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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagatcttgtgtgaagttgtagtaaacatagtatcacaatatgctgcaaaattgttttgacgatatggtgcacattctgaagGAAGCACAAGAGTATGCAGAGAAGAATAATATGGTTTTCATCGAGACATCAGCAAAGACAGCTGATAATATAAACCAAGTATTTGAG

Basic information

species Oryza sativa
transcript LOC_Os03g05740.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g05740.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM5G863105_T01 (Zea mays), 3'ss of exon 2
-----------gtcagatcttgtg--tgaagttgtagtaaacatagtat----cacaatatgctgcaaaattgttttgacgatatggtgcacattctgaagGAAGCACAAGAGTATGCAGAGAAGAATAATATGGTTTTCATCGAGACATCAGCAAAGACAGCTGATAATATAAACCAAGTATTTGAG
           ||| |  ||   |   | | |    |  | |  |  ||    | ||| |  |||| | ||  | ||||| |||||||| || |  ||  ||| ||||| || |||||||||||||| || ||| ||||||| ||||| ||||| |||||||||||||||||||||||| | ||||||
gaccatggaccgtccggcctcagggccggactgtccgccagctcaaaatggcgctcaaca-actgctatatgttattgacaatatggtgtacttgttgcggGATGCACAGGACTATGCAGAGAAGAACAAAATGTTTTTCATTGAGACGTCAGCCAAGACAGCTGATAATATAAACCAACTGTTTGAG

upper sequence: LOC_Os03g05740.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G362088_T02 (Zea mays), 3'ss of exon 7
--------gtcagatcttgtgtgaagttgtagtaaacatagtatcacaatatgctgcaaaattgttttgac------gatatggtgcacattctgaagGAAGCACAAGAGTATGCAGAGAAGAATAATATGGTTTTCATCGAGACATCAGCAAAGACAGCTGATAATATAAACCAAGTATTTGAG
         |  | |||| ||  || |  |||  |   |||| | |     |||| | | ||  | |||||      ||||||||| || |  || |||| || || || || ||||||||||| |||||| ||||||| ||||| || || |||||||||||||||||||||||| | ||||||
gtaagagtatatgctctt-tgccaactgatagatattgtagt-taatggc-tgctactatatgatcttgaccatatggatatggtgtacttgttgcagGATGCGCAGGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAG

upper sequence: LOC_Os03g05740.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA10G35230.3 (Glycine max), 3'ss of exon 6
---gtcagatcttgtgtga---agttgtagtaaacatagtatcacaatatgctgcaaaattgttttgacgatatggtgcacattctgaagGAAGCACAAGAGTATGCAGAGAAGAATAATATGGTTTTCATCGAGACATCAGCAAAGACAGCTGATAATATAAACCAAGTATTTGAG
   ||   |   | ||| |   ||||||  || | | |  || |  || |  | |  |  |  | || |  ||  ||   ||   ||||||| |     || |||||||||||||||  |||| ||||||| |||||||| ||||||||||| |||||||||||  || | ||||||
gtagtgcaacactatgtaatatagttgtcatataaacaaaataatcatttttttctcatatagtatg-ctttactgtttcca---tgaaggatggcactgactatgcagAGAAGAATGGTATGTTTTTCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAG

upper sequence: LOC_Os03g05740.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA20G32320.1 (Glycine max), 3'ss of exon 6
-----gtcagatcttgtg-tgaagttgtagtaaacatagtatcacaatatgctgcaaaattgttttgacgatatggtgcacattctgaagGAAGCACAAGAGTATGCAGAGAAGAATAATATGGTTTTCATCGAGACATCAGCAAAGACAGCTGATAATATAAACCAAGTATTTGAG
     |  | |   |||  |  ||||||  || | | |  || |   | || |       | | |  | | | |  ||       ||||||| |     || ||||||||||||||| ||||| ||||||| |||||||| ||||||||||| |||||||||||  || | ||||||
gtagtgcaacactctgtaatatagttgtcatataaacaaaataattgtttgtttttctcatatatatatgctttactgt-ttccatgaagGATGGCACTGACTATGCAGAGAAGAATGATATGTTTTTCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAG

upper sequence: LOC_Os03g05740.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv13s0019g04680.t01 (Vitis vinifera), 3'ss of exon 6
gtcag-atcttgtgtgaagttgtagtaaacatagtatcacaatatgct-gcaaaat-tgttttgacg-atatggtgcacattct-gaagGAAGCACAAGAGTATGCAGAGAAGAATAATATGGTTTTCATCGAGACATCAGCAAAGACAGCTGATAATATAAACCAAGTATTTGAG
|| ||  || |       ||   | |        | |  | || |  |  |||||| || ||| ||   | |       ||||| |||||| |     || |||||||||||||||  |||| | || || || ||||| ||||||||||||||||| ||||||||  | ||||||
gtgagtgtcatactatttgtctgaatgcttcagcttttcctatgtattcacaaaatgtgctttaacacgtgtttattttattcttgaagGATGGTATTGATTATGCAGAGAAGAATGGTATGTTCTTTATTGAAACATCTGCAAAGACAGCTGATAACATAAACCAGCTGTTTGAG

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|11565095|gb|AU165731.1|AU165731
EST:     TGGTTGGTAATAAAGCTGATCTACATGAAAATCGACATGTATCTTCTCAG                         GAAGCACAAGAGTATGCAGAGAAGAATAATATGGTTTTCATCGAGACATCA
genomic: TGGTTGGTAATAAAGCTGATCTACATGAAAATCGACATGTATCTTCTCAGgtcagatctt ... cattctgaagGAAGCACAAGAGTATGCAGAGAAGAATAATATGGTTTTCATCGAGACATCA
EST: gi|88531758|gb|CI460263.1|CI460263
EST:     GCTGATCTACATGAAAATCGACATGTATCTTCTCAG                         GAAGCACAAGAGTATGCAGAGAAGAATAATATGGTTTTCATCGAGACATCA
genomic: GCTGATCTACATGAAAATCGACATGTATCTTCTCAGgtcagatctt ... cattctgaagGAAGCACAAGAGTATGCAGAGAAGAATAATATGGTTTTCATCGAGACATCA
EST: gi|6782805|gb|C99985.1|C99985
EST:     TGGTTGGTAATAAAGCTGATCTACATGAAAATCGACATGTATCTTCTCAG                         GAAGCACAAGAGTATGCAGAGAAGAATAATATGGTTTTCATCGAGACATCA
genomic: TGGTTGGTAATAAAGCTGATCTACATGAAAATCGACATGTATCTTCTCAGgtcagatctt ... cattctgaagGAAGCACAAGAGTATGCAGAGAAGAATAATATGGTTTTCATCGAGACATCA
EST: gi|55412383|gb|CV724759.1|CV724759
EST:     TGGTTGGTAATAAAGCTGATCTACATGAAAATCGACATGTATCTTCTCAG                         GAAGCACAAGAGTATGCAGAGAAGAATAATATGGTTTTCATCGAGACATCA
genomic: TGGTTGGTAATAAAGCTGATCTACATGAAAATCGACATGTATCTTCTCAGgtcagatctt ... cattctgaagGAAGCACAAGAGTATGCAGAGAAGAATAATATGGTTTTCATCGAGACATCA
EST: gi|300216317|gb|HO088102.1|HO088102
EST:     TGGTTGGTAATAAAGCTGATCTACATGAAAATCGACATGTATCTTCTCAG                         GAAGCACAAGAGTATGCAGAGAAGAATAATATGGTTTTCATCGAGACATCA
genomic: TGGTTGGTAATAAAGCTGATCTACATGAAAATCGACATGTATCTTCTCAGgtcagatctt ... cattctgaagGAAGCACAAGAGTATGCAGAGAAGAATAATATGGTTTTCATCGAGACATCA
EST: gi|25803490|gb|CA759389.1|CA759389
EST:     TGGTTGGTAATAAAGCTGATCTACATGAAAATCGACATGTATCTTCTCAG                         GAAGCACAAGAGTATGCAGAGAAGAATAATATGGTTTTCATCGAGACATCA
genomic: TGGTTGGTAATAAAGCTGATCTACATGAAAATCGACATGTATCTTCTCAGgtcagatctt ... cattctgaagGAAGCACAAGAGTATGCAGAGAAGAATAATATGGTTTTCATCGAGACATCA
EST: gi|3760087|gb|C97345.1|C97345
EST:     GGTTGGTNATAAAGCTGATCTACATAAAAATCGACATGTATCTTCTCCAG                         GAAGCACAAGAGTATGCAGAGAAGAATAATATGGTTTTCATCGAGACATC
genomic: GGTTGGTAATAAAGCTGATCTACATGAAAATCGACATGTATCTTCT-CAGgtcagatctt ... cattctgaagGAAGCACAAGAGTATGCAGAGAAGAATAATATGGTTTTCATCGAGACAT-
EST: gi|33659269|gb|CF281882.1|CF281882
EST:     TGGTTGGTAATAAAGCTGATCTACATGAAAATCGACATGTATCTTCTCAG                         GAAGCACAAGAGTATGCAGAGAAGAATAATATGGTTTTCATCGAGACATCA
genomic: TGGTTGGTAATAAAGCTGATCTACATGAAAATCGACATGTATCTTCTCAGgtcagatctt ... cattctgaagGAAGCACAAGAGTATGCAGAGAAGAATAATATGGTTTTCATCGAGACATCA
EST: gi|88543207|gb|CI473197.1|CI473197
EST:     TGGTTGGTAATAAAGCTGATCTACATGAAAATCGACATGTATCTTCTCAG                         GAAGCACAAGAGTATGCAGAGAAGAATAATATGGTTTTCATCGAGACATCA
genomic: TGGTTGGTAATAAAGCTGATCTACATGAAAATCGACATGTATCTTCTCAGgtcagatctt ... cattctgaagGAAGCACAAGAGTATGCAGAGAAGAATAATATGGTTTTCATCGAGACATCA
EST: gi|88526494|gb|CI454559.1|CI454559
EST:     TGGTAATAAAGCTGATCTACATGAAAATGGACATGTATCTTCTCAG                         GAAGCACAAGAGTATGCAGAGAAGAATAATATGGTTTTCATCGAGACATCA
genomic: TGGTAATAAAGCTGATCTACATGAAAATCGACATGTATCTTCTCAGgtcagatctt ... cattctgaagGAAGCACAAGAGTATGCAGAGAAGAATAATATGGTTTTCATCGAGACATCA
EST: gi|88264996|gb|CI368770.1|CI368770
EST:     TGGTTGGTAATAAAGCTGATCTACATGAAAATCGACATGTATCTTCTCAG                         GAAGCACAAGAGTATGCAGAGAAGAATAATATGGTTTTCATCGAGACATCA
genomic: TGGTTGGTAATAAAGCTGATCTACATGAAAATCGACATGTATCTTCTCAGgtcagatctt ... cattctgaagGAAGCACAAGAGTATGCAGAGAAGAATAATATGGTTTTCATCGAGACATCA
EST: gi|33666789|gb|CF297756.1|CF297756
EST:     TGGTTGGTAATANAGCTGATCTACATGAAAATCGACATGTATCTTCTCAG                         GAAGCACAAGAGTATGCAGAGAAGAATAATATGGTTTTCATCGAGACATCA
genomic: TGGTTGGTAATAAAGCTGATCTACATGAAAATCGACATGTATCTTCTCAGgtcagatctt ... cattctgaagGAAGCACAAGAGTATGCAGAGAAGAATAATATGGTTTTCATCGAGACATCA
EST: gi|88526963|gb|CI455065.1|CI455065
EST:     AAAATCGACATGTATCTTCTCAG                         GAAGCACAAGAGTATGCAGAGAAGAATAATATGGTTTTCATCGAGACATCA
genomic: AAAATCGACATGTATCTTCTCAGgtcagatctt ... cattctgaagGAAGCACAAGAGTATGCAGAGAAGAATAATATGGTTTTCATCGAGACATCA

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: 61 (upstream exon), 68 (downstream exon)
Score: 17

GAACTTCAAAAACATGGTAGTCCTGATATTATCATGGTTTTGGTTGGTAATAAAGCTGATCTACATGAAAATCGACATGTATCTTCTCAGgtcagatctt ... cattctgaagGAAGCACAAGAGTATGCAGAGAAGAATAATATGGTTTTCATCGAGACATCAGCAAAGACAGCTGATAATATAAACCAAGTATTTGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagtatcacaatatgctgcaaaattgttttgacgatatggtgcacattctgaagGAAGCACAAGAGTATGCAGAGAAGAATAATATGGTTTTCATCGAGACATCAGCAAAGACAGCTGATAATATAAACCAAGTATTTGAG
                           ttttgac  putative branch site (score: 17)
                    aaaattgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagatcttgtgtgaagttgtagtaaacatagtatcacaatatgctgcaaaattgttttgacgatatggtgcacattctgaagGAAGCACAAGAGTATGCAGAGAAGAATAATATGGTTTTCATCGAGACATCAGCAAAGACAGCTGATAATATAAACCAAGTATTTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT