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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcttgatattccccttcaattgttaatttttgtagttaccatatgccaagtcatttaggttgctatgcagttaataatcgtattcttgttaacattgcagATTGGTCCTGATCAGATTGAGACTCTGTATCAGTATGCCAAATTTCAGTTTGACTGTGGGAATTACTCATTTGCTGCTCAGTACTTGCATCAATACCGTG

Basic information

species Oryza sativa
transcript LOC_Os07g07250.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g07250.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT3G57290.1 (Arabidopsis thaliana), 3'ss of exon 2
-tcttgatattccccttcaa-ttgttaatttttgtagttaccatatgccaagtcatttaggttgctatgcagttaat----aatcgtatt---cttgttaacattgcagATTGGTCCTGATCAGATTGAGACTCTGTATCAGTATGCCAAATTTCAGTTTGACTGTGGGAATTACTCATTTGCTGCTCAGTACTTGCATCAATACCGTG
 |  |||| |      | || ||||| | |||||| |  |   ||| |  | |   ||  |||  | |   ||  |     |||| |||    |||| |  | |  ||||||||||| || ||||||||| || |||| ||||| ||||| ||||||||||| ||||| || || ||   ||||||| | ||  |  | || ||| |  
gttgtgatttggatgattaagttgtttaattttgt-gaaatgttatccagatttggttttgtttgtgtattgtggaacacaaatcttatatggcttggtgtcttatcagATTGGTCCAGACCAGATTGAGGCTTTGTACCAGTACGCCAAGTTTCAGTTTGAATGTGGCAACTATTCTGGTGCTGCTGATTATCTTTACCAGTACAGGA

upper sequence: LOC_Os07g07250.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv00s0252g00070.t01 (Vitis vinifera), 3'ss of exon 2
tcttgatattccccttcaattgttaatttttgtagttaccatatgccaagtcatttaggttgctatgcagttaataatcgtattcttgttaacattgc-----agATTGGTCCTGATCAGATTGAGACTCTGTATCAGTATGCCAAATTTCAGTTTGACTGTGGGAATTACTCATTTGCTGCTCAGTACTTGCATCAATACCGTG
|| || | ||    ||  ||||||  |  ||    | ||   || | | ||  ||| |||   | ||   |  | |||  ||| | | ||  | || |     ||||||| |  || ||||| ||| |  | |||||||||||||||||||||||||| ||||| || |||||   ||||||| | ||| || |||| ||| | |
tcctgtttttgttgttgtattgttgctaatt----tgacagaattctaggtt-tttgggtctatttggcttacaaaattatatcccttttttcttttctgaccagATTGGCCAGGAGCAGATAGAGGCATTATATCAGTATGCCAAATTTCAGTTTGAATGTGGAAACTACTCTGGTGCTGCTGATTACCTGTATCAGTACAGGG
















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|88433436|gb|CI594250.1|CI594250
EST:     GGCTCACCTCGCTCGGCGAGGCCATCGACAACATCCACCAGAACCAGCAG                         ATTGGTCCTGATCAGATTGAG
genomic: GGCTCACCTCGCTCGGCGAGGCCATCGACAACATCCACCAGAACCAGCAGgtcaggccca ... aacattgcagATTGGTCCTGATCAGATTGAG
EST: gi|88369514|gb|CI582709.1|CI582709
EST:     GGCTCACCTCGCTCGGCGAGGCCATCGACAACATCCACCAGAACCAGCAG                         ATTGGTCCTGATCAGATTGAGACTCTGTATCAGTATGCCAAATTTCAGTTT
genomic: GGCTCACCTCGCTCGGCGAGGCCATCGACAACATCCACCAGAACCAGCAGgtcaggccca ... aacattgcagATTGGTCCTGATCAGATTGAGACTCTGTATCAGTATGCCAAATTTCAGTTT
EST: gi|88373406|gb|CI614742.1|CI614742
EST:     TGCTCACCTCGCTCGGAGAGGCCATAGACAACATCCACCAGAACCAGGAG                         ATTGGTCCTGAT
genomic: -GCTCACCTCGCTCGGCGAGGCCATCGACAACATCCACCAGAACCAGCAGgtcaggccca ... aacattgcagATTGGTCCTGAT
EST: gi|33682160|gb|CF310399.1|CF310399
EST:     GGCTCACCTCGCTCGGCGAGGCCATCGACAACATCCACCAGAACCAGCAG                         ATTGGTCCTGATCAGATTGAGACTCTGTATCAGTATGCCAAATTTCAGTTT
genomic: GGCTCACCTCGCTCGGCGAGGCCATCGACAACATCCACCAGAACCAGCAGgtcaggccca ... aacattgcagATTGGTCCTGATCAGATTGAGACTCTGTATCAGTATGCCAAATTTCAGTTT
EST: gi|29616632|gb|CB621644.1|CB621644
EST:     GGCTCACCTCGCTCGGCGAGGCCATCGACAACATCCACCAGAACCAGCAG                         ATTGGTCCTGATCAGATTGAGACTCTGTATCAGTGTGCCAAATTTCAGTTT
genomic: GGCTCACCTCGCTCGGCGAGGCCATCGACAACATCCACCAGAACCAGCAGgtcaggccca ... aacattgcagATTGGTCCTGATCAGATTGAGACTCTGTATCAGTATGCCAAATTTCAGTTT
EST: gi|88431185|gb|CI574356.1|CI574356
EST:     GGCTCACCTCGCTCGGCGAGGCCATCGACAACATCCACCAGAACCAGCAG                         ATTGGTCCTGATCAGATTGA
genomic: GGCTCACCTCGCTCGGCGAGGCCATCGACAACATCCACCAGAACCAGCAGgtcaggccca ... aacattgcagATTGGTCCTGATCAGATTGA
EST: gi|88432308|gb|CI565341.1|CI565341
EST:     GGCTCACCTCGCTCGGCGAGGCCATCGGCAACATCCACCAGAAC-AGGAG                         ATTGGTCCTGATCAGATTGAGACTCTGTATCAGTATGCCAAATTTCAGTTT
genomic: GGCTCACCTCGCTCGGCGAGGCCATCGACAACATCCACCAGAACCAGCAGgtcaggccca ... aacattgcagATTGGTCCTGATCAGATTGAGACTCTGTATCAGTATGCCAAATTTCAGTTT
EST: gi|88417364|gb|CI579025.1|CI579025
EST:     GGCTCACCTCGCTCGGCGAGGC-ATCGACAACATCCACCAGAACCAGCAG                         ATTGGTCCTGAT
genomic: GGCTCACCTCGCTCGGCGAGGCCATCGACAACATCCACCAGAACCAGCAGgtcaggccca ... aacattgcagATTGGTCCTGAT
EST: gi|88423051|gb|CI613352.1|CI613352
EST:     GGCTCACCTCGCTCGGCGAGGC-ATAGACAACATCCACCAGAACCAGCAG                         ATTGGTCCTGATCAGATTGAGACTCTGTATCAGTA
genomic: GGCTCACCTCGCTCGGCGAGGCCATCGACAACATCCACCAGAACCAGCAGgtcaggccca ... aacattgcagATTGGTCCTGATCAGATTGAGACTCTGTATCAGTA
EST: gi|88407742|gb|CI607876.1|CI607876
EST:     GGCTCACCTCGCTCGGCGAGGCCATCGACAACATCCACCAGAACCAGCAG                         ATTGGTCCTGATCAGATTGAGACTCTGTATCAGTATGCCAAATTTCAGTTT
genomic: GGCTCACCTCGCTCGGCGAGGCCATCGACAACATCCACCAGAACCAGCAGgtcaggccca ... aacattgcagATTGGTCCTGATCAGATTGAGACTCTGTATCAGTATGCCAAATTTCAGTTT
EST: gi|88373282|gb|CI614618.1|CI614618
EST:     GGCTCACCTCGCTCGGCGAGGCCATCGACAACATCCACCAGAACCAGCAG                         ATTGGTCCTGATCAGATTGAGATTCTGTATCAGTATGCCAAATTTCAGTTT
genomic: GGCTCACCTCGCTCGGCGAGGCCATCGACAACATCCACCAGAACCAGCAGgtcaggccca ... aacattgcagATTGGTCCTGATCAGATTGAGACTCTGTATCAGTATGCCAAATTTCAGTTT
EST: gi|29660022|gb|CB656297.1|CB656297
EST:     GGCTCACCTCGCTCGGCGAGGCCATCGACAACATCCACCAGAACCAGCAG                         ATTGGTCCTGATCAGATTGAGACTCTGTATCAGTATGCCAAATTTCAGTTT
genomic: GGCTCACCTCGCTCGGCGAGGCCATCGACAACATCCACCAGAACCAGCAGgtcaggccca ... aacattgcagATTGGTCCTGATCAGATTGAGACTCTGTATCAGTATGCCAAATTTCAGTTT

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: 30 (upstream exon), 75 (downstream exon)
Score: 10

CGACGACGTCCCCGAGGACATGGTCAAGCGCCGCGCCGAGGTCGTCTCCAGGCTCACCTCGCTCGGCGAGGCCATCGACAACATCCACCAGAACCAGCAGgtcaggccca ... aacattgcagATTGGTCCTGATCAGATTGAGACTCTGTATCAGTATGCCAAATTTCAGTTTGACTGTGGGAATTACTCATTTGCTGCTCAGTACTTGCATCAATACCGTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccaagtcatttaggttgctatgcagttaataatcgtattcttgttaacattgcagATTGGTCCTGATCAGATTGAGACTCTGTATCAGTATGCCAAATTTCAGTTTGACTGTGGGAATTACTCATTTGCTGCTCAGTACTTGCATCAATACCGTG
                                         tgttaac  putative branch site (score: 10)
                         ttaataatcgtatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcttgatattccccttcaattgttaatttttgtagttaccatatgccaagtcatttaggttgctatgcagttaataatcgtattcttgttaacattgcagATTGGTCCTGATCAGATTGAGACTCTGTATCAGTATGCCAAATTTCAGTTTGACTGTGGGAATTACTCATTTGCTGCTCAGTACTTGCATCAATACCGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - -cccttca
- - - - - - - - - - - - - - - - - - - -catatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctatgca