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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaccccggttgaaactcaacgaaattcgtcaccgggatcctttccccccccccccccccctcaccggattcttgagtttctcgcgcttgtttcgctcaccatgtcttggttggggttctctgatctctctccctcttctgtagAGATTCGACCGGGCTCGCCGGTTCGCGCCGGCCGCCGCCATGTCGACGTCGTCGGGGCCGAAGGAGGCGCCGGCAAACAACCCGGGCCTCCAGGCGCCGT

Basic information

species Oryza sativa
transcript LOC_Os05g22970.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g22970.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G125310_T01 (Zea mays), 3'ss of exon 1
gtaaccccggttgaaactcaacgaaattcgtcaccgggatcctttccccccccccccccccctcaccg--gattcttgagtttctcgcgcttgtttcgctcaccatgtcttggttggggttctctgatctctctccctcttctgtagAGATTCGACCGGGCTCGCCGGTTCGCGCCGGCCGCCGCCATGTCGACGTCGTCGGGGCCGAAGGAGGCGCCGGCAAACAACCCGGGCCTCCAGGC-GCCGT--
                                    |   | | | ||   |            |  |  |||| | | |  | |||| |  ||||| ||||||||  |  | | ||  || |||              ||  |||||||||||| |||| |||||||||||||||   |||||||||| |||| || || || || ||||||||||| || || ||||| || |||||| | |  ||  
------------------------------------gtcccgtgttccgtactggaggatttggattgatgattatggtgactttcgctcaggtttcactcaccattccccgttgggaattttcttga-----------tttcgtagAGATTCGATCGGGTTCGCCGGTTCGCGCC---CGCCGCCATGGCGACTTCCTCAGGACCAAAGGAGGCGCCAGCGAATAACCCTGGGCTCCAGACCGAGGTCG
















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|33818513|gb|CF335087.1|CF335087
EST:     TCCGCCGTCTCTCCTCGGCGGCGAACGTCTCCCGCTTTGCCCAGCTCAAG                         AGATTCGACCGGGCTCGCCGGTTCGCGCCGGCCGCCGCCATGTCGACGTCG
genomic: TCCGCCGTCTCTCCTCGGCGGCGAACGTCTCCCGCTTTGCCCAGCTCAAGgtaaccccgg ... tcttctgtagAGATTCGACCGGGCTCGCCGGTTCGCGCCGGCCGCCGCCATGTCGACGTCG
EST: gi|88343329|gb|CI627289.1|CI627289
EST:     TCCGCCGTCTCTCCTCGGCGGCGAACGTCTCCCGCTTTGCCCAGTTCAAG                         AGATTCGACCGGGCTCGCCGGTTCGCGCCGGCCGCCGCCATGTCGACGTCG
genomic: TCCGCCGTCTCTCCTCGGCGGCGAACGTCTCCCGCTTTGCCCAGCTCAAGgtaaccccgg ... tcttctgtagAGATTCGACCGGGCTCGCCGGTTCGCGCCGGCCGCCGCCATGTCGACGTCG
EST: gi|33819107|gb|CF335378.1|CF335378
EST:     TCCGCCGTCTCTCCTCGGCGGCGAACGTCTCCCGCTTTGCCCAGCTCAAG                         AGATTCGACCGGGCTCGCCGGTTCGCGCCGGCCGCCGCCATGTCGACGTCG
genomic: TCCGCCGTCTCTCCTCGGCGGCGAACGTCTCCCGCTTTGCCCAGCTCAAGgtaaccccgg ... tcttctgtagAGATTCGACCGGGCTCGCCGGTTCGCGCCGGCCGCCGCCATGTCGACGTCG
EST: gi|88364009|gb|CI610353.1|CI610353
EST:     TCCGCCGTCTCTCCTCGGCGGCGAACGTCTCCCGCTTTGCCCAGCTCAAG                         AGATTCGACCGGGCTCGCCGGTTCGCGCCGGGCGACGCCATGTCGACGTCG
genomic: TCCGCCGTCTCTCCTCGGCGGCGAACGTCTCCCGCTTTGCCCAGCTCAAGgtaaccccgg ... tcttctgtagAGATTCGACCGGGCTCGCCGGTTCGCGCCGGCCGCCGCCATGTCGACGTCG
EST: gi|88396511|gb|CI600994.1|CI600994
EST:     TCCGCCGTCTCTCTTCGGCGGCGAACGTCTCCCGTTTTGCCCAGTTCAAG                         AGATTCGACCGGGCTCGCCGGTTCGCGCCGGCCGCCGCCATGTCGACTTCG
genomic: TCCGCCGTCTCTCCTCGGCGGCGAACGTCTCCCGCTTTGCCCAGCTCAAGgtaaccccgg ... tcttctgtagAGATTCGACCGGGCTCGCCGGTTCGCGCCGGCCGCCGCCATGTCGACGTCG
EST: gi|38478143|gb|CF962276.1|CF962276
EST:     GCCGTCTCTCCTCGGCGGCGAACGTCTCCCGCTTTG-CCAGCTCAAG                         AGATTCGA-CGGGGTCGCCGGTTCGCGCCGGCCGCCGCCATGTCGACGTCG
genomic: GCCGTCTCTCCTCGGCGGCGAACGTCTCCCGCTTTGCCCAGCTCAAGgtaaccccgg ... tcttctgtagAGATTCGACCGGGCTCGCCGGTTCGCGCCGGCCGCCGCCATGTCGACGTCG
EST: gi|66918847|gb|CX105695.1|CX105695
EST:     TCCGCCGTCTCTCCTCGGCGGCGAACGTCTCCCGCTTTGGCCAGCTCAAG                         AGATTCGACCGGGCTCGCCGGTTCGCGCCGGCCGCCGCCATGTCGACGTCG
genomic: TCCGCCGTCTCTCCTCGGCGGCGAACGTCTCCCGCTTTGCCCAGCTCAAGgtaaccccgg ... tcttctgtagAGATTCGACCGGGCTCGCCGGTTCGCGCCGGCCGCCGCCATGTCGACGTCG
EST: gi|38482501|gb|CF966535.1|CF966535
EST:     TCCGCCGTCTCTCCTCGGCGGCGAACGTCTCCCGCTTTGCCCAGCTCAAG                         AGATTCGACCGGGCTCGCCGGTTCGCGCCGGCCGCCGCCATGTCGACGTCG
genomic: TCCGCCGTCTCTCCTCGGCGGCGAACGTCTCCCGCTTTGCCCAGCTCAAGgtaaccccgg ... tcttctgtagAGATTCGACCGGGCTCGCCGGTTCGCGCCGGCCGCCGCCATGTCGACGTCG
EST: gi|87021271|gb|CI295330.1|CI295330
EST:     TCCGCCGTCTCTCCTCGGCGGCGAACGTCTCCCGCTTTGCCCAGCTCAAG                         AGATTCGACCGGGCTCGCCGGTTCGCGCCGGCCGCCGCCATGTCGACGTCG
genomic: TCCGCCGTCTCTCCTCGGCGGCGAACGTCTCCCGCTTTGCCCAGCTCAAGgtaaccccgg ... tcttctgtagAGATTCGACCGGGCTCGCCGGTTCGCGCCGGCCGCCGCCATGTCGACGTCG
EST: gi|88329315|gb|CI653229.1|CI653229
EST:     TCCGCCGTCTCTCCTCGGCGGCGAACGTCTCCCGCTTTGCCCAGCTCAAG                         AGATTCGACCGGGCTCGCCGGTTCGCGCCGGCCGCCGCCATGTCGACGTCG
genomic: TCCGCCGTCTCTCCTCGGCGGCGAACGTCTCCCGCTTTGCCCAGCTCAAGgtaaccccgg ... tcttctgtagAGATTCGACCGGGCTCGCCGGTTCGCGCCGGCCGCCGCCATGTCGACGTCG
EST: gi|25800681|gb|CA756642.1|CA756642
EST:     TCCGCCGTCTCTCCTCGGCGGCGAACGTCTCCCGCTTTGCCCAGCTCAAG                         AGATTCGACCGGGCTCGCCGGTTCGCGCCGGCCGCCGCCATGTCGACGTCG
genomic: TCCGCCGTCTCTCCTCGGCGGCGAACGTCTCCCGCTTTGCCCAGCTCAAGgtaaccccgg ... tcttctgtagAGATTCGACCGGGCTCGCCGGTTCGCGCCGGCCGCCGCCATGTCGACGTCG
EST: gi|33813839|gb|CF332805.1|CF332805
EST:     TCCGCCGTCTCTCCTCGGCGGCGAACGTCTCCCGCTTTGCCCAGCTCAAG                         AGATTCGACCGGGCTCGCCGGTTCGCGCCGGCCGCCGCCATGTCGACGTCG
genomic: TCCGCCGTCTCTCCTCGGCGGCGAACGTCTCCCGCTTTGCCCAGCTCAAGgtaaccccgg ... tcttctgtagAGATTCGACCGGGCTCGCCGGTTCGCGCCGGCCGCCGCCATGTCGACGTCG
EST: gi|88364025|gb|CI610369.1|CI610369
EST:     TCCGCCGTCTCTCCTCGGCGGCGAACGTCTCCCGCTTTGCCCAGCTCAAG                         AGATTCGACCGGGCTCGCCGGTTCGCGCCGGCCGGCGCCATGTCGACGTCG
genomic: TCCGCCGTCTCTCCTCGGCGGCGAACGTCTCCCGCTTTGCCCAGCTCAAGgtaaccccgg ... tcttctgtagAGATTCGACCGGGCTCGCCGGTTCGCGCCGGCCGCCGCCATGTCGACGTCG
EST: gi|58687672|gb|CK076359.1|CK076359
EST:     TCCGCCGTCTCTCCTCGGCGGCGAACGTCTCCCGCTTTGCCCAGCTCAAG                         AGATTCGACCGGGCTCGCCGGTTCGCGCCGGCCGCCGCCATGTCGACGTCG
genomic: TCCGCCGTCTCTCCTCGGCGGCGAACGTCTCCCGCTTTGCCCAGCTCAAGgtaaccccgg ... tcttctgtagAGATTCGACCGGGCTCGCCGGTTCGCGCCGGCCGCCGCCATGTCGACGTCG
EST: gi|33815680|gb|CF333691.1|CF333691
EST:     TCCGCCGTCTCTCCTCGGCGGCGAACGTCTCCCGCTTTGCCCAGCTCAAG                         AGATTCGACCGGGCTCGCCGGTTCGCGCCGGCCGCCGCC-TGNTCGACGTC
genomic: TCCGCCGTCTCTCCTCGGCGGCGAACGTCTCCCGCTTTGCCCAGCTCAAGgtaaccccgg ... tcttctgtagAGATTCGACCGGGCTCGCCGGTTCGCGCCGGCCGCCGCCATG-TCGACGTC
EST: gi|88314674|gb|CI606742.1|CI606742
EST:     TCCGCCGTCTCTCCTCGGCGGCGAACGTCTCCCGCTTTGCCCAGCTCAAG                         AGATTCGACCGGGCTCGCCGGTTCGCGCCGGCCGCCGCCATGTCGACGTCG
genomic: TCCGCCGTCTCTCCTCGGCGGCGAACGTCTCCCGCTTTGCCCAGCTCAAGgtaaccccgg ... tcttctgtagAGATTCGACCGGGCTCGCCGGTTCGCGCCGGCCGCCGCCATGTCGACGTCG
EST: gi|88725675|gb|CI748934.1|CI748934
EST:     TCCGCCGTCTCTCCTCGGCGGCGAACGTCTCCCGCTTTGCCCAGCTCAAG                         AGATTCGACCGGGCTCGCCGGTTCGCGCCGGCCGCCGCCATGTCGACGTCG
genomic: TCCGCCGTCTCTCCTCGGCGGCGAACGTCTCCCGCTTTGCCCAGCTCAAGgtaaccccgg ... tcttctgtagAGATTCGACCGGGCTCGCCGGTTCGCGCCGGCCGCCGCCATGTCGACGTCG
EST: gi|88575843|gb|CI669988.1|CI669988
EST:     TCCGCCGTCTCTCCTCGGCGGCGAACGTCTCCCGCTTTGCCCAGCTCAAG                         AGATTCGACCGGGCTCGCCGGTTCGCGCCGGCCGCCGCCATGTCGACGTCG
genomic: TCCGCCGTCTCTCCTCGGCGGCGAACGTCTCCCGCTTTGCCCAGCTCAAGgtaaccccgg ... tcttctgtagAGATTCGACCGGGCTCGCCGGTTCGCGCCGGCCGCCGCCATGTCGACGTCG
EST: gi|58588133|gb|CF986441.1|CF986441
EST:     TCCGCCGTCTCTCCTCGGCGGCGAACGTCTCCCGCTTTGCCCAGGTCAAG                         AGATTCGACCGGGCTCGCCGTGTTCGCGCCGGCCGCCGCCATGTCGACGTC
genomic: TCCGCCGTCTCTCCTCGGCGGCGAACGTCTCCCGCTTTGCCCAGCTCAAGgtaaccccgg ... tcttctgtagAGATTCGACCGGGCTCGCCG-GTTCGCGCCGGCCGCCGCCATGTCGACGTC
EST: gi|88401847|gb|CI591174.1|CI591174
EST:     TCCGCCGTCTCTCCTCGGCGGCGAACGTCTCCCGCTTTGCCCAGCTCAAG                         AGATTCGACCGGGCTCGCCGGTTCGCGCCGGCCGCCGCCATGTCGACGTCG
genomic: TCCGCCGTCTCTCCTCGGCGGCGAACGTCTCCCGCTTTGCCCAGCTCAAGgtaaccccgg ... tcttctgtagAGATTCGACCGGGCTCGCCGGTTCGCGCCGGCCGCCGCCATGTCGACGTCG
EST: gi|88331273|gb|CI639684.1|CI639684
EST:     TCCGCCGTCTCTCCTCGGCGGCGAACGTCTCCCGCTTTGCCCAGCTCAAG                         AGATTCGACCGGGCTCGCCGGTTCGCGCCGGCCGCCGCCATGTCGACGTCG
genomic: TCCGCCGTCTCTCCTCGGCGGCGAACGTCTCCCGCTTTGCCCAGCTCAAGgtaaccccgg ... tcttctgtagAGATTCGACCGGGCTCGCCGGTTCGCGCCGGCCGCCGCCATGTCGACGTCG
EST: gi|58692806|gb|CK081493.1|CK081493
EST:     CTCCTCGGCGGCGAACGTCTCCCGCTTTGCCCAGCTCAAG                         AGATTCGACCGGGCTCGCCGGTTCGCGCCGGCCGCCGCCATGTCGACGTCG
genomic: CTCCTCGGCGGCGAACGTCTCCCGCTTTGCCCAGCTCAAGgtaaccccgg ... tcttctgtagAGATTCGACCGGGCTCGCCGGTTCGCGCCGGCCGCCGCCATGTCGACGTCG
EST: gi|88330299|gb|CI658610.1|CI658610
EST:     TCCGCCGTCTCTCCTCGGCGGCGAACGTCTCCCGCTTTGCCCAGCTCAAG                         AGATTCGACCGGGCTCGCCGGTTCGCGCCGGCCGCCGCCATGTCGACGTCG
genomic: TCCGCCGTCTCTCCTCGGCGGCGAACGTCTCCCGCTTTGCCCAGCTCAAGgtaaccccgg ... tcttctgtagAGATTCGACCGGGCTCGCCGGTTCGCGCCGGCCGCCGCCATGTCGACGTCG
EST: gi|9457296|gb|AU063064.2|AU063064
EST:     CGGCGGCGAACGTCTCCCGCTTTGCCCAGCTCAAG                         AGATTCGACCGGGCTCGCCGGTTCGCGCCGGCCGCCGCCATGTCGACGTCG
genomic: CGGCGGCGAACGTCTCCCGCTTTGCCCAGCTCAAGgtaaccccgg ... tcttctgtagAGATTCGACCGGGCTCGCCGGTTCGCGCCGGCCGCCGCCATGTCGACGTCG

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: 75 (upstream exon), 73 (downstream exon)
Score: 125

CGCCGCCGCCATCGCCGCCGCTTCACTGCTCCCCTCCTCCGCCTTCGCTCTCCGCCGTCTCTCCTCGGCGGCGAACGTCTCCCGCTTTGCCCAGCTCAAGgtaaccccgg ... tcttctgtagAGATTCGACCGGGCTCGCCGGTTCGCGCCGGCCGCCGCCATGTCGACGTCGTCGGGGCCGAAGGAGGCGCCGGCAAACAACCCGGGCCTCCAGGCGCCGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttcgctcaccatgtcttggttggggttctctgatctctctccctcttctgtagAGATTCGACCGGGCTCGCCGGTTCGCGCCGGCCGCCGCCATGTCGACGTCGTCGGGGCCGAAGGAGGCGCCGGCAAACAACCCGGGCCTCCAGGCGCCGT
                           ttctctgatctctctc  CT-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaccccggttgaaactcaacgaaattcgtcaccgggatcctttccccccccccccccccctcaccggattcttgagtttctcgcgcttgtttcgctcaccatgtcttggttggggttctctgatctctctccctcttctgtagAGATTCGACCGGGCTCGCCGGTTCGCGCCGGCCGCCGCCATGTCGACGTCGTCGGGGCCGAAGGAGGCGCCGGCAAACAACCCGGGCCTCCAGGCGCCGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG