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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtttttcatgtcatatttatgtttaaatagctgatgctttgctgtgaattttataaagattcaactctcatataatagGTTGCTCGCCACCCAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAG

Basic information

species Oryza sativa
transcript LOC_Os01g01710.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g01710.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G056975_T02 (Zea mays), 3'ss of exon 4
gtgagtt-tttcatgtcatatt-tatgtttaaatagctgatgctttgctgtgaa--ttttataaagattcaactctcatataatagGTTGCTCGCCACCCAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAG
|| ||   |||| | | ||  | | | | | |||| ||   | |||||| ||||  |||   ||| ||||||| || ||    |||||||||||||| |||||||||||||||||||| || ||||||||||| |||||||| ||||||
gtaagacatttcttatgatcctatgtatgtgaataactataggtttgctctgaaaatttctcaaatattcaacccttat----tagGTTGCTCGCCATCCAGATGCAGTTACAGTTGTCACAGGGATAGTAGGTTGTGCAGGGCTGAAG

upper sequence: LOC_Os01g01710.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G036290_T01 (Zea mays), 3'ss of exon 4
gtgagttt-ttcatgtcatatt-tatgtttaaatagctgatgctttgctgtgaattttat-aaagattcaactctcatataatagGTTGCTCGCCACCCAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAG
|| ||    ||| | | ||  | | | | | |||| || | | |||||| | || ||| | ||| | ||||| ||   || |||||| ||||| ||||| |||||| |||||||||| || |||||||||||||||||||| ||||||
gtaaggcgattcttatgatcctatgtctgtgaataactaaaggtttgctctaaaatttctcaaatactcaacccttgaatgatagGTCGCTCGACACCCGGATGCAATTACAGTTGTCACAGGGATAGTAGGGTGTGCAGGGCTGAAG

upper sequence: LOC_Os01g01710.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA05G02190.1 (Glycine max), 3'ss of exon 4
-------gtgagtttttc---atgtcatatttatgtttaaatagctgatgctttgctgtgaattttataaagattcaactctcatataat-agGTTGCTCGCCACCCAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAG
        || |||| |    ||||  || || |||||| | |||  ||  |||| |     ||| |||| | |  | |    ||||  | |||||||||| ||||||||||||||||  || || || || |||||||| |||||||||||||||
gtggacattgggtttattcatatgtggtaattttgtttagagagccaat-ttttgtt-----tttcataa-gctatagcatatatattctcagGTTGCTCGTCACCCAGATGCAGTTAGTGTAGTCACAGGAATAGTAGGCTGTGCAGGACTGAAG

upper sequence: LOC_Os01g01710.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA17G09740.1 (Glycine max), 3'ss of exon 4
gtgagtttttcatgtcat-atttatgtttaaatagctgatgctttgctgtgaattttataaagattcaactctcatataat-agGTTGCTCGCCACCCAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAG
|||    | |  | |  | || |   || |  | | | |        | ||  ||| |||| | |  | ||   ||||  | |||||||||| |||||||||||||| |  || || || || |||||||| |||||||||||||||
gtggacatctggtttattcatatgcattaattttgtttagagccaattttgtttttcataa-gctatagcttaaatattctcagGTTGCTCGTCACCCAGATGCAGTCAGTGTAGTCACAGGAATAGTAGGCTGTGCAGGACTGAAG

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|38474648|gb|CF958781.1|CF958781
EST:     TGTGATTGGAAGCCAGAAATTTATTCCTGGTGAGCAAGGTTGTCATAGAG                         GTTGCTCGCCAACCC-GATGCAGTTACAGTTGTTACTGGGATAGTAGGGTG
genomic: TGTGATTGGAAGCCAGAAATT-ATTCCTGGTGAGCAAGGT-GTCATAGAGgtgagttttt ... catataatagGTTGCTCGCCA-CCCAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTG
EST: gi|58607529|gb|CK035562.1|CK035562
EST:     ATTGTGATTGGAAGCCAGAAATTATTCCTGGTGAGCAAGGTGTCATAGAG                         GTTGCTCGCCACCCAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGT
genomic: ATTGTGATTGGAAGCCAGAAATTATTCCTGGTGAGCAAGGTGTCATAGAGgtgagttttt ... catataatagGTTGCTCGCCACCCAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGT
EST: gi|58689337|gb|CK078024.1|CK078024
EST:     ATTGTGATTGGAAGCCAGAAATTATTCCTGGTGAGCAAGGTGTCATAGAG                         GTTGCTCGCCAACCAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGT
genomic: ATTGTGATTGGAAGCCAGAAATTATTCCTGGTGAGCAAGGTGTCATAGAGgtgagttttt ... catataatagGTTGCTCGCCACCCAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGT
EST: gi|86905401|gb|CI285364.1|CI285364
EST:     ATTGTGATTGGAAGCCAGAAATTATTCCTGGTGAGCAAGGTGTCATAGAG                         GTTGCTCGCCACCCAGATGCAGTTACAGTTGTTACTGGGATA
genomic: ATTGTGATTGGAAGCCAGAAATTATTCCTGGTGAGCAAGGTGTCATAGAGgtgagttttt ... catataatagGTTGCTCGCCACCCAGATGCAGTTACAGTTGTTACTGGGATA
EST: gi|33676538|gb|CF304777.1|CF304777
EST:     ATTGTGATTGGAAGCCAGAAATTATTCCTGGTGAGCAAGGTGTCATAGAG                         GTTGCTCGCCACCCAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGGTG
genomic: ATTGTGATTGGAAGCCAGAAATTATTCCTGGTGAGCAAGGTGTCATAGAGgtgagttttt ... catataatagGTTGCTCGCCACCCAGATGCAGTTACAGTTGTTACTGGGATAGTAGGG-TG
EST: gi|29613664|gb|CB618677.1|CB618677
EST:     ATTGTGATTGGAAGCCAGAAATTATTCCTGGTGAGCAAGGTGTCATAGAG                         GTTGCTCGCCACCCAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGT
genomic: ATTGTGATTGGAAGCCAGAAATTATTCCTGGTGAGCAAGGTGTCATAGAGgtgagttttt ... catataatagGTTGCTCGCCACCCAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGT
EST: gi|29620639|gb|CB625650.1|CB625650
EST:     ATTGTGATTGGAAGCCAGAAATTATTCCTGGTGAGCAAGGTGTCATAGAG                         GTTGCTCGCCACCCAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGT
genomic: ATTGTGATTGGAAGCCAGAAATTATTCCTGGTGAGCAAGGTGTCATAGAGgtgagttttt ... catataatagGTTGCTCGCCACCCAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGT
EST: gi|29688464|gb|CB684739.1|CB684739
EST:     ATTGTGATTGGAAGCCAGAAATTATTCCTGGTGAGCAAGGTGTCATAGAG                         GTTGCTCGCCACCCAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGT
genomic: ATTGTGATTGGAAGCCAGAAATTATTCCTGGTGAGCAAGGTGTCATAGAGgtgagttttt ... catataatagGTTGCTCGCCACCCAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGT
EST: gi|29681868|gb|CB678143.1|CB678143
EST:     ATTGTGATTGGAAGCCAGAAATTATTCCTGGTGAGCAAGGTGTCATAGAG                         GTTGCTCGCCACCCAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGT
genomic: ATTGTGATTGGAAGCCAGAAATTATTCCTGGTGAGCAAGGTGTCATAGAGgtgagttttt ... catataatagGTTGCTCGCCACCCAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGT
EST: gi|58696138|gb|CK084825.1|CK084825
EST:     ATTGTGATTGGAAGCCAGAAATTATTCCTGGTGAGCAAGGTGTCATAGAG                         GTTGCTCGCCACCCAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGT
genomic: ATTGTGATTGGAAGCCAGAAATTATTCCTGGTGAGCAAGGTGTCATAGAGgtgagttttt ... catataatagGTTGCTCGCCACCCAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGT
EST: gi|58688271|gb|CK076958.1|CK076958
EST:     ATTGTGATTGGAAGCCAGAAATTATTCCTGGTGAGCAAGGTGTCATAGAG                         GTTGCTCGCCACCCAGATGCAGTTACAGTTGTTACTGGG
genomic: ATTGTGATTGGAAGCCAGAAATTATTCCTGGTGAGCAAGGTGTCATAGAGgtgagttttt ... catataatagGTTGCTCGCCACCCAGATGCAGTTACAGTTGTTACTGGG
EST: gi|29617049|gb|CB622061.1|CB622061
EST:     ATTGTGATTGGAAGCCAGAAATTATTCCTGGTGAGCAAGGTGTCATAGAG                         GTTGCTCGCCACCCAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGT
genomic: ATTGTGATTGGAAGCCAGAAATTATTCCTGGTGAGCAAGGTGTCATAGAGgtgagttttt ... catataatagGTTGCTCGCCACCCAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGT
EST: gi|33663679|gb|CF294646.1|CF294646
EST:     ATTGTGATTGGAAGCCAGAAATTATTCCTGGTGAGCAAGGTGTCATAGAG                         GTTGCTCGCCACCCAGATGCAGTTACAGTTGTTACTGGGAT
genomic: ATTGTGATTGGAAGCCAGAAATTATTCCTGGTGAGCAAGGTGTCATAGAGgtgagttttt ... catataatagGTTGCTCGCCACCCAGATGCAGTTACAGTTGTTACTGGGAT
EST: gi|29620626|gb|CB625637.1|CB625637
EST:     ATTGTGATTGGAAGCCAGAAATTATTCCTGGTGAGCAAGGTGTCATAGAG                         GTTGCTCGCCACCCAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGT
genomic: ATTGTGATTGGAAGCCAGAAATTATTCCTGGTGAGCAAGGTGTCATAGAGgtgagttttt ... catataatagGTTGCTCGCCACCCAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGT
EST: gi|58607277|gb|CK035310.1|CK035310
EST:     ATTGTGATTGGAAGCCAGAAATTATTCCTGGTGAGCAAGGTGTCATAGAG                         GTTGCTCGCCAGCCAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGT
genomic: ATTGTGATTGGAAGCCAGAAATTATTCCTGGTGAGCAAGGTGTCATAGAGgtgagttttt ... catataatagGTTGCTCGCCACCCAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGT
EST: gi|58588201|gb|CF986509.1|CF986509
EST:     ATTGTGATTGGAAGCCAGAAATTATTCCTGGTGAGCAAGGTGTCATAGAG                         GTTGCTCGCCACCCAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGT
genomic: ATTGTGATTGGAAGCCAGAAATTATTCCTGGTGAGCAAGGTGTCATAGAGgtgagttttt ... catataatagGTTGCTCGCCACCCAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGT
EST: gi|29620641|gb|CB625652.1|CB625652
EST:     ATTGTGATTGGAAGCCAGAAATTATTCCTGGTGAGCAAGGTGTCATAGAG                         GTTGCTCGCCACCCAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGT
genomic: ATTGTGATTGGAAGCCAGAAATTATTCCTGGTGAGCAAGGTGTCATAGAGgtgagttttt ... catataatagGTTGCTCGCCACCCAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGT
EST: gi|33381852|gb|CF197195.1|CF197195
EST:     ATTGTGATTGGAAGCCAGAAATTATTCCTGGTGAGCAAGGTGTCATAGAG                         GTTGCTCGCCACCCAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGT
genomic: ATTGTGATTGGAAGCCAGAAATTATTCCTGGTGAGCAAGGTGTCATAGAGgtgagttttt ... catataatagGTTGCTCGCCACCCAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGT
EST: gi|58688021|gb|CK076708.1|CK076708
EST:     ATTGTGATTGGAAGCCAGAAATTATTCCTGGTGAGCAAGGTGTCATAGAG                         GTTGCTCGCCACCCAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGT
genomic: ATTGTGATTGGAAGCCAGAAATTATTCCTGGTGAGCAAGGTGTCATAGAGgtgagttttt ... catataatagGTTGCTCGCCACCCAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGT
EST: gi|58589270|gb|CF987578.1|CF987578
EST:     ATTGTGATTGGAAGCCAGAAATTATTCCTGGTGAGCAAGGTGTCATAGAG                         GTTGCTCGCCACCCAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGT
genomic: ATTGTGATTGGAAGCCAGAAATTATTCCTGGTGAGCAAGGTGTCATAGAGgtgagttttt ... catataatagGTTGCTCGCCACCCAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGT
EST: gi|58690161|gb|CK078848.1|CK078848
EST:     ATTGTGATTGGAAGCCAGAAATTATTCCTGGTGAGCAAGGTGTCATAGAG                         GTTGCTCGCCACCCAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGT
genomic: ATTGTGATTGGAAGCCAGAAATTATTCCTGGTGAGCAAGGTGTCATAGAGgtgagttttt ... catataatagGTTGCTCGCCACCCAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGT

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), 75 (downstream exon)
Score: 78

TGCTGTAAGAAATGAGTCATTAGTTGATGAGCTAAAGGAAGCCTTAGCTGATTGTGATTGGAAGCCAGAAATTATTCCTGGTGAGCAAGGTGTCATAGAGgtgagttttt ... catataatagGTTGCTCGCCACCCAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaatagctgatgctttgctgtgaattttataaagattcaactctcatataatagGTTGCTCGCCACCCAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAG
     agctgat  putative branch site (score: 78)
                                         ctctcat  putative PPT
                       aattttataaagattc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtttttcatgtcatatttatgtttaaatagctgatgctttgctgtgaattttataaagattcaactctcatataatagGTTGCTCGCCACCCAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG