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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtaactgacctggcaattcatcaagtgaagaatttttccccctttttccgaaaccgaataattattgactggatgatgaactcataatcctattcttcagGTGTTGGCAGAGGATGAAAACAATGTGAAAGCATTGTTCAGACGAGGAAAAGCAAGAGCTGAACTTGGTCAGACAGAATCAGCGAGGGAGGACTTCCTGA

Basic information

species Oryza sativa
transcript LOC_Os11g05090.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g05090.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv13s0064g00580.t01 (Vitis vinifera), 3'ss of exon 7
gtaactgacctggcaattcat-caagtgaagaatttttccccctttttccgaaaccgaataat-tattgactggatgatgaactcataatcctattcttcagGTGTTGGCAGAGGATGAAAACAATGTGAAAGCATTGTTCAGACGAGGAAAAGCAAGAGCTGAACTTGGTCAGACAGAATCAGCGAGGGAGGACTTCCTGA
    ||  | ||   |  ||  ||     | | | ||   |  | ||  | |    | | |   | |    ||  | |   | |   |          | |||| ||||||||||||||||||||||| || ||||| || |||||||||||||| ||||| |||||||| || |||||  | ||  | |||||||||   |
--ttctctcatgcacacacacacacacacacagtattgttctttcttatcaactgaggacaggatgtcagatgacttactcaattggatgatggggtcttagGTATTGGCAGAGGATGAAAACAATGTCAAGGCATTATTTAGACGAGGAAAAGCTAGAGCAGAACTTGGGCAAACAGATGCTGCCCGTGAGGACTTCAGTA
















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|22307879|gb|BQ909101.1|BQ909101
EST:     GCCTAATCAAACTGAAGAGATTCGATGAAGCTATCGCACAGTGTAGTATT                         GTGTTGGCAGAGGATGAAAACAATGTGAAAGCATTGTTCAGACGAGGAAAA
genomic: GCCTAATCAAACTGAAGAGATTCGATGAAGCTATCGCACAGTGTAGTATTgtaagttttt ... tattcttcagGTGTTGGCAGAGGATGAAAACAATGTGAAAGCATTGTTCAGACGAGGAAAA
EST: gi|112786266|gb|EE590427.1|EE590427
EST:     GCCTAATCAAACTGAAGAGATTCGATGAAGCTATCGCACAGTGTAGTATT                         GTGTTGGCAGAGGATGAAAACAATGTGAAAGCATTGTTCAGACGAGGAAAA
genomic: GCCTAATCAAACTGAAGAGATTCGATGAAGCTATCGCACAGTGTAGTATTgtaagttttt ... tattcttcagGTGTTGGCAGAGGATGAAAACAATGTGAAAGCATTGTTCAGACGAGGAAAA
EST: gi|86489425|gb|CI132058.1|CI132058
EST:     GATTCGATGAAGCTATCGCACAGTGTAGTATT                         GTGTTGGCAGAGGATGAAAACAATGTGAAAGCATTGTTCAGACGAGGAAAA
genomic: GATTCGATGAAGCTATCGCACAGTGTAGTATTgtaagttttt ... tattcttcagGTGTTGGCAGAGGATGAAAACAATGTGAAAGCATTGTTCAGACGAGGAAAA
EST: gi|29687302|gb|CB683577.1|CB683577
EST:     GCCTAATCAAACTGAAGAGATTCGATGAAGCTATCGCACAGTGTAGTATT                         GTGTTGGCAGAGGATGAAAACAATGTGAAAGCATTGTTCAGACGAGGAAAA
genomic: GCCTAATCAAACTGAAGAGATTCGATGAAGCTATCGCACAGTGTAGTATTgtaagttttt ... tattcttcagGTGTTGGCAGAGGATGAAAACAATGTGAAAGCATTGTTCAGACGAGGAAAA
EST: gi|29663324|gb|CB659599.1|CB659599
EST:     GCCTAATCAAACTGAAGAGATTCGATGAAGCTATCGCACAGTGTAGTATT                         GTGTTGGCAGAGGATGAAAACAATGTGAAAGCATTGTTCAGACGAGGAAAA
genomic: GCCTAATCAAACTGAAGAGATTCGATGAAGCTATCGCACAGTGTAGTATTgtaagttttt ... tattcttcagGTGTTGGCAGAGGATGAAAACAATGTGAAAGCATTGTTCAGACGAGGAAAA
EST: gi|86503286|gb|CI145919.1|CI145919
EST:     GAAGAGATTCGATGAAGCTATCGCACAGTGTAGTATT                         GTGTTGCCAGAGGATGAAAACCATGTGAAATCATTGTTCAGACGAGGAAAA
genomic: GAAGAGATTCGATGAAGCTATCGCACAGTGTAGTATTgtaagttttt ... tattcttcagGTGTTGGCAGAGGATGAAAACAATGTGAAAGCATTGTTCAGACGAGGAAAA
EST: gi|27546946|gb|CA765208.2|CA765208
EST:     GCCTAATCAAACTGAAGAGATTCGATGAAGCTATCGCACAGTGTAGTATT                         T
genomic: GCCTAATCAAACTGAAGAGATTCGATGAAGCTATCGCACAGTGTAGTATTgtaagttttt ... tattcttcag-
EST: gi|27546946|gb|CA765208.2|CA765208
EST:     GCCTAATCAAACTGAAGAGATTCGATGAAGCTATCGCACAGTGTAGTATT                         T
genomic: GCCTAATCAAACTGAAGAGATTCGATGAAGCTATCGCACAGTGTAGTATTgtaagttttt ... tattcttcag-
EST: gi|86500924|gb|CI143557.1|CI143557
EST:     ACTGAAGAGATTCGATGAAGCTATCGCACAGTGTAGTATT                         GTGTTGGCAGAGGATGAAAACAATGTGAAAGCATTGTTCAGACGAGGAAAA
genomic: ACTGAAGAGATTCGATGAAGCTATCGCACAGTGTAGTATTgtaagttttt ... tattcttcagGTGTTGGCAGAGGATGAAAACAATGTGAAAGCATTGTTCAGACGAGGAAAA
EST: gi|58693730|gb|CK082417.1|CK082417
EST:     GCCTAATCAAACTGAAGAGATTCGATGAAGCTATCGCACAGTGTAGTATT                         GTGTTGGCAGAGGATGAAAACAATGTGAAAGCATTGTTCAGACGAGGAAAA
genomic: GCCTAATCAAACTGAAGAGATTCGATGAAGCTATCGCACAGTGTAGTATTgtaagttttt ... tattcttcagGTGTTGGCAGAGGATGAAAACAATGTGAAAGCATTGTTCAGACGAGGAAAA

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: 45 (upstream exon), 35 (downstream exon)
Score: 3

AGATATGGCCTTGGCTGTGAAAAATCCATGTCATCTCAACATGGCCGCATGCCTAATCAAACTGAAGAGATTCGATGAAGCTATCGCACAGTGTAGTATTgtaagttttt ... tattcttcagGTGTTGGCAGAGGATGAAAACAATGTGAAAGCATTGTTCAGACGAGGAAAAGCAAGAGCTGAACTTGGTCAGACAGAATCAGCGAGGGAGGACTTCCTGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccgaaaccgaataattattgactggatgatgaactcataatcctattcttcagGTGTTGGCAGAGGATGAAAACAATGTGAAAGCATTGTTCAGACGAGGAAAAGCAAGAGCTGAACTTGGTCAGACAGAATCAGCGAGGGAGGACTTCCTGA
                 tattgac  putative branch site (score: 3)
                                          tcctattcttc  putative PPT
           aataattattgact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaactgacctggcaattcatcaagtgaagaatttttccccctttttccgaaaccgaataattattgactggatgatgaactcataatcctattcttcagGTGTTGGCAGAGGATGAAAACAATGTGAAAGCATTGTTCAGACGAGGAAAAGCAAGAGCTGAACTTGGTCAGACAGAATCAGCGAGGGAGGACTTCCTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - -tgacctg
- - - - - - - - - - - - - - - - - - - - - - - - - aaaccga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgactgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgaa