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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgacaggatggcaatttccctctccctttattgactacttttatttaccattatgatctccagcattaattatgaggatgctttctcttttcttctgcagATACTTGATAGCCTTGCACACGACAGATTATCAACATCCTATGCTCTTCCTCAACACCATTGCAGTTGTTGTGCTGGTTGTTGCAAAACTACCGAACATG

Basic information

species Oryza sativa
transcript LOC_Os04g47970.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g47970.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA07G05940.1 (Glycine max), 3'ss of exon 2
tgacaggatggcaatttccctctcccttta---ttgactacttttatttaccattatgatctccagca-ttaattatgaggatgctttctcttttctt-----ctg-cagATACTTGATAGCCTTGCACACGACAGATTATCAACATCCTATGCTCTTCCTCAACACCATTGCAGTTGTTGTGCTGGTTGTTGCAAAACTACCGAACATG
          | |||||         |  |   | ||     | || |||  ||| | |    ||  | ||| |||      |  ||| | || | ||      || ||| |||||||||||||  ||||| ||||| |||||  |||| |||||  || |||||||  |||||||  |||||||||||||||||||  | ||  |||||
----------gaaattttgtatattttgaaggttagatagactatagttagaattttaaaactcaatagttatttactgccttcttttttgttcttttgctcattgtcagGTACTTGATAGCCTCACACACAACAGACTATCAGAATCCAATGCTGCTCTTCAACACTGTTGCAGTGATTGTGCTGGTTGTTGCAAAGTTCCCCCACATG

upper sequence: LOC_Os04g47970.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA16G02540.1 (Glycine max), 3'ss of exon 2
tgacaggatggcaatttccctctccctttattgactacttt-tatttaccattatgatctccagcattaattatgaggatgctttctcttttcttctg--------cagATACTTGATAGCCTTGCACACGACAGATTATCAACATCCTATGCTCTTCCTCAACACCATTGCAGTTGTTGTGCTGGTTGTTGCAAAACTACCGAACATG
           | || |         |  || || ||   | || |||  ||| | |     || | | |||    |  |   || | | | ||| ||        ||| |||||||||||||  ||||| ||||| |||||  |||| ||| ||||  |||||||  |||||||  |||||||||||||||||||  | ||  |||||
---------ttccatattttgaagggtagatagagtagagtgtagttagaattttaaaacttagtagttatttactgtgtttcttttttgtacttttggtgattgtcagGTACTTGATAGCCTCACACACAACAGACTATCAGAATCCAATGTTCTTATTCAACACTGTTGCAGTGATTGTGCTGGTTGTTGCAAAGTTCCCCCACATG

upper sequence: LOC_Os04g47970.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA16G01830.1 (Glycine max), 3'ss of exon 2
tgacaggatggcaatttccctctccctttattgactacttt-tatttaccattatgatctccagcattaattatgaggatgctttctcttttcttctg--------cagATACTTGATAGCCTTGCACACGACAGATTATCAACATCCTATGCTCTTCCTCAACACCATTGCAGTTGTTGTGCTGGTTGTTGCAAAACTACCGAACATG
           | || |         |  || || ||   | || |||  ||| | |    ||| | | |||    |  |   || | | | ||| ||        ||| |||||||||||||  ||||| ||||| |||||  |||| ||| ||||  |||||||  |||||||  |||||||||||||||||||  | ||  |||||
---------ttctatattttgaagggtagatagagtagagtatagttagaattttaaaactcagtagttatttactgtgtttcttttttgtacttttggtgattgtcagGTACTTGATAGCCTCACACACAACAGACTATCAGAATCCAATGTTCTTATTCAACACTGTTGCAGTGATTGTGCTGGTTGTTGCAAAGTTCCCCCACATG

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|87033865|gb|CI188489.1|CI188489
EST:     AAGCAGCTTACTCGCAACAGAAAATTTCTGGCCGTGGTTCCTTTGGTCCT                         ATACTTGATAGCCTTGCACACGACAGATTATCAACATCCTATGCTCTTCCT
genomic: AAGCAGCTTACTCGCAACAGAAAATTTCTGACCGTGGTTCCTTTGGTCCTgtaagaataa ... tcttctgcagATACTTGATAGCCTTGCACACGACAGATTATCAACATCCTATGCTCTTCCT
EST: gi|88519048|gb|CI446702.1|CI446702
EST:     AAGCAGCTTACTCGCAACAGAAAATTTCTGACCGTGGTTCCTTTGGTCCT                         ATACTTGATAGCCTTGCACACGACAGATTATCAACATCCTATGCTCTTCCT
genomic: AAGCAGCTTACTCGCAACAGAAAATTTCTGACCGTGGTTCCTTTGGTCCTgtaagaataa ... tcttctgcagATACTTGATAGCCTTGCACACGACAGATTATCAACATCCTATGCTCTTCCT
EST: gi|33656903|gb|CF279517.1|CF279517
EST:     AGCAGCTTACTCGCAACAGAAAATTTNCTGACCGTGGTTCCTTTGGTCCT                         ATACTTGATAGCCTTGCACACGACAGATTATCAACATCCTATGCTCTTCCT
genomic: AGCAGCTTACTCGCAACAGAAAATTT-CTGACCGTGGTTCCTTTGGTCCTgtaagaataa ... tcttctgcagATACTTGATAGCCTTGCACACGACAGATTATCAACATCCTATGCTCTTCCT
EST: gi|86542403|gb|CI182609.1|CI182609
EST:     AAGCAGCTTACTCGCAACAGAAAATTTCTGACCGTGGTTCCTTTGGTCCT                         ATACTTGATAGCCTTGCACACGACAGATTATCAACATCCTATGCTCTTCCT
genomic: AAGCAGCTTACTCGCAACAGAAAATTTCTGACCGTGGTTCCTTTGGTCCTgtaagaataa ... tcttctgcagATACTTGATAGCCTTGCACACGACAGATTATCAACATCCTATGCTCTTCCT
EST: gi|27578337|gb|CB001032.1|CB001032
EST:     AAGCAGCTTACTCGCAACAGAAAATTTCTGACCGTGGTTCCTTTGGTCCT                         ATACTTGATAGCCTTGCACACGACAGATTATCAACATCCTATGCTCTTCCT
genomic: AAGCAGCTTACTCGCAACAGAAAATTTCTGACCGTGGTTCCTTTGGTCCTgtaagaataa ... tcttctgcagATACTTGATAGCCTTGCACACGACAGATTATCAACATCCTATGCTCTTCCT
EST: gi|86902849|gb|CI312226.1|CI312226
EST:     AAGCAGCTTACTCGCAACAGAAAATTTCTGACCGTGGTTCCTTTGGTCCT                         ATACTTGATAGCCTTGCACACGACAGATTATCAACATCCTATGCTCTTCCT
genomic: AAGCAGCTTACTCGCAACAGAAAATTTCTGACCGTGGTTCCTTTGGTCCTgtaagaataa ... tcttctgcagATACTTGATAGCCTTGCACACGACAGATTATCAACATCCTATGCTCTTCCT
EST: gi|33655516|gb|CF278130.1|CF278130
EST:     AAGCAGCTTACTCGCAACAGAAAATTTCTGACCGTGGTTCCTTTGGTCCT                         ATACTTGATAGCCTTGCACACGACAGATTATCAACATCCTATGCTCTTCCT
genomic: AAGCAGCTTACTCGCAACAGAAAATTTCTGACCGTGGTTCCTTTGGTCCTgtaagaataa ... tcttctgcagATACTTGATAGCCTTGCACACGACAGATTATCAACATCCTATGCTCTTCCT
EST: gi|88489263|gb|CI426535.1|CI426535
EST:     AAGCAGCTTACTCGCAACAGAAAATTTCTGACCGTGGTTCCTTTGGTCCT                         ATACTTGATAGCCTTGCACACGACAGATTATCAACATCCTATGCTCTTCCT
genomic: AAGCAGCTTACTCGCAACAGAAAATTTCTGACCGTGGTTCCTTTGGTCCTgtaagaataa ... tcttctgcagATACTTGATAGCCTTGCACACGACAGATTATCAACATCCTATGCTCTTCCT
EST: gi|88988512|gb|CI037748.1|CI037748
EST:     AAGCAGCTTACTCGCAACAGAAAATTTCTGACCGTGGTTCCTTTGGTCCT                         ATACTTGATAGCCTTGCACACGACAGATTATCAACATCCTATGCTCTTCCT
genomic: AAGCAGCTTACTCGCAACAGAAAATTTCTGACCGTGGTTCCTTTGGTCCTgtaagaataa ... tcttctgcagATACTTGATAGCCTTGCACACGACAGATTATCAACATCCTATGCTCTTCCT
EST: gi|86542372|gb|CI182578.1|CI182578
EST:     AAGCAGCTTACTCGCAACAGAAAATTTCTGACCGTGGTTCCTTTGGTCCT                         ATACTTGATAGCCTTGCACACGACAGATTATCAACATCCTATGCTCTTCCT
genomic: AAGCAGCTTACTCGCAACAGAAAATTTCTGACCGTGGTTCCTTTGGTCCTgtaagaataa ... tcttctgcagATACTTGATAGCCTTGCACACGACAGATTATCAACATCCTATGCTCTTCCT
EST: gi|88491173|gb|CI428445.1|CI428445
EST:     AAGCAGCTTACTCGCAACAGAAAATTTCTGACCGTGGTTCCTTTGGTCCT                         ATACTTGATAGCCTTGCACACGACAGATTATCAACATCCTATGCTCTTCCT
genomic: AAGCAGCTTACTCGCAACAGAAAATTTCTGACCGTGGTTCCTTTGGTCCTgtaagaataa ... tcttctgcagATACTTGATAGCCTTGCACACGACAGATTATCAACATCCTATGCTCTTCCT
EST: gi|27578317|gb|CB001012.1|CB001012
EST:     AAGCAGCTTACTCGCAACAGAAAATTTCTGACCGTGGTTCCTTTGGTCCT                         ATACTTGATAGCCTTGCACACGACAGATTATCAACATCCTATGCTCTTCCT
genomic: AAGCAGCTTACTCGCAACAGAAAATTTCTGACCGTGGTTCCTTTGGTCCTgtaagaataa ... tcttctgcagATACTTGATAGCCTTGCACACGACAGATTATCAACATCCTATGCTCTTCCT
EST: gi|33664469|gb|CF295436.1|CF295436
EST:     AGCAGCTTACTCGCAACAGAAAAATTTCTGACCGTGGTTCCTTTGGTCCT                         ATACTTGATAGCCTTGCACACGACAGATTATCAACATCCTAT-CTCTTCCT
genomic: AGCAGCTTACTCGCAACAG-AAAATTTCTGACCGTGGTTCCTTTGGTCCTgtaagaataa ... tcttctgcagATACTTGATAGCCTTGCACACGACAGATTATCAACATCCTATGCTCTTCCT
EST: gi|88241938|gb|CI241787.1|CI241787
EST:     AAGCAGCTTACTCGCAACAGAAAATTTCTGACCGTGGTTCCTTTGGTCCT                         ATACTTGATAGCCTTGCACACGACAGATTATCAACATCCTATGCTCTTCCT
genomic: AAGCAGCTTACTCGCAACAGAAAATTTCTGACCGTGGTTCCTTTGGTCCTgtaagaataa ... tcttctgcagATACTTGATAGCCTTGCACACGACAGATTATCAACATCCTATGCTCTTCCT

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: 69 (upstream exon), 55 (downstream exon)
Score: 49

ACCAGGGGATGTATAATAGATTGACTTGGTGGGAGCAAATGGACAATGGGAAGCAGCTTACTCGCAACAGAAAATTTCTGACCGTGGTTCCTTTGGTCCTgtaagaataa ... tcttctgcagATACTTGATAGCCTTGCACACGACAGATTATCAACATCCTATGCTCTTCCTCAACACCATTGCAGTTGTTGTGCTGGTTGTTGCAAAACTACCGAACATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taccattatgatctccagcattaattatgaggatgctttctcttttcttctgcagATACTTGATAGCCTTGCACACGACAGATTATCAACATCCTATGCTCTTCCTCAACACCATTGCAGTTGTTGTGCTGGTTGTTGCAAAACTACCGAACATG
                  cattaat  putative branch site (score: 49)
                                 tgctttctcttttctt  putative PPT
                   attaattatga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgacaggatggcaatttccctctccctttattgactacttttatttaccattatgatctccagcattaattatgaggatgctttctcttttcttctgcagATACTTGATAGCCTTGCACACGACAGATTATCAACATCCTATGCTCTTCCTCAACACCATTGCAGTTGTTGTGCTGGTTGTTGCAAAACTACCGAACATG

- - - - - - - - - - - - - - - - - - - - - - - - - ttatgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctccagc