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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taaaatcgtagtcccaaatgtatattaggaattacgacatgcatggtacttgataaagacatttgcagcagattccaatgttgattttttgcttgtgcagCCTCCTGAAGTCTGGAACGGTGGCGTTGGGTTTGTGTCACAGGACATGATTAAAGCTCATTTGCCAGCACCTGCCGAGGACATTCAA

Basic information

species Oryza sativa
transcript LOC_Os01g59930.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g59930.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G133213_T01 (Zea mays), 3'ss of exon 7
-----taaaatcgtagtccc---aaatgtatattaggaattacgacat-gcatggtacttgataaagacatttgcagcagattccaatgttgattttttgcttgtgcagCCTCCTGAAGTCTGGAACGGTGGCGTTGGGTTTGTGTCACAGGACATGATTAAAGCTCATTTGCCAGCACCTGCCGAGGACATTCAA
     | || |  |  |||    |||| |   ||| |   ||| |  | |||   |  ||   ||||||||  |    | |   || ||||     ||| |||||||||||||||||   |||||||||||| ||||||||||||||  |||| |||||  || ||||||  ||||| ||||| ||||||||||| 
tcatttgaagttattatcctgagaaatctgctttacgttatactaattagcacattgtttc-caaagacatccgacataca---cagtgtt-----tttacttgtgcagCCTCCTGAGAACTGGAACGGTGGTGTTGGGTTTGTGTCTAAGGAAATGATCCAATCTCATTGTCCAGCGCCTGCTGAGGACATTCAG

upper sequence: LOC_Os01g59930.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv08s0056g01150.t01 (Vitis vinifera), 3'ss of exon 7
--taaaatcg---tagtcccaaatgtatattaggaattacgacatgcatggtacttgataaagacatttgcagcagattccaatgttgattttttgcttgtgcagCCTCCTGAAGTCTGGAACGGTGGCGTTGGGTTTGTGTCACAGGACATGATTAAAGCTCATTTGCCAGCACCTGCCGAGGACATTCAA
  | | |||    |||  |    | || | |  |   || |  |||  || |  ||  ||     ||||   | | ||| |    | || |  |  ||    |||||||||||||  |||||||||||||| |||||||| ||  |||| ||||| || || ||||  || ||||||||    |||||| | 
attcacatcaggctagctctccttttacaat--gttgtatgtgatgattgtttttttttatttttattttatgta-attgctgcttggactact--ctcccacagCCTCCTGAAGCATGGAACGGTGGCGTCGGGTTTGTATCCAAGGAAATGATCAAGGCCCATTGCCCTGCACCTGCATCTGACATTAAG
















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|117244284|gb|CT843075.1|CT843075
EST:     TGGCCAAAACCTACCCTGATCGCTTTAAGATCTACTATGTCTTGAATCAG                         CCTCCTGAAGTCTGGAACGGTGGCGTTGGGTTTGTGTCACAGGACATGATT
genomic: TGGCCAAAACCTACCCTGATCGCTTTAAGATCTACTATGTCTTGAATCAGgtgaacccta ... gcttgtgcagCCTCCTGAAGTCTGGAACGGTGGCGTTGGGTTTGTGTCACAGGACATGATT
EST: gi|15852322|gb|BI805118.1|BI805118
EST:     TACTATGTCTTGAATCAG                         CCTCCTGAAGTCTGGAACGGTGGCCTTGGGTTTGTGTCACAGGACATGATT
genomic: TACTATGTCTTGAATCAGgtgaacccta ... gcttgtgcagCCTCCTGAAGTCTGGAACGGTGGCGTTGGGTTTGTGTCACAGGACATGATT
EST: gi|88201419|gb|CI201774.1|CI201774
EST:     TGGCCCAAACCTACCCTGATCGCTTTAAGATCTACTATGTCTTGAATCAG                         CCTCCTGAAGTCTGGAACGGTGGCGTTGGGTTTGTGTCACAGGACATGATT
genomic: TGGCCAAAACCTACCCTGATCGCTTTAAGATCTACTATGTCTTGAATCAGgtgaacccta ... gcttgtgcagCCTCCTGAAGTCTGGAACGGTGGCGTTGGGTTTGTGTCACAGGACATGATT
EST: gi|3767653|gb|AU031680.1|AU031680
EST:     TGGCCAAAACCTACCCTGATCGCTTTAAGATCTACTATGTCTTGAATCAG                         CCTCCTGAAGTCTGGAACGNTGGCGTTGGGTTTGTGTCACAGGACATGATT
genomic: TGGCCAAAACCTACCCTGATCGCTTTAAGATCTACTATGTCTTGAATCAGgtgaacccta ... gcttgtgcagCCTCCTGAAGTCTGGAACGGTGGCGTTGGGTTTGTGTCACAGGACATGATT
EST: gi|88987863|gb|CI017952.1|CI017952
EST:     TGGCCAAAACCTACCCTGATCGCTTTAAGATCTACTATGTCTTGAATCAG                         CCTCCTGAAGTCTGGAACGGTGGCGTTGGGTTTGTGTCACAGGACATGATT
genomic: TGGCCAAAACCTACCCTGATCGCTTTAAGATCTACTATGTCTTGAATCAGgtgaacccta ... gcttgtgcagCCTCCTGAAGTCTGGAACGGTGGCGTTGGGTTTGTGTCACAGGACATGATT
EST: gi|88214448|gb|CI214297.1|CI214297
EST:     TGGCCAAAACCTACCCTGATCGCTTTAAGATCTACTATGTCTTGAATCAG                         CCTCCTGAAGTCTGGAACGGTGGCGTTGGGTTTGTGTCACAGGACATGATT
genomic: TGGCCAAAACCTACCCTGATCGCTTTAAGATCTACTATGTCTTGAATCAGgtgaacccta ... gcttgtgcagCCTCCTGAAGTCTGGAACGGTGGCGTTGGGTTTGTGTCACAGGACATGATT
EST: gi|58689499|gb|CK078186.1|CK078186
EST:     TGGCCAAAACCTACCCTGATCGCTTTAAGATCTACTATGTCTTGAATCAG                         CCTCCTGAAGTCTGGAACGGTGGCGTTGGGTTTGTGTCACAGGACATGATT
genomic: TGGCCAAAACCTACCCTGATCGCTTTAAGATCTACTATGTCTTGAATCAGgtgaacccta ... gcttgtgcagCCTCCTGAAGTCTGGAACGGTGGCGTTGGGTTTGTGTCACAGGACATGATT
EST: gi|88832171|gb|CI017405.1|CI017405
EST:     TGGCCAAAACCTACCCTGATCGCTTTAAGATCTACTATGTCTTGAATCAG                         CCTCCTGAAGTCTGGAACGGTGGCGTTGGGTTTGTGTCACAGGACATGATT
genomic: TGGCCAAAACCTACCCTGATCGCTTTAAGATCTACTATGTCTTGAATCAGgtgaacccta ... gcttgtgcagCCTCCTGAAGTCTGGAACGGTGGCGTTGGGTTTGTGTCACAGGACATGATT
EST: gi|11171266|gb|AU163705.1|AU163705
EST:     TGGCCAAAACCTACCCTGATCGCTTTAAGATCTACTATGTCTTGAATCAG                         CCTCCTGAAGTCTGGAACGGTGGCGTTGGGTTTGTGTCACAGGACATGATT
genomic: TGGCCAAAACCTACCCTGATCGCTTTAAGATCTACTATGTCTTGAATCAGgtgaacccta ... gcttgtgcagCCTCCTGAAGTCTGGAACGGTGGCGTTGGGTTTGTGTCACAGGACATGATT
EST: gi|88839184|gb|CI378108.1|CI378108
EST:     TGCCCAAAACCTACCCTGATCGCTTTAAAATCTACTATGTCTTGAATCAC                         CCTCCTGAAGTCTGGAACGGTGGCGTTGGGTTTGTGTCACAGGACATGATT
genomic: TGGCCAAAACCTACCCTGATCGCTTTAAGATCTACTATGTCTTGAATCAGgtgaacccta ... gcttgtgcagCCTCCTGAAGTCTGGAACGGTGGCGTTGGGTTTGTGTCACAGGACATGATT
EST: gi|88214584|gb|CI214433.1|CI214433
EST:     TGGCCTAAACCTACCCTGATCGCTTTAAGATCTACTATGTCTTGAATCAG                         CCTCCTGAAGTCTGGAACGGTGGCGTTGGGTTTGTGTCACAGGACATGATT
genomic: TGGCCAAAACCTACCCTGATCGCTTTAAGATCTACTATGTCTTGAATCAGgtgaacccta ... gcttgtgcagCCTCCTGAAGTCTGGAACGGTGGCGTTGGGTTTGTGTCACAGGACATGATT
EST: gi|58678583|gb|CK067270.1|CK067270
EST:     TGGCCAAAACCTACCCTGATCGCTTTAAGATCTACTATGTCTTGAATCAG                         CCTCCTGAAGTCTGGAACGGTGGCGTTGGGTTTGTGTCACAGGACATGATT
genomic: TGGCCAAAACCTACCCTGATCGCTTTAAGATCTACTATGTCTTGAATCAGgtgaacccta ... gcttgtgcagCCTCCTGAAGTCTGGAACGGTGGCGTTGGGTTTGTGTCACAGGACATGATT
EST: gi|56158135|gb|C73512.2|C73512
EST:     TGGCCAAAACCTACCCTGATCGCTTTAAGATCTACTATGTCTTGAATCAG                         CCTCCTGAAGTCTGGAACGGTGGCGTTGGGTTTGTGTCACAGGACATGATT
genomic: TGGCCAAAACCTACCCTGATCGCTTTAAGATCTACTATGTCTTGAATCAGgtgaacccta ... gcttgtgcagCCTCCTGAAGTCTGGAACGGTGGCGTTGGGTTTGTGTCACAGGACATGATT
EST: gi|88848493|gb|CI087015.1|CI087015
EST:     TGGCCAAAACCTACCCTGATCGCTTTAAGATCTACTATGTCTTGAATCAG                         CCTCCTGAAGTCTGGAACGGTGGCGTTGGGTTTGTGTCACAGGACATGATT
genomic: TGGCCAAAACCTACCCTGATCGCTTTAAGATCTACTATGTCTTGAATCAGgtgaacccta ... gcttgtgcagCCTCCTGAAGTCTGGAACGGTGGCGTTGGGTTTGTGTCACAGGACATGATT
EST: gi|88847923|gb|CI006109.1|CI006109
EST:     TATGTCTTGAATCAG                         CCTCCTGAAGTCTGGAACGGTGGCGTTGGGTTTGTGTCACAGGACATGATT
genomic: TATGTCTTGAATCAGgtgaacccta ... gcttgtgcagCCTCCTGAAGTCTGGAACGGTGGCGTTGGGTTTGTGTCACAGGACATGATT
EST: gi|86418467|gb|CI032676.1|CI032676
EST:     TGGCCAAAACCTACCCTGATCGCTTTAAGATCTACTATGTCTTGAATCAG                         CCTCCTGAAGTCTGGAACGGTGGCGTTGGGTTTGTGTCACAGGACATGATT
genomic: TGGCCAAAACCTACCCTGATCGCTTTAAGATCTACTATGTCTTGAATCAGgtgaacccta ... gcttgtgcagCCTCCTGAAGTCTGGAACGGTGGCGTTGGGTTTGTGTCACAGGACATGATT
EST: gi|58608501|gb|CK036534.1|CK036534
EST:     TGGCCAAAACCTACCCTGATCGCTTTAAGATCTACTATGTCTTGAATCAG                         CCTCGCTGAAGTCTGGAACGGTGGCGTTGGGTTTGTGTCACAGGACATGAT
genomic: TGGCCAAAACCTACCCTGATCGCTTTAAGATCTACTATGTCTTGAATCAGgtgaacccta ... gcttgtgcagCCTC-CTGAAGTCTGGAACGGTGGCGTTGGGTTTGTGTCACAGGACATGAT
EST: gi|88988656|gb|CI039075.1|CI039075
EST:     TGGCCNAAACCTACCCTGATCGCTTTAAGATCTACTATGTCTTGAATCAG                         CCTCCTGAAGTCTGGAACGGTGGCGTTGGGTTTGTGTCACAGGACATGATT
genomic: TGGCCAAAACCTACCCTGATCGCTTTAAGATCTACTATGTCTTGAATCAGgtgaacccta ... gcttgtgcagCCTCCTGAAGTCTGGAACGGTGGCGTTGGGTTTGTGTCACAGGACATGATT
EST: gi|86545731|gb|CI185937.1|CI185937
EST:     ACCCTGATCGCTTGAAGATCTACTATGTCTTGAATCAG                         CCTCCTGAAGTCTGGAACGGTGGCGTTGGGTTTGTGTCACAGGACATGATT
genomic: ACCCTGATCGCTTTAAGATCTACTATGTCTTGAATCAGgtgaacccta ... gcttgtgcagCCTCCTGAAGTCTGGAACGGTGGCGTTGGGTTTGTGTCACAGGACATGATT

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: 74 (upstream exon), 74 (downstream exon)
Score: 63

GAAGAACTGGACAACATGGCCAAAACCTACCCTGATCGCTTTAAGATCTACTATGTCTTGAATCAGgtgaacccta ... gcttgtgcagCCTCCTGAAGTCTGGAACGGTGGCGTTGGGTTTGTGTCACAGGACATGATTAAAGCTCATTTGCCAGCACCTGCCGAGGACATTCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtacttgataaagacatttgcagcagattccaatgttgattttttgcttgtgcagCCTCCTGAAGTCTGGAACGGTGGCGTTGGGTTTGTGTCACAGGACATGATTAAAGCTCATTTGCCAGCACCTGCCGAGGACATTCAA
                                 tgttgat  putative branch site (score: 63)
                                       ttttttgctt  CT-rich tract
                               aatgttgatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taaaatcgtagtcccaaatgtatattaggaattacgacatgcatggtacttgataaagacatttgcagcagattccaatgttgattttttgcttgtgcagCCTCCTGAAGTCTGGAACGGTGGCGTTGGGTTTGTGTCACAGGACATGATTAAAGCTCATTTGCCAGCACCTGCCGAGGACATTCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - -tgcatgg
- - - - - - - - - - - - - - - - - - - - - - - - - -gataaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcagca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgttga