatgcagACTATAGTTCAAGCCCTAACAACAGCAAGAGAGCACTTGACCAAATCTCTT
EST: gi|88526854|gb|CI454945.1|CI454945
EST:     GGTGCTACTTCACTCGCTGAGCAG                         ACTATAGTTCAAGCCCTAACAACAGCAAGAGAGCACTTGACCAAATCTCTT
genomic: GGTGCTACTTCACTCGCTGAGCAGgtaagtttta ... ctgaatgcagACTATAGTTCAAGCCCTAACAACAGCAAGAGAGCACTTGACCAAATCTCTT
EST: gi|33820857|gb|CF336233.1|CF336233
EST:     AAAAGGTGTCAGCACATGGAATAGAAGGTGCTACTTCACTCGCTGAGCAG                         ACTATAGTTCAAGCCCTAACAACAGCAAGAGAGCACTTGACCAAATCTCTT
genomic: AAAAGGTGTCAGCACATGGAATAGAAGGTGCTACTTCACTCGCTGAGCAGgtaagtttta ... ctgaatgcagACTATAGTTCAAGCCCTAACAACAGCAAGAGAGCACTTGACCAAATCTCTT
EST: gi|163918457|gb|EG713211.1|EG713211
EST:     AAAAGGTGTCAGCACATGGAATAGAAGGTGCTACTTCACTCGCTGAGCAG                         ACTATAGTTCAAGCCCTAACAACAGCAAGAGAGCACTTGACCAAATCTCTT
genomic: AAAAGGTGTCAGCACATGGAATAGAAGGTGCTACTTCACTCGCTGAGCAGgtaagtttta ... ctgaatgcagACTATAGTTCAAGCCCTAACAACAGCAAGAGAGCACTTGACCAAATCTCTT
EST: gi|88535403|gb|CI464201.1|CI464201
EST:     AGGTGGTACTTCACTCGCTGAGCAG                         ACTATAGTTCAAGCCCTAACAACAGCAAGAGAGCACTTGACCAAATCTCTT
genomic: AGGTGCTACTTCACTCGCTGAGCAGgtaagtttta ... ctgaatgcagACTATAGTTCAAGCCCTAACAACAGCAAGAGAGCACTTGACCAAATCTCTT
EST: gi|88524799|gb|CI453746.1|CI453746
EST:     AAAGGGTGTCAGCACATGGAATAGAAGGTGGTACTTCACTCNCTGAGCAG                         ACTATAGTTCAAGCCCTAACAACAGCAAGAGAGCACTTGACCAAATCTCTT
genomic: AAA-GGTGTCAGCACATGGAATAGAAGGTGCTACTTCACTCGCTGAGCAGgtaagtttta ... ctgaatgcagACTATAGTTCAAGCCCTAACAACAGCAAGAGAGCACTTGACCAAATCTCTT
EST: gi|218500698|gb|FG952590.1|FG952590
EST:     AAAAGGTGTCAGCACATGGAATAGAAGGTGCTACTTCACTCGCTGAGCAG                         ACTATAGTTCAAGCCCTAACAACAGCAAGAGAGCACTTGACCAAATCTCTT
genomic: AAAAGGTGTCAGCACATGGAATAGAAGGTGCTACTTCACTCGCTGAGCAGgtaagtttta ... ctgaatgcagACTATAGTTCAAGCCCTAACAACAGCAAGAGAGCACTTGACCAAATCTCTT
EST: gi|88531839|gb|CI460354.1|CI460354
EST:     AAAAGGTGTCAGCACATGGAATAGAAGGTGCTACTTCACTCGCTGAGCAG                         ACTATAGTTCAAGCCCTAACAACAGCAAGAGAGCACTTGACCAAATCTCTT
genomic: AAAAGGTGTCAGCACATGGAATAGAAGGTGCTACTTCACTCGCTGAGCAGgtaagtttta ... ctgaatgcagACTATAGTTCAAGCCCTAACAACAGCAAGAGAGCACTTGACCAAATCTCTT
EST: gi|88533791|gb|CI460457.1|CI460457
EST:     AAAAGGTGTCAGCACATGGAATAGAAGGTGCTACTTCACTCGCTGAGCAG                         ACTATAGTTCAAGCCCTAACAACAGCAAGAGAGCACTTGACCAAATCTCTT
genomic: AAAAGGTGTCAGCACATGGAATAGAAGGTGCTACTTCACTCGCTGAGCAGgtaagtttta ... ctgaatgcagACTATAGTTCAAGCCCTAACAACAGCAAGAGAGCACTTGACCAAATCTCTT
EST: gi|88383090|gb|CI538118.1|CI538118
EST:     AAAAGGTGTCAGCACATGGAATAGAAGGTGCTACTTCACTCGCTGAGCAG                         ACTATAGTTCAAGCCCTAACAACAGCAAGAGAGCACTTGACCAAATCTCTT
genomic: AAAAGGTGTCAGCACATGGAATAGAAGGTGCTACTTCACTCGCTGAGCAGgtaagtttta ... ctgaatgcagACTATAGTTCAAGCCCTAACAACAGCAAGAGAGCACTTGACCAAATCTCTT
EST: gi|88545337|gb|CI474890.1|CI474890
EST:     GGTGTCAGCACATGGAATAGAAGGTGCTACTTCACTCGCTGAGCAG                         ACTATAGTTCAAGCCCTAACAACAGCAAGAGAGCACTTGACCAAATTTCTT
genomic: GGTGTCAGCACATGGAATAGAAGGTGCTACTTCACTCGCTGAGCAGgtaagtttta ... ctgaatgcagACTATAGTTCAAGCCCTAACAACAGCAAGAGAGCACTTGACCAAATCTCTT

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: 72 (upstream exon), 66 (downstream exon)
Score: 13

GATTGTCCTGGAAACAGAAGGAAGTGTGATAGCTGAAAAGGTGTCAGCACATGGAATAGAAGGTGCTACTTCACTCGCTGAGCAGgtaagtttta ... ctgaatgcagACTATAGTTCAAGCCCTAACAACAGCAAGAGAGCACTTGACCAAATCTCTTCTTATGTGATGTGCTCTGCTTTTGGAGCTGAAGATGGAGTAGCATCCCG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATTGTCCTGGAAACAGAAGGAAGTGTGATAGCTGAAAAGGTGTCAGCACATGGAATAGAAGGTGCTACTTCACTCGCTGAGCAGgtaagttttagccatgatcttactaaaggaagctgttcggtttaaccaaacataacgagttattgctctctgaatgcag

- - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG