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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attttttctttgtttgcaggatattagtttgtactaatgctactcattgtagttattgcttcatgatttgttgatctgattccaagttttacgtttgtagGAAGCCCTTTTTATCAGTCATGTACGGACGCATGCCAAAGAAGAGTAACAATACCAAGTATTATGAGGTGCTTGGTGTATCTAAGACAGCAACCCAGGAT

Basic information

species Oryza sativa
transcript LOC_Os02g43930.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g43930.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G118731_T01 (Zea mays), 3'ss of exon 1
----------attttttctttgtttgcaggatattagtttgtactaatgctactcattgtagttattgcttcatgatttgttgatctgattccaagttttacgtttgtagGAAGCCCTTTTTATCAGTCATGTACGGACGCATGCCAAAGAAGAGTA---ACAATACCAAGTATTATGAGGTGCTTGGTGTATCTAAGACAGCAACCCAGGAT
          | |   |  |  |||| |   || | |    |  |  |   | | ||| | ||||||        ||   ||||  |||||   |||||| ||||  ||| |||  | | ||||||  |||||  ||||||||||||| ||||||||   |||||||||||||||| ||||| |||||||| |||||||| ||||  |||   
actgctacagagtaccttctcttttgaaaagtactggcacttttt--tatcatttattattgttatta-------atcgcttgagttgattt-gagttttccgttcatagCAAGTACCTATTATCAACCATGTTTGGACGCATGCCAAGGAAGAGTAGTAACAATACCAAGTATTACGAGGTTCTTGGTGTGTCTAAGACCGCAAGTCAG---
















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|88343932|gb|CI654968.1|CI654968
EST:     CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCG                         GAAGCCCTTTTTATCAGTCATGTACGGACGCATGCCAAAGAAGAGTAACAA
genomic: CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCGgtgaggaagc ... acgtttgtagGAAGCCCTTTTTATCAGTCATGTACGGACGCATGCCAAAGAAGAGTAACAA
EST: gi|58655503|gb|CK044183.1|CK044183
EST:     CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCG                         GAAGCCCTTTTTATCAGTCATGTACGGACGCATGCCAAAGAAGAGTAACAA
genomic: CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCGgtgaggaagc ... acgtttgtagGAAGCCCTTTTTATCAGTCATGTACGGACGCATGCCAAAGAAGAGTAACAA
EST: gi|33796281|gb|CF324007.1|CF324007
EST:     CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCG                         GAAGCCCTTTTTATCAGTCATGTACGGACGCATGCCAAAGAAGAGTAACAA
genomic: CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCGgtgaggaagc ... acgtttgtagGAAGCCCTTTTTATCAGTCATGTACGGACGCATGCCAAAGAAGAGTAACAA
EST: gi|29631437|gb|CB636446.1|CB636446
EST:     CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCG                         GAAGCCCTTTTTATCAGTCATGTACGGACGCATGCCAAAGAAGAGTAACAA
genomic: CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCGgtgaggaagc ... acgtttgtagGAAGCCCTTTTTATCAGTCATGTACGGACGCATGCCAAAGAAGAGTAACAA
EST: gi|58602101|gb|CK012629.1|CK012629
EST:     CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCG                         GAAGCCCTTTTTATCAGTCATGTACGGACGCATGCCAAAGAAGAGTAACAA
genomic: CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCGgtgaggaagc ... acgtttgtagGAAGCCCTTTTTATCAGTCATGTACGGACGCATGCCAAAGAAGAGTAACAA
EST: gi|58687630|gb|CK076317.1|CK076317
EST:     GGTCGCTTCTTCCTCTTCCG                         GAAGCCCTTTTTATCAGTCATGTACGGACGCATGCCAAAGAAGAGTAACAA
genomic: GGTCGCTTCTTCCTCTTCCGgtgaggaagc ... acgtttgtagGAAGCCCTTTTTATCAGTCATGTACGGACGCATGCCAAAGAAGAGTAACAA
EST: gi|58663897|gb|CK052583.1|CK052583
EST:     CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCG                         GAAGCCCTTTTTATCAGTCATGTACGGACGCATGCCAAAGAAGAGTAACAA
genomic: CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCGgtgaggaagc ... acgtttgtagGAAGCCCTTTTTATCAGTCATGTACGGACGCATGCCAAAGAAGAGTAACAA
EST: gi|58604589|gb|CK015117.1|CK015117
EST:     CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCG                         GAAGCCCTTTTTATCAGTCATGTACGGACGCATGCCAAAGAAGAGTAACAA
genomic: CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCGgtgaggaagc ... acgtttgtagGAAGCCCTTTTTATCAGTCATGTACGGACGCATGCCAAAGAAGAGTAACAA
EST: gi|58600729|gb|CK011257.1|CK011257
EST:     CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCG                         GAAGCCCTTTTTATCAGTCATGTACGGACGCATGCCAAAGAAGAGTAACAA
genomic: CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCGgtgaggaagc ... acgtttgtagGAAGCCCTTTTTATCAGTCATGTACGGACGCATGCCAAAGAAGAGTAACAA
EST: gi|58658345|gb|CK051083.1|CK051083
EST:     GGTGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCG                         GAAGCCCTTTTTATCAGTCATGTACGGACGCATGCCAAAGAAGAGTAACAG
genomic: GG-GCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCGgtgaggaagc ... acgtttgtagGAAGCCCTTTTTATCAGTCATGTACGGACGCATGCCAAAGAAGAGTAACAA
EST: gi|58664824|gb|CK053510.1|CK053510
EST:     CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCC-                         ---GCCCTTTTTATCAGTCATGTACGGACGCATGCCAAAGAAGAGTAACAA
genomic: CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCGgtgaggaagc ... acgtttgtagGAAGCCCTTTTTATCAGTCATGTACGGACGCATGCCAAAGAAGAGTAACAA
EST: gi|29619928|gb|CB624940.1|CB624940
EST:     CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCG                         GAAGCCCTTTTTATCAGTCATGTACGGACGCATGCCAAAGAAGAGTAACAA
genomic: CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCGgtgaggaagc ... acgtttgtagGAAGCCCTTTTTATCAGTCATGTACGGACGCATGCCAAAGAAGAGTAACAA
EST: gi|58666150|gb|CK054836.1|CK054836
EST:     CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCG                         GAAGCCCTTTTTATCAGTCATGTACGGACGCATGCCAAAGAAGAGTAACAA
genomic: CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCGgtgaggaagc ... acgtttgtagGAAGCCCTTTTTATCAGTCATGTACGGACGCATGCCAAAGAAGAGTAACAA
EST: gi|58601753|gb|CK012281.1|CK012281
EST:     CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCG                         GAAGCCCTTTTTATCAGTCATGTACGGACGCATGCCAAAGAAGAGTAACAA
genomic: CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCGgtgaggaagc ... acgtttgtagGAAGCCCTTTTTATCAGTCATGTACGGACGCATGCCAAAGAAGAGTAACAA
EST: gi|58679094|gb|CK067781.1|CK067781
EST:     CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCG                         GAAGCCCTTTTTATCAGTCATGTACGGACGCATGCCAAAGAAGAGTAACAA
genomic: CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCGgtgaggaagc ... acgtttgtagGAAGCCCTTTTTATCAGTCATGTACGGACGCATGCCAAAGAAGAGTAACAA
EST: gi|29673001|gb|CB669276.1|CB669276
EST:     CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCG                         GAAGCCCTTTTTATCAGTCATGTACGGACGCATGCCAAAGAAGAGTAACAA
genomic: CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCGgtgaggaagc ... acgtttgtagGAAGCCCTTTTTATCAGTCATGTACGGACGCATGCCAAAGAAGAGTAACAA
EST: gi|58660176|gb|CK048856.1|CK048856
EST:     CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCG                         GAAGCCCTTTTTATCAGTCATGTACGGACGCATGCCAAAGAAGAGTAACAA
genomic: CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCGgtgaggaagc ... acgtttgtagGAAGCCCTTTTTATCAGTCATGTACGGACGCATGCCAAAGAAGAGTAACAA
EST: gi|29683463|gb|CB679738.1|CB679738
EST:     GCTTCTTCCTCTTCCG                         GAAGCCCTTTTTATCAGTCATGTACGGACGCATGCCAAAGAAGAGTAACAA
genomic: GCTTCTTCCTCTTCCGgtgaggaagc ... acgtttgtagGAAGCCCTTTTTATCAGTCATGTACGGACGCATGCCAAAGAAGAGTAACAA
EST: gi|58661196|gb|CK049876.1|CK049876
EST:     GGAGCGGTCGCTTCTTCCTCTTCCG                         GAAGCCCTTTTTATCAGTCATGTACGGACGCATGCCAAAGAAGAGTAACAA
genomic: GGAGCGGTCGCTTCTTCCTCTTCCGgtgaggaagc ... acgtttgtagGAAGCCCTTTTTATCAGTCATGTACGGACGCATGCCAAAGAAGAGTAACAA
EST: gi|58589635|gb|CF987943.1|CF987943
EST:     CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTGCG                         GAAGCCCTTTTTATCAGTCATGTACGTGACGCATGCCAAAGAAGAGTAACA
genomic: CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCGgtgaggaagc ... acgtttgtagGAAGCCCTTTTTATCAGTCATGTACG-GACGCATGCCAAAGAAGAGTAACA

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: 72 (upstream exon), 71 (downstream exon)
Score: 66

AGAGCTCCTCTTCTCCTCCACGGCGGCTGCGCGGCGTCGTCCCGCTCCACCGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCGgtgaggaagc ... acgtttgtagGAAGCCCTTTTTATCAGTCATGTACGGACGCATGCCAAAGAAGAGTAACAATACCAAGTATTATGAGGTGCTTGGTGTATCTAAGACAGCAACCCAGGAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgtagttattgcttcatgatttgttgatctgattccaagttttacgtttgtagGAAGCCCTTTTTATCAGTCATGTACGGACGCATGCCAAAGAAGAGTAACAATACCAAGTATTATGAGGTGCTTGGTGTATCTAAGACAGCAACCCAGGAT
                            atctgat  putative branch site (score: 66)
                                      aagtttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attttttctttgtttgcaggatattagtttgtactaatgctactcattgtagttattgcttcatgatttgttgatctgattccaagttttacgtttgtagGAAGCCCTTTTTATCAGTCATGTACGGACGCATGCCAAAGAAGAGTAACAATACCAAGTATTATGAGGTGCTTGGTGTATCTAAGACAGCAACCCAGGAT

- - - - - tgtttgc
- - - - - - - - - - - - - - - - - - -tgctact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgattc