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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgttgaaattccagcaggatattgtaacgtcctcttgttgtcttttttgccgtatgggctatggctggctgctacattcacttgttagcctgatattgttcttgcaagttttatgtatgctgaacccatgaccttgtttttaatcagGCCGATCTTGAGGAAGTCAGTGCTCTGTATTTGGACGCTAAATCATCGGCTCGTCTCCTTCAGGAGCAGCAAGGAAGATACATTACTTAAATTTCTCTTG

Basic information

species Oryza sativa
transcript LOC_Os07g08170.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g08170.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G032267_T01 (Zea mays), 3'ss of exon 11
gtatgtgttgaaattccagcaggatattgtaacgtcctcttgttgtcttttttgccgtatgggctatggctggctgctacattcacttgttagcctgatattgttcttgcaagttttatgtatgctgaacccatgaccttgtttttaatcagGCCGATCTTGAGGAAGTCAGTGCTCTGTATTTGGACGCTAAATCATCGGCTCGTCTCCTTCAGGAGCAGCAAGGAAGATACATTACTTAAATTTCTCTTG
                                                | | | |||   | ||| |    |   |||       ||||||   ||   |   || ||   |  | |     |  |  ||  ||   | || | |  ||||||| || || ||||||||||| |  || |||||||| || ||||| |||||||| || || |||||||| |||| ||||||||| || || | ||   |  
---------------------------------------------gtatatctaccgaccgagctttcatcgtgagctggtc---cttgttc-tctcgcaagcttattatgacctctggtcttattatacatatatacatggtctctatcagGCTGACCTCGAGGAAGTCAGCGGGCTCTATTTGGATGCCAAATCCTCGGCTCGCCTGCTCCAGGAGCAACAAGAAAGATACATCACCTAGACTTGCATCT

upper sequence: LOC_Os07g08170.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G018697_T03 (Zea mays), 3'ss of exon 12
gtatgtgttgaaattccagcaggatattgtaacgtcctcttgttgtcttttttgccgtatgggctatggctggctgctacattcacttgttagcctgatattgttcttgcaagttttatgtatgctgaacccatgaccttgtttttaatcagGCCGATCTTGAGGAAGTCAGTGCTCTGTATTTGGACGCTAAATCATCGGCTCGTCTCCTTCAGGAGCAGCAAGGAAGATACATTACTTAAATTTCTCTTG
                                                                |||  ||| |       |   | |   | |      ||||||  |||||| |||||    || | |  ||     ||||    ||||||| ||||| |||||||||||||  || |||||||| || ||||| |||||||| || || |||||||| |||| ||||||||| || || ||||      
---------------------------------------------------------------gtatatctgccgagcttttgttcctacaaactgatccttgttcccgcaagtcttatgatctctaagcttata--tatgttccctatcagGCTGATCTCGAGGAAGTCAGTGGGCTCTATTTGGATGCCAAATCCTCGGCTCGGCTGCTCCAGGAGCAACAAGAAAGATACATCACCTAGATTT------

upper sequence: LOC_Os07g08170.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G018697_T04 (Zea mays), 3'ss of exon 5
gtatgtgttgaaattccagcaggatattgtaacgtcctcttgttgtcttttttgccgtatgggctatggctggctgctacattcacttgttagcctgatattgttcttgcaagttttatgtatgctgaacccatgaccttgtttttaatcagGCCGATCTTGAGGAAGTCAGTGCTCTGTATTTGGACGCTAAATCATCGGCTCGTCTCCTTCAGGAGCAGCAAGGAAGATACATTACTTAAATTTCTCTTG
                                                                |||  ||| |       |   | |   | |      ||||||  |||||| |||||    || | |  ||     ||||    ||||||| ||||| |||||||||||||  || |||||||| || ||||| |||||||| || || |||||||| |||| ||||||||| || || ||||   |  
---------------------------------------------------------------gtatatctgccgagcttttgttcctacaaactgatccttgttcccgcaagtcttatgatctctaagcttata--tatgttccctatcagGCTGATCTCGAGGAAGTCAGTGGGCTCTATTTGGATGCCAAATCCTCGGCTCGGCTGCTCCAGGAGCAACAAGAAAGATACATCACCTAGATTTGGATCT

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|88384720|gb|CI556598.1|CI556598
EST:     GGGAGAGAGAAGATCAGCAAG                         GCCGATCTTGAGGAAGTCAGTGCTCTGTATTTGGACGCTAAATCATCGGCT
genomic: GGGAGAGAGAAGATCAGCAAGgtatgtgttg ... ttttaatcagGCCGATCTTGAGGAAGTCAGTGCTCTGTATTTGGACGCTAAATCATCGGCT
EST: gi|88961514|gb|CI096795.1|CI096795
EST:     CACCCGCCAGTGTAGTTGCAAAGGCTAATGGGAGAGAGAAGATCAGCAAG                         GCCGATCTTGAGGAAGTCAGTGCTCTGTATTTGGACGCTAAATCATCGGCT
genomic: CACCCGCCAGTGTAGTTGCAAAGGCTAATGGGAGAGAGAAGATCAGCAAGgtatgtgttg ... ttttaatcagGCCGATCTTGAGGAAGTCAGTGCTCTGTATTTGGACGCTAAATCATCGGCT
EST: gi|89168320|gb|CI109524.1|CI109524
EST:     CACCCGCCAGTGTAGTTGCAAAGGCTAATGGGAGAGAGAAGATCAGCAAG                         GCCGATCTTGAGGAAGTCAGTGCTCTGTATTTGGACGCTAAATCATCGGCT
genomic: CACCCGCCAGTGTAGTTGCAAAGGCTAATGGGAGAGAGAAGATCAGCAAGgtatgtgttg ... ttttaatcagGCCGATCTTGAGGAAGTCAGTGCTCTGTATTTGGACGCTAAATCATCGGCT
EST: gi|88443802|gb|CI552347.1|CI552347
EST:     CAGTGTAGTTGCAAAGGCTAATGGGAGAGAGAAGATCAGCAAG                         GCCGATCTTGAGGAAGTCAGTGCTCTGTATTTGGACGCTAAATCATCGGCT
genomic: CAGTGTAGTTGCAAAGGCTAATGGGAGAGAGAAGATCAGCAAGgtatgtgttg ... ttttaatcagGCCGATCTTGAGGAAGTCAGTGCTCTGTATTTGGACGCTAAATCATCGGCT
EST: gi|86496777|gb|CI139410.1|CI139410
EST:     CACCCGCCAGTGTAGTTGCAAAGGCTAATGGGAGAGAGAAGATCAGCAAG                         GCCGATCTTGAGGAAGTCAGTGCTCTGTATTTGGACGCTAAATCATCGGCT
genomic: CACCCGCCAGTGTAGTTGCAAAGGCTAATGGGAGAGAGAAGATCAGCAAGgtatgtgttg ... ttttaatcagGCCGATCTTGAGGAAGTCAGTGCTCTGTATTTGGACGCTAAATCATCGGCT
EST: gi|88222413|gb|CI222369.1|CI222369
EST:     CACCCGCCAGTGTAGTTGCAAAGGCTAATGGGAGAGAGAAGATCAGCAAG                         GCCGATCTTGAGGAAGTCAGTGCTCTGTATTTGGACGCTAAATCATCGGCT
genomic: CACCCGCCAGTGTAGTTGCAAAGGCTAATGGGAGAGAGAAGATCAGCAAGgtatgtgttg ... ttttaatcagGCCGATCTTGAGGAAGTCAGTGCTCTGTATTTGGACGCTAAATCATCGGCT
EST: gi|22307047|gb|BQ908269.1|BQ908269
EST:     GAAGATCAGCAAG                         GCCGATCTTGAGGAAGTCAGTGCTCTGTATTTGGACGCTANAATCATCGGC
genomic: GAAGATCAGCAAGgtatgtgttg ... ttttaatcagGCCGATCTTGAGGAAGTCAGTGCTCTGTATTTGGACGCTA-AATCATCGGC
EST: gi|86838938|gb|CI330353.1|CI330353
EST:     CACCCGCCAGTGTATTTGCAAAGGCTAATGGGAGAGAAAAGATCAGCAAG                         GCCGATCTTGAGGAAGTCAGTGCTCTGTATTTGGACGCTAAATCATCGGCT
genomic: CACCCGCCAGTGTAGTTGCAAAGGCTAATGGGAGAGAGAAGATCAGCAAGgtatgtgttg ... ttttaatcagGCCGATCTTGAGGAAGTCAGTGCTCTGTATTTGGACGCTAAATCATCGGCT
EST: gi|33807423|gb|CF329586.1|CF329586
EST:     CACCCGCCAGTGTAGTTGCAAAGGCTAATGGGAGAGAGAAGATCAGCAAG                         GCCGATCTTGAGGAAGTCAGTGCTCTGTATTTGGACGCTAAATCATCGGCT
genomic: CACCCGCCAGTGTAGTTGCAAAGGCTAATGGGAGAGAGAAGATCAGCAAGgtatgtgttg ... ttttaatcagGCCGATCTTGAGGAAGTCAGTGCTCTGTATTTGGACGCTAAATCATCGGCT
EST: gi|4715602|gb|AU056718.1|AU056718
EST:     CACCCGCCAGTGTAGTTGCAAAGGCTAATGGGAGAGAGAAGATCAGCAAG                         GCCGATCTTGAGGAAGTCAGTGCTCTGTATTTGGACGCTAAATCATCGGCT
genomic: CACCCGCCAGTGTAGTTGCAAAGGCTAATGGGAGAGAGAAGATCAGCAAGgtatgtgttg ... ttttaatcagGCCGATCTTGAGGAAGTCAGTGCTCTGTATTTGGACGCTAAATCATCGGCT
EST: gi|86487502|gb|CI130135.1|CI130135
EST:     CACCCGCCAGTGTAGTTGCAAAGGCTAATGGGAGAGAGAAGATCAGCAAG                         GCCGATCTTGAGGAAGTCAGTGCTCTGTATTTGGACGCTAAATCATCGGCT
genomic: CACCCGCCAGTGTAGTTGCAAAGGCTAATGGGAGAGAGAAGATCAGCAAGgtatgtgttg ... ttttaatcagGCCGATCTTGAGGAAGTCAGTGCTCTGTATTTGGACGCTAAATCATCGGCT

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: 41 (upstream exon), 53 (downstream exon)
Score: 2

GCATGCTATTCAGTTGCTATCACCCGCCAGTGTAGTTGCAAAGGCTAATGGGAGAGAGAAGATCAGCAAGgtatgtgttg ... ttttaatcagGCCGATCTTGAGGAAGTCAGTGCTCTGTATTTGGACGCTAAATCATCGGCTCGTCTCCTTCAGGAGCAGCAAGGAAGATACATTACTTAAATTTCTCTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atattgttcttgcaagttttatgtatgctgaacccatgaccttgtttttaatcagGCCGATCTTGAGGAAGTCAGTGCTCTGTATTTGGACGCTAAATCATCGGCTCGTCTCCTTCAGGAGCAGCAAGGAAGATACATTACTTAAATTTCTCTTG
 gcctgat  putative branch site (score: 2)
                                       ccttgttttt  putative PPT
                                         ttgtttttaat  TA-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgttgaaattccagcaggatattgtaacgtcctcttgttgtcttttttgccgtatgggctatggctggctgctacattcacttgttagcctgatattgttcttgcaagttttatgtatgctgaacccatgaccttgtttttaatcagGCCGATCTTGAGGAAGTCAGTGCTCTGTATTTGGACGCTAAATCATCGGCTCGTCTCCTTCAGGAGCAGCAAGGAAGATACATTACTTAAATTTCTCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA