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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCTATCAAGTTTGTTCTCTCTGGTGCAAACATAATGTGTCCTGGATTGACATCTCCAGGTGGTTCCTTGGATGTTGAAGTTGAGGAGGAAACACCAGTGgtaaaagacttgcctctaaacctctattcatcaactgtagatgcattaagaatgaatctcatctgtaggtggtcatagttaacaatataacatgtttata...

Basic information

species Oryza sativa
transcript LOC_Os01g21180.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g21180.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G180990_T01 (Zea mays), 5'ss of exon 5
CGCTATCAAGTTTGTTCTCTCTGGTGCAAACATAATGTGTCCTGGATTGACATCTCCAGGTGGTTCCTTGGATGTTGAAGTTGAGGAGGAAACACCAGTGgtaaaagacttgcctctaaacctctat-tcatcaactgtagatgcattaagaatgaatctcatctgtaggtggtcatagttaacaatataacatgtttata-
 |||||||| |||||||| ||||| |||||||||||||||||||| ||||| || || |||||| |||| || |  ||||| ||||||||||||||||||||||| | |||      ||  |||||  ||||    |  |||| | | ||   | ||| ||  ||  ||   ||  |    ||| | | ||  ||| ||   
TGCTATCAAATTTGTTCTATCTGGCGCAAACATAATGTGTCCTGGGTTGACTTCACCTGGTGGTGCCTTAGACGACGAAGTCGAGGAGGAAACACCAGTGgtaaatggcttatgctaaattctctaggtcatatgttacagatac-tgaatgttcaatatctacttcagtaagtagtctgcaaccaaaaaat-tgtatacct

upper sequence: LOC_Os01g21180.1 (Oryza sativa), 5'ss of exon 5
lower sequence: AT1G09150.1 (Arabidopsis thaliana), 5'ss of exon 6
CGCTATCAAGTTTGTTCTCTCTGGTGCAAACATAATGTGTCCTGGATTGACATCTCCAGGTGGTTCCTTGGATGTTGAAGTTGAGGAGGAAACACCAGTGgtaaaagacttgcctctaaacctctattcatcaactgtagatgcattaagaatgaatctcatctgtaggtggtcatagttaacaatataacatgtttata
 || || ||||||||||| ||||||||||||||||||||||||||  | ||||| || || ||     |||||   ||||| ||||  ||||  |||||||||  |       |  ||   | ||      ||  | |   || ||  |   |||   | | |  |   |     || ||    |               
TGCCATAAAGTTTGTTCTGTCTGGTGCAAACATAATGTGTCCTGGTCTTACATCCCCGGGAGGCGTTCTGGATCAAGAAGTCGAGGCTGAAAGGCCAGTGgtatgaataaaaacagtatttccctgggttgcatttttgtttgtat--atgctgatcttaaaccatgaat--ctgtatttgtttag--------------
















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|88831835|gb|CI369517.1|CI369517
EST:     CATCTCCAGGTGGTTCCTTGGATTTTGAAGTTGAGGAGGAAACACCAGTG                         GCTATAATGGCTGAAGGCAAACAGCATGCATTGGCAATT-GATATACAAAG
genomic: CATCTCCAGGTGGTTCCTTGGATGTTGAAGTTGAGGAGGAAACACCAGTGgtaaaagact ... tgtttatcagGCTATAATGGCTGAAGGCAAACAGCATGCATTGGCAATTGGATATACAAAG
EST: gi|33688443|gb|CF316682.1|CF316682
EST:     ATCTCCAGGTGGTTCCTTGGATGGTTGAAGTTGAGGAGGAAACACCAGTG                         GCTATAATGGCTGAAGGCAAACAGCATGCATTGGCAATTG
genomic: ATCTCCAGGTGGTTCCTTGGATG-TTGAAGTTGAGGAGGAAACACCAGTGgtaaaagact ... tgtttatcagGCTATAATGGCTGAAGGCAAACAGCATGCATTGGCAATTG
EST: gi|29289887|gb|CB483501.1|CB483501
EST:     CATCTCCAGGTGGTTCCTTGGATGTTGAAGTTGAGGAGGAAACACCAGTG                         GCTATAATGGCTGAAGGCAAACAGCAAGCATTGGC-ATTGGATATACAAAG
genomic: CATCTCCAGGTGGTTCCTTGGATGTTGAAGTTGAGGAGGAAACACCAGTGgtaaaagact ... tgtttatcagGCTATAATGGCTGAAGGCAAACAGCATGCATTGGCAATTGGATATACAAAG
EST: gi|88835943|gb|CI371048.1|CI371048
EST:     TGGTTCCTTGGATGTTGAAGTTGAGGAGGAAACACCAGTG                         GCTATAATGGCTGAAGCCAAACAGCATGCATTGGCAATTGGATATACAAAG
genomic: TGGTTCCTTGGATGTTGAAGTTGAGGAGGAAACACCAGTGgtaaaagact ... tgtttatcagGCTATAATGGCTGAAGGCAAACAGCATGCATTGGCAATTGGATATACAAAG
EST: gi|33812764|gb|CF332270.1|CF332270
EST:     CATCTCCAGGTGGTTCCTTGGATGTTGAAGTTGAGGAGGAAACACCAGTG                         GCTATAATGGCTG
genomic: CATCTCCAGGTGGTTCCTTGGATGTTGAAGTTGAGGAGGAAACACCAGTGgtaaaagact ... tgtttatcagGCTATAATGGCTG
EST: gi|29687412|gb|CB683687.1|CB683687
EST:     CATCTCCAGGTGGTTCCTTGGATGTTGAAGTTGAGGAGGAAACACCAGTG                         GCTATAATGGCTGAAGGCAAACAGCATGCATTGGCAATTGGATATACAAAG
genomic: CATCTCCAGGTGGTTCCTTGGATGTTGAAGTTGAGGAGGAAACACCAGTGgtaaaagact ... tgtttatcagGCTATAATGGCTGAAGGCAAACAGCATGCATTGGCAATTGGATATACAAAG
EST: gi|33682858|gb|CF311097.1|CF311097
EST:     CAGGTGGTTCCTTGGATGTTGAAGTTGAGGAGGAAACACCAGTG                         GCTAATAATGGCTGAAGGCAAACAGCATGCATTGGCAATTGGATATACAAA
genomic: CAGGTGGTTCCTTGGATGTTGAAGTTGAGGAGGAAACACCAGTGgtaaaagact ... tgtttatcagGCT-ATAATGGCTGAAGGCAAACAGCATGCATTGGCAATTGGATATACAAA
EST: gi|88473032|gb|CI410303.1|CI410303
EST:     GAGGAGGAAACACCAGTG                         GCTATAATGGCTGAAGGCAAACAGCATGCATTGGCAATTGGATATACAAAG
genomic: GAGGAGGAAACACCAGTGgtaaaagact ... tgtttatcagGCTATAATGGCTGAAGGCAAACAGCATGCATTGGCAATTGGATATACAAAG
EST: gi|88531796|gb|CI460307.1|CI460307
EST:     ATGTTGAAGTTGAGGAGGAAACACCAGTG                         GCTATAATGGCTGAAGGCAAACAGCATGCATTGGCAATTGGATATACAAAG
genomic: ATGTTGAAGTTGAGGAGGAAACACCAGTGgtaaaagact ... tgtttatcagGCTATAATGGCTGAAGGCAAACAGCATGCATTGGCAATTGGATATACAAAG
EST: gi|218488231|gb|FG951457.1|FG951457
EST:     CATCTCCAGGTGGTTCCTTGGATGTTGAAGTTGAGGAGGAAACACCAGTG                         GCTATAATGGCTGAAGGCAAACAGCATGCATTGGCAATTGGATATACAAAG
genomic: CATCTCCAGGTGGTTCCTTGGATGTTGAAGTTGAGGAGGAAACACCAGTGgtaaaagact ... tgtttatcagGCTATAATGGCTGAAGGCAAACAGCATGCATTGGCAATTGGATATACAAAG
EST: gi|88852472|gb|CI374240.1|CI374240
EST:     TTGAGGAGGAAACACCAGTG                         GCTATAAT-GCTGAA-GCAAACAGCATGCATT-GCAATTGGATATACAAAG
genomic: TTGAGGAGGAAACACCAGTGgtaaaagact ... tgtttatcagGCTATAATGGCTGAAGGCAAACAGCATGCATTGGCAATTGGATATACAAAG
EST: gi|86522655|gb|CI162861.1|CI162861
EST:     ATCTCCAGGTGGTTCCTTGGATGTTGAAGTTGAGGAGGAAACACNCAGTG                         GCTATAATGGCTGAANGGCAAACAGCATGCATTGGCAATTGGATATACAA
genomic: ATCTCCAGGTGGTTCCTTGGATGTTGAAGTTGAGGAGGAAACAC-CAGTGgtaaaagact ... tgtttatcagGCTATAATGGCTGAA-GGCAAACAGCATGCATTGGCAATTGGATATACAA
EST: gi|88514235|gb|CI441741.1|CI441741
EST:     AGGAGGAAACACCAGTG                         GCTATAATGGCTGAAGGCAAACAGCATGCATTGGCAATTGGATATACAAAG
genomic: AGGAGGAAACACCAGTGgtaaaagact ... tgtttatcagGCTATAATGGCTGAAGGCAAACAGCATGCATTGGCAATTGGATATACAAAG
EST: gi|58030638|gb|CX728181.1|CX728181
EST:     CATCTCCAGGTGGTTCCTTGGATGTTGAAGTTGAGGAGGAAACACCAGTG                         GCTATAATGGCTGAAGGCAAACAGCATGCATTGGCAATTGGATATACAAAG
genomic: CATCTCCAGGTGGTTCCTTGGATGTTGAAGTTGAGGAGGAAACACCAGTGgtaaaagact ... tgtttatcagGCTATAATGGCTGAAGGCAAACAGCATGCATTGGCAATTGGATATACAAAG
EST: gi|88508109|gb|CI435615.1|CI435615
EST:     CATCTCCAGGTGGTTCCTTGGATGTTGAAGTTGAGGAGGAAACACCAGTG                         GCTATAATGGCTGAAGGCAAACAGCATGCATTGGCAATTGGATATACAAAG
genomic: CATCTCCAGGTGGTTCCTTGGATGTTGAAGTTGAGGAGGAAACACCAGTGgtaaaagact ... tgtttatcagGCTATAATGGCTGAAGGCAAACAGCATGCATTGGCAATTGGATATACAAAG
EST: gi|55412623|gb|CV724999.1|CV724999
EST:     CATCTCCAGGTGGTTCCTTGGATGTTGAAGTTGAGGAGGAAACACCAGTG                         GCTATAATGGCTGAAGGCAAACAGCATGCATTGGCAATTGGATATACAAAG
genomic: CATCTCCAGGTGGTTCCTTGGATGTTGAAGTTGAGGAGGAAACACCAGTGgtaaaagact ... tgtttatcagGCTATAATGGCTGAAGGCAAACAGCATGCATTGGCAATTGGATATACAAAG
EST: gi|88549468|gb|CI479359.1|CI479359
EST:     TGAANTTGAGGAGGAAACACCAGTG                         GCTATAATGGCTGAAGGCAAACAGCATGCATTGGCAATTGGATATACAAAG
genomic: TGAAGTTGAGGAGGAAACACCAGTGgtaaaagact ... tgtttatcagGCTATAATGGCTGAAGGCAAACAGCATGCATTGGCAATTGGATATACAAAG
EST: gi|33665495|gb|CF296462.1|CF296462
EST:     CATCTCCAGGTGGTTCCTTGGATGTTGAAGTTGAGGAGGAAACACCAGTG                         GCTATAATGGCTGAAGGCAAGCAGCATGCATTGGCAATTGGATATACAAAG
genomic: CATCTCCAGGTGGTTCCTTGGATGTTGAAGTTGAGGAGGAAACACCAGTGgtaaaagact ... tgtttatcagGCTATAATGGCTGAAGGCAAACAGCATGCATTGGCAATTGGATATACAAAG
EST: gi|66917257|gb|CX104105.1|CX104105
EST:     CATCTCCAGGTGGTTCCTTGGATGTTGAAGTTGAGGAGGAAACACCAGTG                         GCTATAATGGCTGAAGGCAAACAGCATGCATTGGCCATTGGATATACAAAG
genomic: CATCTCCAGGTGGTTCCTTGGATGTTGAAGTTGAGGAGGAAACACCAGTGgtaaaagact ... tgtttatcagGCTATAATGGCTGAAGGCAAACAGCATGCATTGGCAATTGGATATACAAAG
EST: gi|88484301|gb|CI421572.1|CI421572
EST:     GGTTCCTTGGATGTTGAAGTTGAGGAGGAAACACCAGTG                         GCTATAATGGCTGAAGGCAAACAGCATGCATTGGCAATTGGATATACAAAG
genomic: GGTTCCTTGGATGTTGAAGTTGAGGAGGAAACACCAGTGgtaaaagact ... tgtttatcagGCTATAATGGCTGAAGGCAAACAGCATGCATTGGCAATTGGATATACAAAG

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), 68 (downstream exon)
Score: 33

CGCTATCAAGTTTGTTCTCTCTGGTGCAAACATAATGTGTCCTGGATTGACATCTCCAGGTGGTTCCTTGGATGTTGAAGTTGAGGAGGAAACACCAGTGgtaaaagact ... tgtttatcagGCTATAATGGCTGAAGGCAAACAGCATGCATTGGCAATTGGATATACAAAGATGTCAGCAAAGGACAT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGCTATCAAGTTTGTTCTCTCTGGTGCAAACATAATGTGTCCTGGATTGACATCTCCAGGTGGTTCCTTGGATGTTGAAGTTGAGGAGGAAACACCAGTGgtaaaagacttgcctctaaacctctattcatcaactgtagatgcattaagaatgaatctcatctgtaggtggtcatagttaacaatataacatgtttata

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA