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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtagtgatcattacgtcctttgctatgtcgcaccagcctttcctgattgcaaagcataacattccaatcccaatttaccgaagCTCTGCGAGCGTCTCCCAAGCCCCAATGGCGAATCGGCAGTCGACTGCGATGAGATCTCAAACATGCCGAACCTTTCATTCACCATAGCAAACAAGACCT

Basic information

species Oryza sativa
transcript LOC_Os01g18630.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g18630.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G077233_T06 (Zea mays), 3'ss of exon 9
gtaagtagtgatcattacgtcct--ttgctatgtcgcaccagcctttcctgattgcaa-agcataacattccaatcccaatttac--cgaagCTCTGCGAGCGTCTCCCAAGCCCCAATGGCGAATCGGCAGTCGACTGCGATGAGATCTCAAACATGCCGAACCTTTCATTCACCATAGCAAACAAGACCT
||  | |    |  ||| ||       | | | |         || | | || ||  | |||||    |||  ||   ||| | |   | ||||||| ||||||||||| |||||||||||||| ||  | || || ||| || |||||||||| ||||| || ||| |||||||||||||||||||||| |
gttgggatactttgttatgtttggacagttctatgattgggaactgtacagaatgtgacagcat----ttcttattttaatgtgcattgcagCTCTGTGAGCGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCATCAGATCTCAAAGATGCCAAATCTTGCATTCACCATAGCAAACAAGACTT
















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|86596608|gb|CI286521.1|CI286521
EST:     AGCTCCGACATAACCAAACAAGGGAGCTCATTTTGCAATATGCTGACCAG                         CTCTGCGAGCGTCTCCCAAGCCCCAATGGCGAATCGGCAGTCGACTGCGAT
genomic: AGCTCCGACATAACCAAACAAGGGAGCTCATTTTGCAATATGCTGACCAGgtaagtagtg ... tttaccgaagCTCTGCGAGCGTCTCCCAAGCCCCAATGGCGAATCGGCAGTCGACTGCGAT
EST: gi|29643124|gb|CB648131.1|CB648131
EST:     AGCTCCGACATAACCAAACAAGGGAGCTCATTTTGCAATATGCTGACCAG                         CTCTGCGAGCGTCTCCCAAGCCCCAATGGCGAATCGGCAGTCGACTGCGAT
genomic: AGCTCCGACATAACCAAACAAGGGAGCTCATTTTGCAATATGCTGACCAGgtaagtagtg ... tttaccgaagCTCTGCGAGCGTCTCCCAAGCCCCAATGGCGAATCGGCAGTCGACTGCGAT
EST: gi|29631103|gb|CB636112.1|CB636112
EST:     TGCAATATGTTGACCAG                         CTCTGCGAGCGTCTCCCAAGCCCCAATGGCGAATCGGCAGTCGACTGCGAT
genomic: TGCAATATGCTGACCAGgtaagtagtg ... tttaccgaagCTCTGCGAGCGTCTCCCAAGCCCCAATGGCGAATCGGCAGTCGACTGCGAT
EST: gi|89195188|gb|CI051301.1|CI051301
EST:     AGCTCCGACATAACCAAACAAGGGAGCTCATTTTGCAATATGCTGACCAG                         CTCTGCGAGCGTCTCCCAAGCCCCAATGGCGAATCGGCAGTCGACTGCGAT
genomic: AGCTCCGACATAACCAAACAAGGGAGCTCATTTTGCAATATGCTGACCAGgtaagtagtg ... tttaccgaagCTCTGCGAGCGTCTCCCAAGCCCCAATGGCGAATCGGCAGTCGACTGCGAT
EST: gi|29662754|gb|CB659029.1|CB659029
EST:     AGCTCCGACATAACCAAACAAGGGAGCTCATTTTGCAATATGCTGACCAG                         CTCTGCGAGCGTCTCCCAAGCCCCAATGGCGAATCGGCAGTCGACTGCGAT
genomic: AGCTCCGACATAACCAAACAAGGGAGCTCATTTTGCAATATGCTGACCAGgtaagtagtg ... tttaccgaagCTCTGCGAGCGTCTCCCAAGCCCCAATGGCGAATCGGCAGTCGACTGCGAT
EST: gi|87022160|gb|CI259232.1|CI259232
EST:     AGCTCCGACATAACCAAACAAGGGAGCTCATTTTGCAATATGCTGACCAG                         CTCTGCGAGCGTCTCCCAAGCCCCAATGGCGAATCGGCAGTCGACTGCGAT
genomic: AGCTCCGACATAACCAAACAAGGGAGCTCATTTTGCAATATGCTGACCAGgtaagtagtg ... tttaccgaagCTCTGCGAGCGTCTCCCAAGCCCCAATGGCGAATCGGCAGTCGACTGCGAT
EST: gi|86907659|gb|CI296618.1|CI296618
EST:     TATGCTGACCAG                         CTCTGCGAGCGTCTCCCAAGCCCCAATGGCGAATCGGCAGTCGACTGCGAT
genomic: TATGCTGACCAGgtaagtagtg ... tttaccgaagCTCTGCGAGCGTCTCCCAAGCCCCAATGGCGAATCGGCAGTCGACTGCGAT
EST: gi|218493897|gb|FG949292.1|FG949292
EST:     AGCTCCGACATAACCAAACAAGGGAGCTCATTTTGCAATATGCTGACCAG                         CTCTGCGAGCGTCTCCCAAGCCCCAATGGCGAATCGGCAGTCGACTGCGAT
genomic: AGCTCCGACATAACCAAACAAGGGAGCTCATTTTGCAATATGCTGACCAGgtaagtagtg ... tttaccgaagCTCTGCGAGCGTCTCCCAAGCCCCAATGGCGAATCGGCAGTCGACTGCGAT
EST: gi|29665540|gb|CB661815.1|CB661815
EST:     AGCTCCGACATAACCAAACAAGGGAGCTCATTTTGCAATATGCTGACCAG                         CTCTGCGAGCGTCTCCCAAGCCCCAATGGCGAATCGGCAGTCGACTGCGAT
genomic: AGCTCCGACATAACCAAACAAGGGAGCTCATTTTGCAATATGCTGACCAGgtaagtagtg ... tttaccgaagCTCTGCGAGCGTCTCCCAAGCCCCAATGGCGAATCGGCAGTCGACTGCGAT
EST: gi|29645988|gb|CB650995.1|CB650995
EST:     AGCTCCGACATAACCAAACAAGGGAGCTCATTTTGCAATATGCTGACCAG                         CTCTGCGAGCGTCTCCCAAGCCCCAATGGCGAATCGGCAGTCGACTGCGAT
genomic: AGCTCCGACATAACCAAACAAGGGAGCTCATTTTGCAATATGCTGACCAGgtaagtagtg ... tttaccgaagCTCTGCGAGCGTCTCCCAAGCCCCAATGGCGAATCGGCAGTCGACTGCGAT
EST: gi|29664682|gb|CB660957.1|CB660957
EST:     AGCTCCGACATAACCAAACAAGGGAGCTCATTTTGCAATATGCTGACCAG                         CTCTGCGAGCGTCTCCCAAGCCCCAATGGCGAATCGGCAGTCGACTGCGAT
genomic: AGCTCCGACATAACCAAACAAGGGAGCTCATTTTGCAATATGCTGACCAGgtaagtagtg ... tttaccgaagCTCTGCGAGCGTCTCCCAAGCCCCAATGGCGAATCGGCAGTCGACTGCGAT
EST: gi|87022142|gb|CI259214.1|CI259214
EST:     AGCTCCGACATAACCAAACAAGGGAGCTCATTTTGCAATATGCTGACCAG                         CTCTGCGAGCGTCTCCCAAGCCCCAATGGCGAATCGGCAGTCGACTGCGAT
genomic: AGCTCCGACATAACCAAACAAGGGAGCTCATTTTGCAATATGCTGACCAGgtaagtagtg ... tttaccgaagCTCTGCGAGCGTCTCCCAAGCCCCAATGGCGAATCGGCAGTCGACTGCGAT
EST: gi|88993443|gb|CI257871.1|CI257871
EST:     TTTGCAATATGCTGACCAG                         CTCTGCGAGCGTCTCCCAAGCCCCCAATGGCGAATCGGCAGTCGACTGCGA
genomic: TTTGCAATATGCTGACCAGgtaagtagtg ... tttaccgaagCTCTGCGAGCGTCTCCCAAG-CCCCAATGGCGAATCGGCAGTCGACTGCGA
EST: gi|29639119|gb|CB644128.1|CB644128
EST:     AGCTCCGACATAACCAAACAAGGGAGCTCATTTTGCAATATGCTGACCAG                         CTCTGCGAGCGTCTCCCAAGCCCCAATGGCGAATCGGCAGTCGACTGCGAT
genomic: AGCTCCGACATAACCAAACAAGGGAGCTCATTTTGCAATATGCTGACCAGgtaagtagtg ... tttaccgaagCTCTGCGAGCGTCTCCCAAGCCCCAATGGCGAATCGGCAGTCGACTGCGAT
EST: gi|29683212|gb|CB679487.1|CB679487
EST:     AGCTCCGACATAACCAAACAAGGGAGCTCATTTTGCAATATGCTGACCAG                         CTCTGCGAGCGTCTCCCAAGCCCCAATGGCGAATCGGCAGTCGACTGCGAT
genomic: AGCTCCGACATAACCAAACAAGGGAGCTCATTTTGCAATATGCTGACCAGgtaagtagtg ... tttaccgaagCTCTGCGAGCGTCTCCCAAGCCCCAATGGCGAATCGGCAGTCGACTGCGAT
EST: gi|27578101|gb|CB000796.1|CB000796
EST:     ATTTTGCAATATGCTGACCAG                         CTCTGCGAGCGTCTCCCAAGCCCCAATGGCGAATCGGCAGTCGACTGCGAT
genomic: ATTTTGCAATATGCTGACCAGgtaagtagtg ... tttaccgaagCTCTGCGAGCGTCTCCCAAGCCCCAATGGCGAATCGGCAGTCGACTGCGAT
EST: gi|86828240|gb|CI276836.1|CI276836
EST:     AGCTCCGACATAACCAAACAAGGGAGCTCATTTTGCAATATGCTGACCAG                         CTCTGCGAGCGTCTCCCAAGCCCCAATGGCGAATCGGCAGTCGACTGCGAT
genomic: AGCTCCGACATAACCAAACAAGGGAGCTCATTTTGCAATATGCTGACCAGgtaagtagtg ... tttaccgaagCTCTGCGAGCGTCTCCCAAGCCCCAATGGCGAATCGGCAGTCGACTGCGAT
EST: gi|86254951|gb|CI017071.1|CI017071
EST:     ATATGCTGACCAG                         CTCTGCGAGCGTCTCCCAAGCCCCAATGGCGAATCGGCAGTCGACTGCGAT
genomic: ATATGCTGACCAGgtaagtagtg ... tttaccgaagCTCTGCGAGCGTCTCCCAAGCCCCAATGGCGAATCGGCAGTCGACTGCGAT

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), 61 (downstream exon)
Score: 83

AGATCTTTCCTGCACTGCTTGCGAGATGGCTGTTGTCTGGATACAGAATCAGCTCCGACATAACCAAACAAGGGAGCTCATTTTGCAATATGCTGACCAGgtaagtagtg ... tttaccgaagCTCTGCGAGCGTCTCCCAAGCCCCAATGGCGAATCGGCAGTCGACTGCGATGAGATCTCAAACATGCCGAACCTTTCATTCACCATAGCAAACAAGACCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgcaccagcctttcctgattgcaaagcataacattccaatcccaatttaccgaagCTCTGCGAGCGTCTCCCAAGCCCCAATGGCGAATCGGCAGTCGACTGCGATGAGATCTCAAACATGCCGAACCTTTCATTCACCATAGCAAACAAGACCT
                         gcataac  putative branch site (score: 83)
                           ataacatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtagtgatcattacgtcctttgctatgtcgcaccagcctttcctgattgcaaagcataacattccaatcccaatttaccgaagCTCTGCGAGCGTCTCCCAAGCCCCAATGGCGAATCGGCAGTCGACTGCGATGAGATCTCAAACATGCCGAACCTTTCATTCACCATAGCAAACAAGACCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC