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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctgggctccccgtttcttggttttcacggcaggtgcaaatcgggatctcgtttgttgttagttagttgatggcgttgctttgatggtttgctcgtacagGAATCCTGCCCTTCGGTGAAGAACATCCTTCTGCTGGATTCCGAGGGGAAGCGCGTCGCCGTCAAGTACTACACGGATGATTGGCCTACTCTCTCGGCGA

Basic information

species Oryza sativa
transcript LOC_Os05g38610.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g38610.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM5G883149_T03 (Zea mays), 3'ss of exon 1
gctgggctccccgtttcttggttttc---acggcaggtgcaaatcgggatct-cgtttgttgttagttagttgatggcgttgctttgatggtttgctcg-tacagGAATCCTGCCCTTCGGTGAAGAACATCCTTCTGCTGGATTCCGAGGGGAAGCGCGTCGCCGTCAAGTACTACACGGATGATTGGCCTACTCTCTCGGCGA
    ||||| || ||| ||  || ||    | ||| | || |   ||||||| ||  || || | |        ||     |  | ||  ||||| | | | |||||  ||| ||| ||||||||||||||||| || ||||| ||||||||||||||||||||||| ||||||||||  ||||  |||||||||||||| ||||
---cggctctcctttttttttttctctttgccgcaagcgcta--tgggatctgcgaatggtggtggcctcggtttgttaaagggtcgagcgtttgtttgatgcagGAGACCTTCCCGTCGGTGAAGAACATCCTCCTACTGGACTCCGAGGGGAAGCGCGTCGCCGTGAAGTACTACAGCGATGGCTGGCCTACTCTCTCCGCGA

upper sequence: LOC_Os05g38610.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G431350_T01 (Zea mays), 3'ss of exon 1
gctgggctccccgtttcttggttttcacggcaggtgcaaatcgggatctcgtttgttgttagttagttgatggcgttgctttgatggtttgctcg-tacagGAATCCTGCCCTTCGGTGAAGAACATCCTTCTGCTGGATTCCGAGGGGAAGCGCGTCGCCGTCAAGTACTACACGGATGATTGGCCTACTCTCTCGGCGA
   |||||  || ||| ||  | ||  | ||| |  | |   |   |     | ||||||   | | |  ||     |  ||||   |||| | | | |||||  ||||||| |||||||||||||||||  ||||||| || ||||| |||||||||||||| ||||||||||  ||||| ||||||||||| || ||||
atcgggctgtccctttttttctctttgctgcaagctctatgggatctgcgaatggttgttgcctcgatt-tgttaaagggttgaacctttgtttgatgcagGAGACCTGCCCCTCGGTGAAGAACATCCTCTTGCTGGACTCGGAGGGAAAGCGCGTCGCCGTAAAGTACTACAGCGATGACTGGCCTACTCTATCCGCGA
















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|58696220|gb|CK084907.1|CK084907
EST:     GTCTCGCCTCCCGCCCCGTGGAT-CACCTTGCCGCTCCAGATG                         GAATCCTGCCCTTCGGTGAAGAACATCCTTCTGCTGGATTCCGAGGGGAAG
genomic: GTCTCGCCTCCCGCCCCGTGGATCCACCTTGCCGCTCCAGATGgtacgcgtcc ... gctcgtacagGAATCCTGCCCTTCGGTGAAGAACATCCTTCTGCTGGATTCCGAGGGGAAG
EST: gi|87022689|gb|CI293579.1|CI293579
EST:     CTCCGCCGTCTCGCCTCCCGCCCCGTGGATCCACCTTGCCGCTCCAGATG                         GAATCCTGCCCTTCGGTGAAGAACATCCTTCTGCTGGATTCCGAGGGGAAG
genomic: CTCCGCCGTCTCGCCTCCCGCCCCGTGGATCCACCTTGCCGCTCCAGATGgtacgcgtcc ... gctcgtacagGAATCCTGCCCTTCGGTGAAGAACATCCTTCTGCTGGATTCCGAGGGGAAG
EST: gi|33688934|gb|CF317173.1|CF317173
EST:     CTCCGCCGTCTCGCCTCCCGCCCCGTGGATCCACCTTGCCGCTCCAGATG                         GAATCCTGCCCTTCGGTGAAGAACATCCTTCTGCTGGATTCCGAGGGGAAG
genomic: CTCCGCCGTCTCGCCTCCCGCCCCGTGGATCCACCTTGCCGCTCCAGATGgtacgcgtcc ... gctcgtacagGAATCCTGCCCTTCGGTGAAGAACATCCTTCTGCTGGATTCCGAGGGGAAG
EST: gi|88579853|gb|CI691844.1|CI691844
EST:     CTCCGCCGTCTCGCCTCCCGCCCCGTGGATCCACCTTGCCGCTCCAGATG                         GAATCCTGCCCTTCGGTGAAGAACATCCTTCTGCTGGATTCCGAGGGGAAG
genomic: CTCCGCCGTCTCGCCTCCCGCCCCGTGGATCCACCTTGCCGCTCCAGATGgtacgcgtcc ... gctcgtacagGAATCCTGCCCTTCGGTGAAGAACATCCTTCTGCTGGATTCCGAGGGGAAG
EST: gi|396941400|gb|HO188609.1|HO188609
EST:     CTCCGCCGTCTCGCCTCCCGCCCCGTGGATCCACCTTGCCGCTCCAGATG                         GAATCCTGCCCTTCGGTGAAGAACATCCTTCTGCTGGATTCCGAGGGGAAG
genomic: CTCCGCCGTCTCGCCTCCCGCCCCGTGGATCCACCTTGCCGCTCCAGATGgtacgcgtcc ... gctcgtacagGAATCCTGCCCTTCGGTGAAGAACATCCTTCTGCTGGATTCCGAGGGGAAG
EST: gi|88355336|gb|CI679042.1|CI679042
EST:     CTCCGCCGTCTCGCCTCCCGCCCCGTGGATCCACCTTGCCGCTCCAGATG                         GAATCCTGCCCTTCGGTGAAGAACATCCTTCTGCTGGATTCCGAGGGGAAG
genomic: CTCCGCCGTCTCGCCTCCCGCCCCGTGGATCCACCTTGCCGCTCCAGATGgtacgcgtcc ... gctcgtacagGAATCCTGCCCTTCGGTGAAGAACATCCTTCTGCTGGATTCCGAGGGGAAG
EST: gi|33692848|gb|CF321087.1|CF321087
EST:     CTCCGCCGTCTCGCCTCCCGCCCCGTGGATCCACCTTGCCGCTCCAGATG                         GAATCCTGCCCTTCGGTGAAGAACATCCTTCTGCTGGATTCCGAGGGGAAG
genomic: CTCCGCCGTCTCGCCTCCCGCCCCGTGGATCCACCTTGCCGCTCCAGATGgtacgcgtcc ... gctcgtacagGAATCCTGCCCTTCGGTGAAGAACATCCTTCTGCTGGATTCCGAGGGGAAG
EST: gi|88586226|gb|CI703916.1|CI703916
EST:     CTCCGCCGTCTCGCCTCCCGCCCCGTGGATCCACCTTGCCGCTCCAGATG                         GAATCCTGCCCTTCGGTGAAGAACATCCTTCTGCTGGATTCCGAGGGGAAG
genomic: CTCCGCCGTCTCGCCTCCCGCCCCGTGGATCCACCTTGCCGCTCCAGATGgtacgcgtcc ... gctcgtacagGAATCCTGCCCTTCGGTGAAGAACATCCTTCTGCTGGATTCCGAGGGGAAG
EST: gi|88737539|gb|CI759420.1|CI759420
EST:     CTCCGCCGTCTCGCCTCCCGCCCCGTGGATCCACCTTGCCGCTCCAGATG                         GAATCCTGCCCTTCGGTGAAGAACATCCTTCTGCTGGATTCCGAGGGGAAG
genomic: CTCCGCCGTCTCGCCTCCCGCCCCGTGGATCCACCTTGCCGCTCCAGATGgtacgcgtcc ... gctcgtacagGAATCCTGCCCTTCGGTGAAGAACATCCTTCTGCTGGATTCCGAGGGGAAG
EST: gi|29682909|gb|CB679184.1|CB679184
EST:     CTCCGCCGTCTCGCCTCCCGCCCCGTGGATCCACCTTGCCGCTCCAGATG                         GAATCCTGCCCTTCGGTGAAGAACATCCTTCTGCTGGATTCCGAGGGGAAG
genomic: CTCCGCCGTCTCGCCTCCCGCCCCGTGGATCCACCTTGCCGCTCCAGATGgtacgcgtcc ... gctcgtacagGAATCCTGCCCTTCGGTGAAGAACATCCTTCTGCTGGATTCCGAGGGGAAG
EST: gi|33820855|gb|CF336232.1|CF336232
EST:     CTCCGCCGTCTCGCCTCCCGCCCCGTGGATCCACCTTGCCGCTCCAGATG                         GAATCCTGCCCTTCGGTGAAGAACATCCTTCTGCTGGATTCCGAGGGGAAG
genomic: CTCCGCCGTCTCGCCTCCCGCCCCGTGGATCCACCTTGCCGCTCCAGATGgtacgcgtcc ... gctcgtacagGAATCCTGCCCTTCGGTGAAGAACATCCTTCTGCTGGATTCCGAGGGGAAG
EST: gi|33678548|gb|CF306787.1|CF306787
EST:     CTCCGCCGTCTCGCCTCCCGCCCCGTGGATCCACCTTGCCGCTCCAGATG                         GAATCCTGCCCTTCGGTGAAGAACATCCTTCTGCTGGATTCCGAGGGGAAG
genomic: CTCCGCCGTCTCGCCTCCCGCCCCGTGGATCCACCTTGCCGCTCCAGATGgtacgcgtcc ... gctcgtacagGAATCCTGCCCTTCGGTGAAGAACATCCTTCTGCTGGATTCCGAGGGGAAG
EST: gi|218504818|gb|FG952248.1|FG952248
EST:     CTCCGCCGTCTCGCCTCCCGCCCCGTGGATCCACCTTGCCGCTCCAGATG                         GAATCCTGCCCTTCGGTGAAGAACATCCTTCTGCTGGATTCCGAGGGGAAG
genomic: CTCCGCCGTCTCGCCTCCCGCCCCGTGGATCCACCTTGCCGCTCCAGATGgtacgcgtcc ... gctcgtacagGAATCCTGCCCTTCGGTGAAGAACATCCTTCTGCTGGATTCCGAGGGGAAG
EST: gi|88338043|gb|CI677027.1|CI677027
EST:     CTCCGCCGTCTCGCCTCCCGCCCCGTGGATCCACCTTGCCGCTCCAGATG                         GAATCCTGCCCTTCGGTGAAGAACATCCTTCTGCTGGATTCCGAGGGGAAG
genomic: CTCCGCCGTCTCGCCTCCCGCCCCGTGGATCCACCTTGCCGCTCCAGATGgtacgcgtcc ... gctcgtacagGAATCCTGCCCTTCGGTGAAGAACATCCTTCTGCTGGATTCCGAGGGGAAG
EST: gi|38473747|gb|CF957879.1|CF957879
EST:     CTCCGCCGTCTCGCCTCCCGCCCCGTGGATCCACCTTGCCGCTCCAGATG                         GAATCCTGCCCTTCGGTGAAGAACATCCTTCTGCTGGATTCCGAGGGGAAG
genomic: CTCCGCCGTCTCGCCTCCCGCCCCGTGGATCCACCTTGCCGCTCCAGATGgtacgcgtcc ... gctcgtacagGAATCCTGCCCTTCGGTGAAGAACATCCTTCTGCTGGATTCCGAGGGGAAG
EST: gi|58585721|gb|CF984029.1|CF984029
EST:     CTCCGCCGTCTCGCCTCCCGCCCCGTGGATCCACCTTGCCGCTCCAGATG                         GAATCCTGCCCTTCGGTGAAGAACATCCTTCTGCTGGATTCCGAGGGGAAG
genomic: CTCCGCCGTCTCGCCTCCCGCCCCGTGGATCCACCTTGCCGCTCCAGATGgtacgcgtcc ... gctcgtacagGAATCCTGCCCTTCGGTGAAGAACATCCTTCTGCTGGATTCCGAGGGGAAG
EST: gi|88311493|gb|CI572549.1|CI572549
EST:     CTCCGCCGTCTCGCCTCCCGCCCCGTGGATCCACCTTGCCGCTCCAGATG                         GAATCCTGCCCTTCGGTGAAGAACATCCTTCTGCTGGATTCCGAGGGGAAG
genomic: CTCCGCCGTCTCGCCTCCCGCCCCGTGGATCCACCTTGCCGCTCCAGATGgtacgcgtcc ... gctcgtacagGAATCCTGCCCTTCGGTGAAGAACATCCTTCTGCTGGATTCCGAGGGGAAG
EST: gi|88352776|gb|CI678799.1|CI678799
EST:     CTCCGCCGTCTCGCCTCCCGCCCCGTGGATCCACCTTGCCGCTCCAGATG                         GAATCCTGCCCTTCGGTGAAGAACATCCTTCTGCTGGATTCCGAGGGGAAG
genomic: CTCCGCCGTCTCGCCTCCCGCCCCGTGGATCCACCTTGCCGCTCCAGATGgtacgcgtcc ... gctcgtacagGAATCCTGCCCTTCGGTGAAGAACATCCTTCTGCTGGATTCCGAGGGGAAG
EST: gi|88429206|gb|CI690095.1|CI690095
EST:     CTCCGCCGTCTCGCCTCCCGCCCCGTGGATCCACCTTGCCGCTCCAGATG                         GAATCCTGCCCTTCGGTGAAGAACATCCTTCTGCTGGATTCCGAGGGGAAG
genomic: CTCCGCCGTCTCGCCTCCCGCCCCGTGGATCCACCTTGCCGCTCCAGATGgtacgcgtcc ... gctcgtacagGAATCCTGCCCTTCGGTGAAGAACATCCTTCTGCTGGATTCCGAGGGGAAG
EST: gi|88333877|gb|CI645291.1|CI645291
EST:     CTCCGCCGTCTCGCCTCCCGCCCCGTGGATCCACCTTGCCGCTCCAGATG                         GAATCCTGCCCTTCGGTGAAGAACATCCTTCTGCTGGATTCCGAGGGGAAG
genomic: CTCCGCCGTCTCGCCTCCCGCCCCGTGGATCCACCTTGCCGCTCCAGATGgtacgcgtcc ... gctcgtacagGAATCCTGCCCTTCGGTGAAGAACATCCTTCTGCTGGATTCCGAGGGGAAG
EST: gi|88458357|gb|CI695744.1|CI695744
EST:     CTCCGCCGTCTCGCCTCCCGCCCCGTGGATCCACCTTGCCGCTCCAGATG                         GAATCCTGCCCTTCGGTGAAGAACATCCTTCTGCTGGATTCCGAGGGGAAG
genomic: CTCCGCCGTCTCGCCTCCCGCCCCGTGGATCCACCTTGCCGCTCCAGATGgtacgcgtcc ... gctcgtacagGAATCCTGCCCTTCGGTGAAGAACATCCTTCTGCTGGATTCCGAGGGGAAG
EST: gi|33683273|gb|CF311512.1|CF311512
EST:     CTCCGCCGTCTCGCCTCCCGCCCCGTGGATCCACCTTGCCGCTCCAGATG                         GAATCCTGCCCTTCGGTGAAGAACATCCTTCTGCTGGATTCCGAGGGGAAG
genomic: CTCCGCCGTCTCGCCTCCCGCCCCGTGGATCCACCTTGCCGCTCCAGATGgtacgcgtcc ... gctcgtacagGAATCCTGCCCTTCGGTGAAGAACATCCTTCTGCTGGATTCCGAGGGGAAG

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), 71 (downstream exon)
Score: 49

CTTCCTTCGTTGGTCCGCACCTTCTCCCCTCACCCGCCGCCGGGGATCCGCTCCGCCGTCTCGCCTCCCGCCCCGTGGATCCACCTTGCCGCTCCAGATGgtacgcgtcc ... gctcgtacagGAATCCTGCCCTTCGGTGAAGAACATCCTTCTGCTGGATTCCGAGGGGAAGCGCGTCGCCGTCAAGTACTACACGGATGATTGGCCTACTCTCTCGGCGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctcgtttgttgttagttagttgatggcgttgctttgatggtttgctcgtacagGAATCCTGCCCTTCGGTGAAGAACATCCTTCTGCTGGATTCCGAGGGGAAGCGCGTCGCCGTCAAGTACTACACGGATGATTGGCCTACTCTCTCGGCGA
                                 ctttgat  putative branch site (score: 49)
                                          tttgctc  putative PPT
             ttagtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gctgggctccccgtttcttggttttcacggcaggtgcaaatcgggatctcgtttgttgttagttagttgatggcgttgctttgatggtttgctcgtacagGAATCCTGCCCTTCGGTGAAGAACATCCTTCTGCTGGATTCCGAGGGGAAGCGCGTCGCCGTCAAGTACTACACGGATGATTGGCCTACTCTCTCGGCGA

- - ggctccc
- - - - - - -tttcttg
- - - - - - - - - - - - - - - caggtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - gttgtta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gttgctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatggt