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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gggcccattctttgtcttatgcatatccttttgttatatactgtattctatcaccgatttaataatactatctcctaatggaactacatctacttttaagGTTGTCCCTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTTGCACAG

Basic information

species Oryza sativa
transcript LOC_Os04g58620.1
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g58620.1 (Oryza sativa), 3'ss of exon 18
lower sequence: GLYMA18G46420.1 (Glycine max), 3'ss of exon 25
gggcccattctttgtcttatgcatatccttttgttatatactgtattctatcaccgat--ttaataatactatctcctaatggaactacatctacttttaagGTTGTCCCTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTTGCACAG-
       ||  |||| ||| |  |  | ||||||   | | |  |    |  ||  |   ||| | | |   |   |||  | |  | |  | ||||  | ||||||||| |||||||||||||||||||| ||  | || |||||||| ||| | ||| 
-aagagttttgttgtttta-gtcttgctttttgtagcaaaattgaaagaaaaacttaccattagtgaaatgcttatctagagaactttctgccacttgca-ggTTGTCCCGGAGACCTTGGAACCAAGTCTTCAACTAGCAGCTGCTGTGCTTTCTCAGG

upper sequence: LOC_Os04g58620.1 (Oryza sativa), 3'ss of exon 18
lower sequence: GLYMA09G39770.1 (Glycine max), 3'ss of exon 21
gggcccattctttgtcttatgcatatccttttgttatatactgtattctatcaccgat--ttaataatactatctcctaatggaactacatctacttttaagGTTGTCCCTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTTGCACAG
      | | ||  | ||  |  |  | ||||||   | | |  |  | |  ||  |   ||| | | |   |  |   |  |||||   |      |  |||||||||| |||||||||||||||||||| ||  | || |||||||| ||| | |||
--aaagagttttgttgtttagtcttgctttttgtagcaaaattgaaacaaaaacttaccattagtgaaatgcttactctagagaactttctgccacatgcagGTTGTCCCAGAGACCTTGGAACCAAGTCTTCAACTAGCAGCTGCTGTGCTTTCTCAG

upper sequence: LOC_Os04g58620.1 (Oryza sativa), 3'ss of exon 18
lower sequence: GLYMA07G08030.1 (Glycine max), 3'ss of exon 17
------------------------------------------------------------gggcccattctttgtcttatgcatatccttttgttatatactgtattctatcaccgatttaataatactatctcctaatggaactacatct-actttta-agGTTGTCCCTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTTGCACAG
                                                              |    ||  ||  || || |||||     | |||   |   || ||| | |     ||     |  |||||| | ||    || | |||  | |||  |||||||||| |||||||||||||||||||| ||  | || || || || ||||| |||
gtaatattctattaccttttctattatgaatgttatgattgccttatggtataattttggaagtgtttttctttactaatacatatttagat-ttagccaaaatactctgttaat--cttctctgtcttatctctttatctctctgcctcttgcatttgcagGTTGTCCCAGAGACCTTGGAACCAAGTCTTCAACTAGCAGCCGCCGTGCTTGCTCAG

upper sequence: LOC_Os04g58620.1 (Oryza sativa), 3'ss of exon 18
lower sequence: AT4G00630.1 (Arabidopsis thaliana), 3'ss of exon 17
gggcccattctttgtcttatgcatatccttttgttatatactgtattctatcaccgatttaataatactatc-tcctaatggaactacatctacttttaagGTTGTCCCTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTTGCACAG
            |  |||   ||  |  | |  |    | ||||  |    || |  ||| | | ||   |  |   |||     ||||   |||  | ||||||| ||||||||  ||||||||||||| ||||| || ||||||||||||||||||
--------gtaataacttccacaacttttctattctccttctgtcattgcacaacattttcaaagtaaactgattaaaatctcgatacaaaaactcgttagGTTGTTCCTGAGACGCTGGAACCAAGTCTTCAGTTAGCAGCTGCTGTTCTTGCACAG

upper sequence: LOC_Os04g58620.1 (Oryza sativa), 3'ss of exon 18
lower sequence: AT1G01790.1 (Arabidopsis thaliana), 3'ss of exon 18
gggcccattctttgtcttatgcatatccttttgttatatac-tgtattctatcaccgatttaataatactatctcctaatggaactacatctacttttaagGTTGTCCCTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTTGCACAG
 |    | ||   | |   | ||    | | |    ||||  | |  | | |||    |  | ||||| || |||        |  |||   ||||||| ||||||||| |||||  |||| || ||||| |||||||| |||||||||||||| |||
-gtaatactcacagaccccttcactctcatctagactatagatatgctttgtcaatcgtacactaataatacctc-------gatcacaaaaactttta-gGTTGTCCCGGAGACTCTGGAGCCTAGTCTACAGTTGGCAGCTGCTGTTCTTGCTCAG

upper sequence: LOC_Os04g58620.1 (Oryza sativa), 3'ss of exon 18
lower sequence: Vv15s0046g03390.t01 (Vitis vinifera), 3'ss of exon 16
-----------------------------------------------------------------------------gggccca----ttctttgtcttatgcatatccttttgttatatactgta-----ttctatcaccgatttaataatactatctcctaatggaactacatctacttttaa----------gGTTGTCCCTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTTGCACAG
                                                                                 | |    | ||    || || | |||  |     |||||  | |      || | ||  |  ||  | |  ||    |     |     | ||||  || ||||          |||||| || |||||||||||||||||||| ||||| |||||||||||||||||||||
gtatcattaattttactttccctttttctattctgtaattttttgacctcttgggcatttattgcattagttattgaaaatctacaactactaaaactaatacctattatcggagtatattttcttagggtttttgtcttcccttctaaatcaccccttgacttttattttgcatcatctgttaaaaaacatacagGTTGTTCCAGAGACCTTGGAACCAAGTCTGCAGTTAGCTGCTGCTGTTCTTGCACAG

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|88491733|gb|CI429005.1|CI429005
EST:     TTGGAGAAAGCTGGTGCAACAGCG                         GTTGTCCCTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTT
genomic: TTGGAGAAAGCTGGTGCAACAGCGgtaagtatgt ... tacttttaagGTTGTCCCTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTT
EST: gi|29675208|gb|CB671483.1|CB671483
EST:     CGCATGATGTGGATCATGGTGTTAACTTGGAGAAAGCTGGTGCAACAGCG                         GTTGTCCCTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTT
genomic: CGCATGATGTGGATCATGGTGTTAACTTGGAGAAAGCTGGTGCAACAGCGgtaagtatgt ... tacttttaagGTTGTCCCTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTT
EST: gi|12622483|gb|AU172696.1|AU172696
EST:     CGCATNATGTGGATCATGGTGTTAACTTGGAGAAAGCTGGTGCAACAGCG                         GTTGTCCCTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTT
genomic: CGCATGATGTGGATCATGGTGTTAACTTGGAGAAAGCTGGTGCAACAGCGgtaagtatgt ... tacttttaagGTTGTCCCTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTT
EST: gi|25806037|gb|CA761998.1|CA761998
EST:     CGCATGATGTGGATCATGGTGTTAACTTGGAGAAAGCTGGTGCAACAGCG                         GTTGTCCCTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTT
genomic: CGCATGATGTGGATCATGGTGTTAACTTGGAGAAAGCTGGTGCAACAGCGgtaagtatgt ... tacttttaagGTTGTCCCTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTT
EST: gi|29630179|gb|CB635188.1|CB635188
EST:     CATGATGTGGATCATGGTGTTAACTTGGAGAAAGCTGGTGCAACAGCG                         GTTGTCCCTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTT
genomic: CATGATGTGGATCATGGTGTTAACTTGGAGAAAGCTGGTGCAACAGCGgtaagtatgt ... tacttttaagGTTGTCCCTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTT
EST: gi|29674001|gb|CB670276.1|CB670276
EST:     CGCATGATGTGGATCATGGTGTTAACTTGGAGAAAGCTGGTGCAACAGCG                         GTTGTCCCTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTT
genomic: CGCATGATGTGGATCATGGTGTTAACTTGGAGAAAGCTGGTGCAACAGCGgtaagtatgt ... tacttttaagGTTGTCCCTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTT
EST: gi|88247369|gb|CI247218.1|CI247218
EST:     CGCATGATGTGGATCATGGTGTTAACTTGGAGAAAGCTGGTGCAACAGCG                         GTTGTCCCTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTT
genomic: CGCATGATGTGGATCATGGTGTTAACTTGGAGAAAGCTGGTGCAACAGCGgtaagtatgt ... tacttttaagGTTGTCCCTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTT
EST: gi|86430204|gb|CI082627.1|CI082627
EST:     CGCATGATGTGGATCATGGTGTTAACTTGGAGAAAGCTGGTGCAACAGCG                         GTTGTCCCTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTT
genomic: CGCATGATGTGGATCATGGTGTTAACTTGGAGAAAGCTGGTGCAACAGCGgtaagtatgt ... tacttttaagGTTGTCCCTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTT
EST: gi|88502339|gb|CI429845.1|CI429845
EST:     TGGAGAAAGCTGGTGCAACAGCG                         GTTGTCCCTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTT
genomic: TGGAGAAAGCTGGTGCAACAGCGgtaagtatgt ... tacttttaagGTTGTCCCTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTT
EST: gi|86430421|gb|CI082844.1|CI082844
EST:     AAAGCTGGTGCAACAGCG                         GTTGTCCCTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTT
genomic: AAAGCTGGTGCAACAGCGgtaagtatgt ... tacttttaagGTTGTCCCTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTT
EST: gi|88504559|gb|CI432065.1|CI432065
EST:     CTGGTGCAACAGCG                         GTTGTCCCTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTT
genomic: CTGGTGCAACAGCGgtaagtatgt ... tacttttaagGTTGTCCCTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTT

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: 53 (upstream exon), 55 (downstream exon)
Score: 21

TGTCTGGGCTTTGAGCAAATATTTTCCAAATGTGAAGACATTCGTCCGAGCGCATGATGTGGATCATGGTGTTAACTTGGAGAAAGCTGGTGCAACAGCGgtaagtatgt ... tacttttaagGTTGTCCCTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTTGCACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctatcaccgatttaataatactatctcctaatggaactacatctacttttaagGTTGTCCCTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTTGCACAG
                           tcctaat  putative branch site (score: 21)
                                           tctactttt  putative PPT
           atttaataatactatc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gggcccattctttgtcttatgcatatccttttgttatatactgtattctatcaccgatttaataatactatctcctaatggaactacatctacttttaagGTTGTCCCTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTTGCACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- -cccattc
- - - - - - - - ttatgca
- - - - - - - - - - - - - -cttttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctacatc