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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGATGGAATGGATGTTCTTGCTGTGAAGCAGGCATGCAAATTCGCAAAAGAGCATGCTATTGCAAATGGCCCAATTgtgagtaaactttgtcgtgttaatagtatgcatacttatgtagcgcaattatatagatttgctactgttgaactacagtggcttaggattcacatttctt...

Basic information

species Oryza sativa
transcript LOC_Os02g50620.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g50620.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G361693_T01 (Zea mays), 5'ss of exon 3
GTTGATGGAATGGATGTTCTTGCTGTGAAGCAGGCATGCAAATTCGCAAAAGAGCATGCTATTGCAAATGGCCCAATTgtgagtaaactttgtcgt-gttaatagtatgcatacttatgtagcgcaattatatagatttgctactgttgaactacag---tggcttaggattcacatttctt
|||||||||||||||||||||||||||||||| || |||||||| |||||||| |||||| | ||||||||||||||||| ||||   |   || | | | |        ||    |||||||      || |||  |  ||||| ||      | |   |||||| |   |    | |   
GTTGATGGAATGGATGTTCTTGCTGTGAAGCAAGCGTGCAAATTTGCAAAAGATCATGCTGTCGCAAATGGCCCAATTgtaagtactatgaatctttgctgacttctgttatttggatgtagc----ccatgtaggataactactattagggctcggagttggcttggctattctgtgttgc

upper sequence: LOC_Os02g50620.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G140150_T01 (Zea mays), 5'ss of exon 3
GTTGATGGAATGGATGTTCTTGCTGTGAAGCAGGCATGCAAATTCGCAAAAGAGCATGCTATTGCAAATGGCCCAATTgtgagta-----aactttgtcg------tgttaatagtatgcatacttatgtagcgcaattatatagatttgctactgttgaactacagtggcttaggattcacatttctt
|||||||||||||||||||||||||||||||| || |||||||| |||||||| |||||| ||||||||||||||||||||||||     ||  || ||       ||||| | | |||||  |  ||||||   || ||  ||     |||  | | |||  |  |       ||  |          
GTTGATGGAATGGATGTTCTTGCTGTGAAGCAAGCGTGCAAATTTGCAAAAGATCATGCTGTTGCAAATGGCCCAATTgtgagtactatgaatcttttctgacttctgttattgg-atgcac-cccatgtaggagaagtac-tattaaggcttgtttcgaagcaagggaaagaggggattg--------

upper sequence: LOC_Os02g50620.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA02G03080.1 (Glycine max), 5'ss of exon 3
GTTGATGGAATGGATGTTCTTGCTGTGAAGCAGGCATGCAAATTCGCAAAAGAGCATGCTATTGCAAATGGCCCAATTgtgagtaaactttgtcgtgttaatagtatgcatacttatgtagcgcaattatatagatttgctactg----ttgaac-----tacagtggcttaggattcacatttctt
|||||||| ||||||||||||||||| || || || |||||||| ||||| || |||||| |    ||||| ||  ||||||||  | ||| |    ||| |  |||| ||||||   |  | |  || || | ||| | || ||    ||| |      | ||    || | | || ||||     
GTTGATGGTATGGATGTTCTTGCTGTTAAACAAGCTTGCAAATTTGCAAAGGAACATGCTTTGAAGAATGGACCCCTTgtgagttgatttttt----ttactgttatgtatacttgaatttctc--ttctaaaaattagttattggcaattggatgtctattcatctactaaagcttgacataa---

upper sequence: LOC_Os02g50620.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA01G04470.2 (Glycine max), 5'ss of exon 1
----------------------GTTGATGGAATGGATGTTCTTGCTGTGAAGCAGGCATGCAAATTCGCAAAAGAGCATGCTATTGCAAATGGCCCAATTgtgagtaaactttgtcgtgttaatagtatgcatacttatgtagcgcaattatatagatttgctactgttgaactacagtggcttaggattcacatttctt-------
                      |||||||| ||||||||||||||||| || || || |||||||| ||||| || |||||| |    ||||| |   |||||||| |||||| | |      |  |||||||||||   |  | |  || || | |||    | ||   |      ||     |  |  ||    |||        
AGACGAATATTACTTTGTACAGGTTGATGGCATGGATGTTCTTGCTGTTAAACAAGCTTGCAAATTTGCAAAGGAACATGCTTTGAAGAATGGACTCCTTgtgagttaacttttttgc-----tgttatgcatacttgaatttctc--ttctaaaaattaatcattggcaattagatgttatgaatcacccattcatctgctaaagc

upper sequence: LOC_Os02g50620.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv09s0018g01940.t01 (Vitis vinifera), 5'ss of exon 3
GTTGATGGAATGGATGTTCTTGCTGTGAAGCAGGCATGCAAATTCGCAAAAGAGCATGCTATTGCAAATGGCCCAATTgtgagtaaactttgtcg--tgttaatagtatgcatacttatgtagcgcaattatatagatttgctactgttgaactacagtggcttaggattcacatttctt--
|| ||||| |||||||||||||||||||| |||||||||| ||| || || ||||||||| |   |||||| || ||||| |||  ||||   |   ||||   | | || || ||||   |   |  ||  | |    |  |  ||||||  || |    |||     |   | ||||   
GTAGATGGTATGGATGTTCTTGCTGTGAAACAGGCATGCAGATTTGCTAAGGAGCATGCTTTAAAAAATGGACCCATTgtaagtttacttatcctgctgtttccattttgtattcttaaaaattccttttgcaaactactattgttgttga-ttagat---cttctatcttctaattctgca

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|86478591|gb|CI121224.1|CI121224
EST:     GCAAAAGAGCATGCTATTGCAAATGGCCCAATT                         GTTCTTGAAATGGATACCTACAGGTACCATGGCCATTCTATGTCAGATCCC
genomic: GCAAAAGAGCATGCTATTGCAAATGGCCCAATTgtgagtaaac ... ttgtatttagGTTCTTGAAATGGATACCTACAGGTACCATGGCCATTCTATGTCAGATCCC
EST: gi|27577814|gb|CB000509.1|CB000509
EST:     AGCAGGCATGCAAATTCGCAAAAGAGCATGCTATTGCAAATGGCCCAATT                         GTTCTTGAAATGGATACCTACAGGTACCATGGCCATTCTATGTCAGATCCC
genomic: AGCAGGCATGCAAATTCGCAAAAGAGCATGCTATTGCAAATGGCCCAATTgtgagtaaac ... ttgtatttagGTTCTTGAAATGGATACCTACAGGTACCATGGCCATTCTATGTCAGATCCC
EST: gi|86477775|gb|CI120408.1|CI120408
EST:     AGCAGGCATGCAAATTCGCAAAAGAGCATGCTATTGCAAATGGCCCAATT                         GTTCTTGAAATGGATACCTACAGGTACCATGGCCATTCTATGTCAGATCCC
genomic: AGCAGGCATGCAAATTCGCAAAAGAGCATGCTATTGCAAATGGCCCAATTgtgagtaaac ... ttgtatttagGTTCTTGAAATGGATACCTACAGGTACCATGGCCATTCTATGTCAGATCCC
EST: gi|87026831|gb|CI259484.1|CI259484
EST:     AGCAGGCATGCAAATTCGCAAAAGAGCATGCTATTGCAAATGGCCCAATT                         GTTCTTGAAATGGATACCTACAGGTACCATGGCCATTCTATGTCAGATCCC
genomic: AGCAGGCATGCAAATTCGCAAAAGAGCATGCTATTGCAAATGGCCCAATTgtgagtaaac ... ttgtatttagGTTCTTGAAATGGATACCTACAGGTACCATGGCCATTCTATGTCAGATCCC
EST: gi|29678001|gb|CB674276.1|CB674276
EST:     AGCAGGCATGCAAATTCGCAAAAGAGCATGCTATTGCAAATGGCCCAATT                         GTTCTTGAAATGGATACCTACAGGTACCATGGCCATTCTATGTCAGATCCC
genomic: AGCAGGCATGCAAATTCGCAAAAGAGCATGCTATTGCAAATGGCCCAATTgtgagtaaac ... ttgtatttagGTTCTTGAAATGGATACCTACAGGTACCATGGCCATTCTATGTCAGATCCC
EST: gi|33380532|gb|CF195875.1|CF195875
EST:     AGCAGGCATGCAAATTCGCAAAAGAGCATGCTATTGCAAATGGCCCAATT                         GTTCTTGAAATGGATACCTACAGGTACCATGGCCATTCTATGTCNNNTCCC
genomic: AGCAGGCATGCAAATTCGCAAAAGAGCATGCTATTGCAAATGGCCCAATTgtgagtaaac ... ttgtatttagGTTCTTGAAATGGATACCTACAGGTACCATGGCCATTCTATGTCAGATCCC
EST: gi|325494624|gb|JG459148.1|JG459148
EST:     AGCAGGCATGCAAATTCGCAAAAGAGCATGCTATTGCAAATGGCCCAATT                         GGTCTTGAAATGGATACCTACAGGTACCATGGCCATTCTATGTCAGATCCC
genomic: AGCAGGCATGCAAATTCGCAAAAGAGCATGCTATTGCAAATGGCCCAATTgtgagtaaac ... ttgtatttagGTTCTTGAAATGGATACCTACAGGTACCATGGCCATTCTATGTCAGATCCC
EST: gi|29686015|gb|CB682290.1|CB682290
EST:     GCAGGCATGCAAATTCGCAAAAGAGCATGCTATTGNCAA-TGGCCCAATT                         GTTCTTGAAATGGATACCTACAGGTACCATGGCCATTCTATGTCAGATCCC
genomic: GCAGGCATGCAAATTCGCAAAAGAGCATGCTATTG-CAAATGGCCCAATTgtgagtaaac ... ttgtatttagGTTCTTGAAATGGATACCTACAGGTACCATGGCCATTCTATGTCAGATCCC
EST: gi|112785647|gb|EE591127.1|EE591127
EST:     AGCAGGCATGCAAATTCGCAAAAGAGCATGCTATTGCAAATGGCCCAATT                         GTTCTTGAAATGGA
genomic: AGCAGGCATGCAAATTCGCAAAAGAGCATGCTATTGCAAATGGCCCAATTgtgagtaaac ... ttgtatttagGTTCTTGAAATGGA
EST: gi|86490349|gb|CI132982.1|CI132982
EST:     AATGGCCCAATT                         GTTCTTGAAATGGATACCTACAGGTACCATGGCCATTCTATGTCAGATCCC
genomic: AATGGCCCAATTgtgagtaaac ... ttgtatttagGTTCTTGAAATGGATACCTACAGGTACCATGGCCATTCTATGTCAGATCCC
EST: gi|87024021|gb|CI252768.1|CI252768
EST:     AGCAGGCATGCAAATTCGCAAAAGAGCATGCTATTGCAAATGGCCCAATT                         GTTCTTGAAATGGATACCTACAGGTACCATGGCCATTCTATGTCAGATCCC
genomic: AGCAGGCATGCAAATTCGCAAAAGAGCATGCTATTGCAAATGGCCCAATTgtgagtaaac ... ttgtatttagGTTCTTGAAATGGATACCTACAGGTACCATGGCCATTCTATGTCAGATCCC
EST: gi|86480007|gb|CI122640.1|CI122640
EST:     TTGCAAATGGCCCAATT                         GTTCTTGAAATGGATACCTACAGGTACCATGGCCATTCTATGTCAGATCCC
genomic: TTGCAAATGGCCCAATTgtgagtaaac ... ttgtatttagGTTCTTGAAATGGATACCTACAGGTACCATGGCCATTCTATGTCAGATCCC
EST: gi|88361180|gb|CI646204.1|CI646204
EST:     AGCAGGCATGCAAATTCGCAAAAGAGCATGCTATTGCAAATGGCCCAATT                         GTTCTTGAAATGGATACCTACAGGTACCATGGCCATTCTATGTCAGATCCC
genomic: AGCAGGCATGCAAATTCGCAAAAGAGCATGCTATTGCAAATGGCCCAATTgtgagtaaac ... ttgtatttagGTTCTTGAAATGGATACCTACAGGTACCATGGCCATTCTATGTCAGATCCC
EST: gi|58588659|gb|CF986967.1|CF986967
EST:     ATGCTATTGCAAATGGCCCAATT                         GTTCTTGAAATGGATACCTACAGGTACCATGGCCGTGCTATGTCAGATCCC
genomic: ATGCTATTGCAAATGGCCCAATTgtgagtaaac ... ttgtatttagGTTCTTGAAATGGATACCTACAGGTACCATGGCCATTCTATGTCAGATCCC
EST: gi|87018512|gb|CI252266.1|CI252266
EST:     AGCAGGCATGCAAATTCGCAAAAGAGCATGCTATTGCAAATGGCCCAATT                         GTTCTTGAAATGGATACCTACAGGTACCATGGCCATTCTATGTCAGATCCC
genomic: AGCAGGCATGCAAATTCGCAAAAGAGCATGCTATTGCAAATGGCCCAATTgtgagtaaac ... ttgtatttagGTTCTTGAAATGGATACCTACAGGTACCATGGCCATTCTATGTCAGATCCC
EST: gi|87024655|gb|CI259370.1|CI259370
EST:     AGCAGGCATGCAAATTCGCAAAAGAGCATGCTATTGCAAATGGCCCAATT                         GTTCTTGAAATGGATACCTACAGGTACCATGGCCATTCTATGTCAGATCCC
genomic: AGCAGGCATGCAAATTCGCAAAAGAGCATGCTATTGCAAATGGCCCAATTgtgagtaaac ... ttgtatttagGTTCTTGAAATGGATACCTACAGGTACCATGGCCATTCTATGTCAGATCCC
EST: gi|88976948|gb|CI257644.1|CI257644
EST:     GCATGCAAATTCGCAAAAGAGCATGCTATTGCAAATGGCCCAATT                         GTTCTTGAAATGGATACCTACAGGTACCATGGCCATTCTATGTCAGATCCC
genomic: GCATGCAAATTCGCAAAAGAGCATGCTATTGCAAATGGCCCAATTgtgagtaaac ... ttgtatttagGTTCTTGAAATGGATACCTACAGGTACCATGGCCATTCTATGTCAGATCCC
EST: gi|29615723|gb|CB620735.1|CB620735
EST:     AGCAGGCATGCAAATTCGCAAAAGAGCATGCTATTGCAAATGGCCCAATT                         GTTCTTGAAATGGATACCTACAGGTACCATGGCCATTCTATGTCAGATCCC
genomic: AGCAGGCATGCAAATTCGCAAAAGAGCATGCTATTGCAAATGGCCCAATTgtgagtaaac ... ttgtatttagGTTCTTGAAATGGATACCTACAGGTACCATGGCCATTCTATGTCAGATCCC
EST: gi|29686016|gb|CB682291.1|CB682291
EST:     AGCAGGCATGCAAATTCGCAAAAGAGCATGCTATTGCAAATGGCCCAATT                         GTTCTTGAAATGGATACCTACAGGTACCATGGCCATTCTATGTCAGATCCC
genomic: AGCAGGCATGCAAATTCGCAAAAGAGCATGCTATTGCAAATGGCCCAATTgtgagtaaac ... ttgtatttagGTTCTTGAAATGGATACCTACAGGTACCATGGCCATTCTATGTCAGATCCC
EST: gi|29682671|gb|CB678946.1|CB678946
EST:     AGCAGGCATGCAAATTCGCAAAAGAGCATGCTATTGCAAATGGCCCAATT                         GTTCTTGAAATGGATACCTACAGGTACCATGGCCATTCTATGTCAGATCCC
genomic: AGCAGGCATGCAAATTCGCAAAAGAGCATGCTATTGCAAATGGCCCAATTgtgagtaaac ... ttgtatttagGTTCTTGAAATGGATACCTACAGGTACCATGGCCATTCTATGTCAGATCCC
EST: gi|29637300|gb|CB642309.1|CB642309
EST:     AGCAGGCATGCAAATTCGCAAAAGAGCATGCTATTGCAAATGGCCCAATT                         GTTCTTGAAATGGATACCTACAGGTACCATGGCCATTCTATGTCAGATCCC
genomic: AGCAGGCATGCAAATTCGCAAAAGAGCATGCTATTGCAAATGGCCCAATTgtgagtaaac ... ttgtatttagGTTCTTGAAATGGATACCTACAGGTACCATGGCCATTCTATGTCAGATCCC
EST: gi|33800928|gb|CF326337.1|CF326337
EST:     AGCAGGCATGCAAATTCGCAAAAGAGCATGCTATTGCAAATGGCCCAATT                         GTTCTTGAAATGGATACCTACAGGTACCATGGCCATTCTATGTCAGATCCC
genomic: AGCAGGCATGCAAATTCGCAAAAGAGCATGCTATTGCAAATGGCCCAATTgtgagtaaac ... ttgtatttagGTTCTTGAAATGGATACCTACAGGTACCATGGCCATTCTATGTCAGATCCC
EST: gi|29639554|gb|CB644563.1|CB644563
EST:     AGCAGGCATGCAAATTCGCAAAAGAGCATGCTATTGCAAATGGCCCAATT                         GTTCTTGAAATGGATACCTACAGGTACCATGGCCATTCTATGTCAGATCCC
genomic: AGCAGGCATGCAAATTCGCAAAAGAGCATGCTATTGCAAATGGCCCAATTgtgagtaaac ... ttgtatttagGTTCTTGAAATGGATACCTACAGGTACCATGGCCATTCTATGTCAGATCCC
EST: gi|66915210|gb|CX102058.1|CX102058
EST:     AGCAGGCATGCAAATTCGCAAAAGAGCATGCTATTGCAAATGGCCCAATT                         GTTCTTGAAATGGATACCTACAGGTACCATGGCCATTCTATGTCAGATCCC
genomic: AGCAGGCATGCAAATTCGCAAAAGAGCATGCTATTGCAAATGGCCCAATTgtgagtaaac ... ttgtatttagGTTCTTGAAATGGATACCTACAGGTACCATGGCCATTCTATGTCAGATCCC
EST: gi|88828606|gb|CI073476.1|CI073476
EST:     CGCAAAAGAGCATGCTATTGCAAATGGCCCAATT                         GTTCTTGAAATGGATACCTACAGGTACCATGGCCATTCTATGTCAGATCCC
genomic: CGCAAAAGAGCATGCTATTGCAAATGGCCCAATTgtgagtaaac ... ttgtatttagGTTCTTGAAATGGATACCTACAGGTACCATGGCCATTCTATGTCAGATCCC
EST: gi|87026901|gb|CI259554.1|CI259554
EST:     AGCATGCTATTGCAAATGGCCCAATT                         GTTCTTGAAATGGATACCTACAGGTACCATGGCCATTCTATGTCAGATCCC
genomic: AGCATGCTATTGCAAATGGCCCAATTgtgagtaaac ... ttgtatttagGTTCTTGAAATGGATACCTACAGGTACCATGGCCATTCTATGTCAGATCCC
EST: gi|29689207|gb|CB685482.1|CB685482
EST:     AGCAGGCATGCAAATTCGCAAAAGAGCATGCTATTGCAAATGGCCCAATT                         GTTCTTGAAATGGATACCTACAGGTACCATGGCCATTTTATGTCAGATCCC
genomic: AGCAGGCATGCAAATTCGCAAAAGAGCATGCTATTGCAAATGGCCCAATTgtgagtaaac ... ttgtatttagGTTCTTGAAATGGATACCTACAGGTACCATGGCCATTCTATGTCAGATCCC
EST: gi|396941607|gb|HO188264.1|HO188264
EST:     AGCAGGCATGCAAATTCGCAAAAGAGCATGCTATTGCAAATGGCCCAATT                         GTTCTTGAAATGGATACCTACAGGTACCATGGCCATTCTATGTCAGATCCC
genomic: AGCAGGCATGCAAATTCGCAAAAGAGCATGCTATTGCAAATGGCCCAATTgtgagtaaac ... ttgtatttagGTTCTTGAAATGGATACCTACAGGTACCATGGCCATTCTATGTCAGATCCC

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: 54 (upstream exon), 74 (downstream exon)
Score: 138

GTTGATGGAATGGATGTTCTTGCTGTGAAGCAGGCATGCAAATTCGCAAAAGAGCATGCTATTGCAAATGGCCCAATTgtgagtaaac ... ttgtatttagGTTCTTGAAATGGATACCTACAGGTACCATGGCCATTCTATGTCAGATCCCGGAAGCACTTACCGTACCAGGGATGAGATCTCAGGTGTAAGACAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGATGGAATGGATGTTCTTGCTGTGAAGCAGGCATGCAAATTCGCAAAAGAGCATGCTATTGCAAATGGCCCAATTgtgagtaaactttgtcgtgttaatagtatgcatacttatgtagcgcaattatatagatttgctactgttgaactacagtggcttaggattcacatttctt

- - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA