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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttgctaataatgccctgcctttctatcttcaattttttagcattccattggacagtcatttgatgaatttatgtaatgttttgtactttcacaatttagGTACAAGTTTGATGATGAACGAGTGACAAAAGAAGACATGAAGCGGGCATTAGAGGAGCAATACGGTGGCGAGGAAGAG

Basic information

species Oryza sativa
transcript LOC_Os01g56490.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g56490.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA14G04890.1 (Glycine max), 3'ss of exon 11
--gttgctaataatgccctgcctttctatcttcaattttttagcattccattggacagtcatttgatgaat-ttatgtaatgttttgtactttcacaatttagGTACAAGTTTGATGATGAACGAGTGACAAAAGAAGACATGAAGCGGGCATTAGAGGAGCAATACGGTGGCGAGGAAGAG
       |   |  | |||  |    ||| ||   || ||| | ||| ||||    | |  |||  |||    |        |  | || ||  | |  ||||||| || |||||||||||  | ||||| ||||||||||  || |||||||||||||||||||| ||||| |||||||||
gcaacattctgagagtcctttcaccttatttttg-ttattttgtattgcatttcttactgctttactgagcacttcactgcatgctttaattgaata--ttagGTATAAATTTGATGATGAGAGGGTGACTAAAGAAGACACTAAACGGGCATTAGAGGAGCAATATGGTGGTGAGGAAGAG

upper sequence: LOC_Os01g56490.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA20G11330.1 (Glycine max), 3'ss of exon 3
-gttgctaataatgccctgcctttctatcttcaattttttagcattccattggacagtcatttgatgaatttatgtaatgttttgtactttcacaatttagGTACAAGTTTGATGATGAACGAGTGACAAAAGAAGACATGAAGCGGGCATTAGAGGAGCAATACGGTGGCGAGGAAGAG
 |   ||   | |  | |  | |||| |   |  ||||| |     |  |||| | ||         | |   | |       | |         | | |||||||| |||||||||||  | |||||||||||||| |  ||  | ||||| ||||||||||| ||||| |||||||||
tgcaactgggagtcactttaccttcttttcactgttttt-aattcccttttggcccgtgtccctgccattcactatttgtgaatatctgactggcactcagGTACAAATTTGATGATGAGAGGGTGACAAAAGAAGATAATAAAAGAGCATTGGAGGAGCAATATGGTGGTGAGGAAGAG

upper sequence: LOC_Os01g56490.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA02G43930.1 (Glycine max), 3'ss of exon 11
-----gttgcta-ataatgccctgcctttctatcttcaattttttagcattccattggacagt-catttgatgaatttatgtaatgttttgtactttcacaatttagGTACAAGTTTGATGATGAACGAGTGACAAAAGAAGACATGAAGCGGGCATTAGAGGAGCAATACGGTGGCGAGGAAGAG
     ||  ||  |   |    ||   || |   ||  |||| ||     |  | ||  || | || |  |||  || ||  ||||  |   ||| |       |||||| || |||||||||||  | ||||| ||||||||||  || |||||||||||||||||||| |||||||||||||||
tgagagtcccttcaccttcttttgttattttgaattgcatttcttgctgctttactgagcacttcactgcatgctttgattgaatgcatatgactat-------tagGTATAAATTTGATGATGAGAGGGTGACTAAAGAAGACACTAAACGGGCATTAGAGGAGCAATATGGTGGCGAGGAAGAG

upper sequence: LOC_Os01g56490.1 (Oryza sativa), 3'ss of exon 11
lower sequence: AT5G06600.2 (Arabidopsis thaliana), 3'ss of exon 11
---------gttgctaataatgccctgcctttctatcttcaattttttagcattccattggacagtcatttgatgaatttatgtaatgttttgtactttcacaatttagGTACAAGTTTGATGATGAACGAGTGACAAAAGAAGACATGAAGCGGGCATTAGAGGAGCAATACGGTGGCGAGGAAGAG
         |||  | | || | |   | ||| |     |||||| |    ||    ||       |||||  |    | ||  | |  ||   ||||   |  || ||||| || ||||||||||||||||| || || |||||  ||||  |||| || ||||||||||| ||||| || ||||||
tacgctgatgttattcacaaggtcacacgtttttg----caatttgtccaaatcatgttttgtg--catttttt---ctcattaactcgttcaaacttctccttttcagGTATAAATTTGATGATGAACGAGTAACCAAGGAAGATTTGAAAAGGGCTTTGGAGGAGCAATATGGTGGTGAAGAAGAG

upper sequence: LOC_Os01g56490.1 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv13s0073g00610.t01 (Vitis vinifera), 3'ss of exon 11
gttgctaataatgccctgcctttctatcttcaattttttagcattc-cattgg-acagtcatttgatgaatttatgtaatgtt---ttgtactttcacaatttagGTACAAGTTTGATGATGAACGAGTGACAAAAGAAGACATGAAGCGGGCATTAGAGGAGCAATACGGTGGCGAGGAAGAG
     |  | ||   ||    || ||  |    | | | | ||||  || | |    ||   |  ||   ||  | |||  ||   ||| | ||      ||||||| ||| |||||||||||||| |||||||||||||| || ||| ||||| |||||||||| || ||||| |||||||||
-----ttttgattttctattattttaattatggtgtctcatcattttcactagtgtcgtttctgtattttttattctaactttcaattggagttctttgctttagGTTCAAATTTGATGATGAACGGGTGACAAAAGAAGATATTAAGAGGGCACTAGAGGAGCAGTATGGTGGTGAGGAAGAG

upper sequence: LOC_Os01g56490.1 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 11
--gttgctaataatgccctgcctttctatcttcaatttt-ttagcattccattggacagtcatt-tgatgaatttatgtaatgttttgtactttcacaatttagGTACAAGTTTGATGATGAACGAGTGACAAAAGAAGACATGAAGCGGGCATTAGAGGAGCAATACGGTGGCGAGGAAGAG
    |    || |   | |||  | | || |  |  |    ||  |||  |    |||||  |  || || ||  |   |||   |||    ||     || ||||| || |||||||||||| | ||||||||||||||| ||||| |||| || ||||||||||| ||||| || ||||||
aatgtatggatgagtacatgcaatgccatttgtagctaagctacaattttaccctacagttgtcatgctgtataaaaagaataacttgggaattt----ttcagGTATAAATTTGATGATGAAAGGGTGACAAAAGAAGACGTGAAGAGGGCTTTGGAGGAGCAATATGGTGGTGAAGAAGAG

upper sequence: LOC_Os01g56490.1 (Oryza sativa), 3'ss of exon 11
lower sequence: EFJ18164 (Selaginella moellendorffii), 3'ss of exon 9
---gttgctaataatgccctgcctttctatcttcaattttt----tagcattcca--ttggacagtcatttgatgaatttatgtaatgttttgtactttcacaatttagGTACAAGTTTGATGATGAACGAGTGACAAAAGAAGACATGAAGCGGGCATTAGAGGAGCAATACGGTGGCGAGGAAGAG
    || |  ||| || | |   |   ||  ||  | |  |    |  |  |  |  |||  |||   || |    |||   |  | || | ||    |  ||     |||| |||||||| |||||||| |||||||||||||| |  ||  | |   | ||||||||||| ||||| ||||| || 
gtactttcagatactgacttaggtagttagttttgaatgctaaaatgacgctagaagttgatcaggttttcggaacattctcgctaagtctcgtttcctggca-----gGTATAAGTTTGACGATGAACGCGTGACAAAAGAAGAAACCAAAAGAGTTCTCGAGGAGCAATATGGTGGAGAGGAGGAA

upper sequence: LOC_Os01g56490.1 (Oryza sativa), 3'ss of exon 11
lower sequence: EFJ14291 (Selaginella moellendorffii), 3'ss of exon 9
---gttgctaataatgccctgcctttctatcttcaattttt----tagcattcca--ttggacagtcatttgatgaatttatgtaatgttttgtactttcacaatttagGTACAAGTTTGATGATGAACGAGTGACAAAAGAAGACATGAAGCGGGCATTAGAGGAGCAATACGGTGGCGAGGAAGAG
    || |  ||| || | |   |   ||  ||  | |  |    |  |  |  |  |||  |||   ||||    |||   |  | || | ||  | |  ||     |||| |||||||| |||||||| |||||||||||||| |  || || |   | ||||||||||| ||||| ||||| || 
gtactttcagatactgacttaggtagttagttttgaatgctaaaatgacgctagaagttgatcaggtttttggaacattctcgctaagtctcgttttctggca-----gGTATAAGTTTGACGATGAACGCGTGACAAAAGAAGAAACCAAACGAGTTCTCGAGGAGCAATATGGTGGAGAGGAGGAA

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|86899049|gb|CI296221.1|CI296221
EST:     CATGGTGGACACTACTACGCCTTTATACGCCCGGCACTTTCAGATATATG                         GTACAAGTTTGATGATGAACGAGTGACAAAAGAAGACATGAAGCGGGCATT
genomic: CATGGTGGACACTACTACGCCTTTATACGCCCGGCACTTTCAGATATATGgtacatctaa ... cacaatttagGTACAAGTTTGATGATGAACGAGTGACAAAAGAAGACATGAAGCGGGCATT
EST: gi|89163644|gb|CI100534.1|CI100534
EST:     CATGGTGGACACTACTACGCCTTTATACGCCCGGCACTTTCAGATATATG                         GTACAAGTTTGATGATGAACGAGTGACAAAAGAAGACATGAAGCGGGCATT
genomic: CATGGTGGACACTACTACGCCTTTATACGCCCGGCACTTTCAGATATATGgtacatctaa ... cacaatttagGTACAAGTTTGATGATGAACGAGTGACAAAAGAAGACATGAAGCGGGCATT
EST: gi|88223226|gb|CI223075.1|CI223075
EST:     CATGGTGGACACTACTACGCCTTTATACGCCCGGCACTTTCAGATATATG                         GTACAAGTTTGATGATGAACGAGTGACAAAAGAAGACATGAAGCGGGCATT
genomic: CATGGTGGACACTACTACGCCTTTATACGCCCGGCACTTTCAGATATATGgtacatctaa ... cacaatttagGTACAAGTTTGATGATGAACGAGTGACAAAAGAAGACATGAAGCGGGCATT
EST: gi|29639377|gb|CB644386.1|CB644386
EST:     CATGGTGGACACTACTACGCCTTTATACGCCCGGCACTTTCAGATATATG                         GTACAAGTTTGATGATGAACGAGTGACAAAAGAAGACATGAAGCGGGCATT
genomic: CATGGTGGACACTACTACGCCTTTATACGCCCGGCACTTTCAGATATATGgtacatctaa ... cacaatttagGTACAAGTTTGATGATGAACGAGTGACAAAAGAAGACATGAAGCGGGCATT
EST: gi|8955595|gb|BE229401.1|BE229401
EST:     CATGGTGGACACTACTACGCCTTTATACGCCCGGCACTTTCAGATATATG                         GTACAAGTTTGATGATGAACGAGTGACAAAAGAAGACATGAAGCGGGCATT
genomic: CATGGTGGACACTACTACGCCTTTATACGCCCGGCACTTTCAGATATATGgtacatctaa ... cacaatttagGTACAAGTTTGATGATGAACGAGTGACAAAAGAAGACATGAAGCGGGCATT
EST: gi|58692924|gb|CK081611.1|CK081611
EST:     CATGGTGGACACTACTACGCCTTTATACACCCGGCACTTTCAGATATATG                         GTACAAGTTTGATGATGAACGAGTGACAAAAGAAGACATGAAGCGGGCATT
genomic: CATGGTGGACACTACTACGCCTTTATACGCCCGGCACTTTCAGATATATGgtacatctaa ... cacaatttagGTACAAGTTTGATGATGAACGAGTGACAAAAGAAGACATGAAGCGGGCATT
EST: gi|86260523|gb|CI066396.1|CI066396
EST:     CATGGTGGACACTACTACGCCTTTATACGCCCGGCACTTTCAGATATATG                         GTACAAGTTTGATGATGAACGAGTGACAAAAGAAGACATGAAGCGGGCATT
genomic: CATGGTGGACACTACTACGCCTTTATACGCCCGGCACTTTCAGATATATGgtacatctaa ... cacaatttagGTACAAGTTTGATGATGAACGAGTGACAAAAGAAGACATGAAGCGGGCATT
EST: gi|86504086|gb|CI146719.1|CI146719
EST:     CATGGTGGACACTACTACGCCTTTATACGCCCGGCACTTTCAGATATATG                         GTACAAGTTTGATGATGAACGAGTGACAAAAGAAGACATGAAGCGGGCATT
genomic: CATGGTGGACACTACTACGCCTTTATACGCCCGGCACTTTCAGATATATGgtacatctaa ... cacaatttagGTACAAGTTTGATGATGAACGAGTGACAAAAGAAGACATGAAGCGGGCATT

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: 51 (upstream exon), 75 (downstream exon)
Score: 11

CGTACTTGTTCATAGTGGTGGTGGTCATGGTGGACACTACTACGCCTTTATACGCCCGGCACTTTCAGATATATGgtacatctaa ... cacaatttagGTACAAGTTTGATGATGAACGAGTGACAAAAGAAGACATGAAGCGGGCATTAGAGGAGCAATACGGTGGCGAGGAAGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccattggacagtcatttgatgaatttatgtaatgttttgtactttcacaatttagGTACAAGTTTGATGATGAACGAGTGACAAAAGAAGACATGAAGCGGGCATTAGAGGAGCAATACGGTGGCGAGGAAGAG
             atttgat  putative branch site (score: 11)
                                       tactttc  putative PPT
                     aatttatgtaatgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgctaataatgccctgcctttctatcttcaattttttagcattccattggacagtcatttgatgaatttatgtaatgttttgtactttcacaatttagGTACAAGTTTGATGATGAACGAGTGACAAAAGAAGACATGAAGCGGGCATTAGAGGAGCAATACGGTGGCGAGGAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- tgctaat
- - - - -aatgccc
- - - - - - - - tgccttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttttg