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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catacgtgtcatccacttattttgtttttgtaatcatatgtacaattcaatggcatgtacttgtgtccctggactcacatatttcctgctctcttttcagCTAAGATTCCCTTTCCATTGACTCCGCGATTCAGGGGAATGCTGCAAAACGGGATAGACCTGAGTACTGTTGATGTGAGCTATGTTAGCAGCCGTTCATG

Basic information

species Oryza sativa
transcript LOC_Os09g32220.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g32220.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G014313_T02 (Zea mays), 3'ss of exon 4
-catacgtgtcatccacttattttgtttttgtaatcatatgt-aca-attcaatggcatgtacttgtgtccctggactcacatatttcctgctctcttttcagCTAAGATTCCCTTTCCATTGACTCCGCGATTCAGGGGAATGCTGCAAAACGGGATAGACCTGAGTACTGTTGATGTGAGCTATGTTAGCAGCCGTTCATG
 || || | | ||   ||| |  ||||||||| ||||| ||| | | || | || | ||||| |||   |     |||||||||| | |   | |||||||||| || || |||||||||||||||| | |||||||||||||||||||||| ||||| |||||||| ||||||||||| ||||||||||| ||||| |||||
ccacacatattatttgcttctgctgtttttgttatcatgtgttatatatcctatcgtatgtagttgaagcat---actcacatatatgcaaatatcttttcagCAAAAATCCCCTTTCCATTGACTCAGAGATTCAGGGGAATGCTGCAAAATGGGATTGACCTGAGCACTGTTGATGTCAGCTATGTTAGTAGCCGGTCATG

upper sequence: LOC_Os09g32220.1 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ16947 (Selaginella moellendorffii), 3'ss of exon 4
catacgtgtcatccacttattttgtttttgtaatcatatgtacaattcaatggcatgtacttgtgtccctggactcacatatttcctgctctcttttcagCTAAGATTCCCTTTCCATTGACTCCGCGATTCAGGGGAATGCTGCAAAACGGGATAGACCTGAGTACTGTTGATGTGAGCTATGTTAGCAGCCGTTCATG
                                                |||    | |||  |  |  ||    ||    | | | |  | |   | |||| || ||||| || ||  | || |   ||||| | || ||| ||||||| || || ||| ||||  | || |||||||||||||| ||||||||||||||
----------------------------------------------gtaatactttataccagcctttct----tctttaagtgcatcgtttgcctgcagCCAAAATTCCTTTCCCGCTCACGCAAAGATTCCGAGGGATGTTGCAAAATGGAATCGACTTGAGCTCGGTGGATGTGAGCTATGTCAGCAGCCGTTCATG

upper sequence: LOC_Os09g32220.1 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ16068 (Selaginella moellendorffii), 3'ss of exon 4
catacgtgtcatccacttattttgtttttgtaatcatatgtacaattcaatggcatgtacttgtgtccctggactcacatatttcctgctctcttttcagCTAAGATTCCCTTTCCATTGACTCCGCGATTCAGGGGAATGCTGCAAAACGGGATAGACCTGAGTACTGTTGATGTGAGCTATGTTAGCAGCCGTTCATG
                                                |||    | ||     | |  |   ||   |  |     | |  | |  |||| || ||||| || ||  | || |   ||||| | || ||| ||||||| || || ||| ||||  | || |||||||||||||| ||||||||||||||
----------------------------------------------gtaatactttttatacaagcctttcttctt-tacgtgcatcgtttgcctg-cagCCAAAATTCCTTTCCCGCTCACGCAAAGATTCCGAGGGATGTTGCAAAATGGAATCGACTTGAGCTCGGTGGATGTGAGCTATGTCAGCAGCCGTTCATG

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|86511384|gb|CI154017.1|CI154017
EST:     TTCTTTTCGGGCTGTGTTGCAG                         CTAAGATTCCCTTTCCATTGACTCCGCGATTCAGGGGAATGCTGCAAAACG
genomic: TTCTTTTCGGGTTTTGTTGCAGgtatgcactt ... ctcttttcagCTAAGATTCCCTTTCCATTGACTCCGCGATTCAGGGGAATGCTGCAAAACG
EST: gi|58686514|gb|CK075201.1|CK075201
EST:     ACACTTACATTTGCATGGGTGAACTTCTTCTTTTCAGGTTTTGTTGCAG                         CTAAGATTCCCTTTCCATTGACTCCGCGATTCAGGGGAATGCTGCAAAACG
genomic: ACACTTACATTTGCATGGGTGAACTTCTTCTTTTCGGGTTTTGTTGCAGgtatgcactt ... ctcttttcagCTAAGATTCCCTTTCCATTGACTCCGCGATTCAGGGGAATGCTGCAAAACG
EST: gi|66920739|gb|CX107587.1|CX107587
EST:     GACACTTACATTTGCATGGGTGAACTTCTTCTTTTCGGGTTTTGTTGCAG                         CTAAGATTCCCTTTCCATTGACTCCGCGATTCAGGGGAATGCTGCAAAACG
genomic: GACACTTACATTTGCATGGGTGAACTTCTTCTTTTCGGGTTTTGTTGCAGgtatgcactt ... ctcttttcagCTAAGATTCCCTTTCCATTGACTCCGCGATTCAGGGGAATGCTGCAAAACG
EST: gi|88206181|gb|CI206030.1|CI206030
EST:     GACACTTACATTTGCATGGGTG-ACTTCTTCTTTTCGGGTTTTGTTGCAG                         CTAAGATTCCCTTTCCATGGACTCCGCGATTCAGGGGAATGCTGCAAAACG
genomic: GACACTTACATTTGCATGGGTGAACTTCTTCTTTTCGGGTTTTGTTGCAGgtatgcactt ... ctcttttcagCTAAGATTCCCTTTCCATTGACTCCGCGATTCAGGGGAATGCTGCAAAACG
EST: gi|87032311|gb|CI264092.1|CI264092
EST:     ACACTTACATTTGCATGGGTG-ACTTCTTCTTTTCGGGTTTTGTTGCAG                         CTAAGATTCCCTTTCCATNGACTCCGCGATTCAGGGGAATGCTGCAAAACG
genomic: ACACTTACATTTGCATGGGTGAACTTCTTCTTTTCGGGTTTTGTTGCAGgtatgcactt ... ctcttttcagCTAAGATTCCCTTTCCATTGACTCCGCGATTCAGGGGAATGCTGCAAAACG
EST: gi|25806351|gb|CA762312.1|CA762312
EST:     ACACTTACATTTGCATGGGTGAACTTCTTCTTTTCAGGTTTTGTTGCAG                         CTAAGATTCCCTTTCCATTGACTCCGCGATTCAGGGGAATGCTGCAAAACG
genomic: ACACTTACATTTGCATGGGTGAACTTCTTCTTTTCGGGTTTTGTTGCAGgtatgcactt ... ctcttttcagCTAAGATTCCCTTTCCATTGACTCCGCGATTCAGGGGAATGCTGCAAAACG
EST: gi|4716728|gb|AU057844.1|AU057844
EST:     TGAACTTCTTCTTTTCGGGTTTTGTTGCAG                         CTAAGATTCCCTTTCCATTGACTCCGCGATTCAGGGGAATGCTGCAAAACG
genomic: TGAACTTCTTCTTTTCGGGTTTTGTTGCAGgtatgcactt ... ctcttttcagCTAAGATTCCCTTTCCATTGACTCCGCGATTCAGGGGAATGCTGCAAAACG
EST: gi|86506491|gb|CI149124.1|CI149124
EST:     ACACTTACATTTGCATGGGTGAACTTCTTCTTTTCGGGTTTTGTTGCAG                         CTAAGATTCCCTTTCCATTGACTCCGCGATTCAGGGGAATGCTGCAAAACG
genomic: ACACTTACATTTGCATGGGTGAACTTCTTCTTTTCGGGTTTTGTTGCAGgtatgcactt ... ctcttttcagCTAAGATTCCCTTTCCATTGACTCCGCGATTCAGGGGAATGCTGCAAAACG
EST: gi|86854905|gb|CI260973.1|CI260973
EST:     ACACTTACATTTGCATGGGTG-ACTTCTTCTTTTCGGGTTTTGTTGCAG                         CTAAGATTCCCTTTCCATTGACTCCGCGATTCAGGGGAATGCTGCAAAACG
genomic: ACACTTACATTTGCATGGGTGAACTTCTTCTTTTCGGGTTTTGTTGCAGgtatgcactt ... ctcttttcagCTAAGATTCCCTTTCCATTGACTCCGCGATTCAGGGGAATGCTGCAAAACG
EST: gi|33688252|gb|CF316491.1|CF316491
EST:     ACACTTACATTTGCATAGGTGAACTTCTTCTTTTCGGGTTTTGTTGCAG                         CTAAGATTCCCTTTCCATTGACTCCGCGATTCAGGGGAATGCT
genomic: ACACTTACATTTGCATGGGTGAACTTCTTCTTTTCGGGTTTTGTTGCAGgtatgcactt ... ctcttttcagCTAAGATTCCCTTTCCATTGACTCCGCGATTCAGGGGAATGCT
EST: gi|86543296|gb|CI183502.1|CI183502
EST:     ACACTTACATTTGCATGGGTGAACTTCTTCTTTTCGGGTTTTGTTGCAG                         CTAAGATTCCCTTTCCATTGACTCCGCGATTCAGGGGAATGCTGCAAAACG
genomic: ACACTTACATTTGCATGGGTGAACTTCTTCTTTTCGGGTTTTGTTGCAGgtatgcactt ... ctcttttcagCTAAGATTCCCTTTCCATTGACTCCGCGATTCAGGGGAATGCTGCAAAACG
EST: gi|117242276|gb|CT842928.1|CT842928
EST:     ACACTTACATTTGCATGGGTGAACTTCTTCTTTTCGGGTTTTGTTGCAG                         CTAAGATTCCCTTTCCATTGACTCCGCGATTCAGGGGAATGCTGCAAAACG
genomic: ACACTTACATTTGCATGGGTGAACTTCTTCTTTTCGGGTTTTGTTGCAGgtatgcactt ... ctcttttcagCTAAGATTCCCTTTCCATTGACTCCGCGATTCAGGGGAATGCTGCAAAACG
EST: gi|86417257|gb|CI031466.1|CI031466
EST:     CTTACATTTGCATGGGTG-ACTTCTTCTTTTCGGGTTTTGTTGCAG                         CTAAGATTCCCTTTCCATTGACTCCGCGATTCAGGGGAATGCTGCAAAACG
genomic: CTTACATTTGCATGGGTGAACTTCTTCTTTTCGGGTTTTGTTGCAGgtatgcactt ... ctcttttcagCTAAGATTCCCTTTCCATTGACTCCGCGATTCAGGGGAATGCTGCAAAACG
EST: gi|33665107|gb|CF296074.1|CF296074
EST:     GACACTTACATTTGCATGGGTGAACTTCTTCTTTTCGGGTTTTGTTGCAG                         CTAAGATTCCCTTTCCATTGACTCCGCGATTCAGGGGAATGCTGCAAAACG
genomic: GACACTTACATTTGCATGGGTGAACTTCTTCTTTTCGGGTTTTGTTGCAGgtatgcactt ... ctcttttcagCTAAGATTCCCTTTCCATTGACTCCGCGATTCAGGGGAATGCTGCAAAACG
EST: gi|86251662|gb|CI016951.1|CI016951
EST:     GACACTTACATTTGCATGGGTG-ACTTCTTCTTTTCGGGTTTTGTTGCAG                         CTAAGATTCCCTTTCCATTGACTCCGCGATTCAGGGGAATGCTGCAAAACG
genomic: GACACTTACATTTGCATGGGTGAACTTCTTCTTTTCGGGTTTTGTTGCAGgtatgcactt ... ctcttttcagCTAAGATTCCCTTTCCATTGACTCCGCGATTCAGGGGAATGCTGCAAAACG

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: 49 (upstream exon), 75 (downstream exon)
Score: 63

ACACTTACATTTGCATGGGTGAACTTCTTCTTTTCGGGTTTTGTTGCAGgtatgcactt ... ctcttttcagCTAAGATTCCCTTTCCATTGACTCCGCGATTCAGGGGAATGCTGCAAAACGGGATAGACCTGAGTACTGTTGATGTGAGCTATGTTAGCAGCCGTTCATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcaatggcatgtacttgtgtccctggactcacatatttcctgctctcttttcagCTAAGATTCCCTTTCCATTGACTCCGCGATTCAGGGGAATGCTGCAAAACGGGATAGACCTGAGTACTGTTGATGTGAGCTATGTTAGCAGCCGTTCATG
                          gactcac  putative branch site (score: 63)
                                catatttcctgctctc  CT-rich tract
                               acatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catacgtgtcatccacttattttgtttttgtaatcatatgtacaattcaatggcatgtacttgtgtccctggactcacatatttcctgctctcttttcagCTAAGATTCCCTTTCCATTGACTCCGCGATTCAGGGGAATGCTGCAAAACGGGATAGACCTGAGTACTGTTGATGTGAGCTATGTTAGCAGCCGTTCATG

- - - - -catccac
- - - - - - - - - - - -gtttttg
- - - - - - - - - - - - - - - - - catatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - gcatgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttgtgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccctgga