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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtacttattagatgcatttattttatgttctcttaaaatggaagtctattggcttttacatcatttggagaagcactgactaatagttagtagaagctgatatctccatttcatgtttcagGCGTTTCATGAATCAATATTTCTTGCTGATAGCATGCCTCCAACTGTGGTCACTTATCACTCCTGTAAATCCTGCAAGCACATGGGGCCCGCTTATTTTT

Basic information

species Oryza sativa
transcript LOC_Os11g25980.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g25980.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G411940_T01 (Zea mays), 3'ss of exon 4
gtttgtacttattagatgcatttattttatgttctcttaaaatggaagtctattggcttttacatcatttggagaagcactgactaata--gttagtagaagctgatatctccatttcatgtttcagGCGTTTCATGAATCAATATTTCTTGCTGATAGCATGCCTCCAACTGTGGTCACTTATCACTCCTGTAAATCCTGCAAGCACATGGGGCCCGCTTATTTTT
                || |   || | ||| | ||         |||  | || |   ||     | ||| | |||   | | |  ||    | | | ||| |  ||| |   |||  ||||||||||| ||||||||||||||||||||| ||||||| || || ||||| |||||||||||||||||||||||||||||||| || |||||||| ||||| |||
---------------ctgaaaaaatctcatgatttc---------aagcatgttagaccttgttgtaattgcataagt--taattggtacgaatggaaaaagttactatttat-tttggtgtttcagGCGCTTCATGAATCAATATTTCTTGTTGATAGCTTGTCTGCAACTATGGTCACTTATCACTCCTGTAAATCCTGCAAGTACCTGGGGCCCACTTATATTT

upper sequence: LOC_Os11g25980.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT5G44240.1 (Arabidopsis thaliana), 3'ss of exon 2
gtttgtacttattagatgcatttattttatgttctcttaaaatggaagtctattggcttttacatcatttggagaagcactgactaatagttagtagaagctgatatctccatttcatgtttcagGCGTTTCATGAATCAATATTTCTTGCTGATAGCATGCCTCCAACTGTGGTCACTTATCACTCCTGTAAATCCTGCAAGCACATGGGGCCCGCTTATTTTT
           | |     ||| |||| || |  | ||  ||||    | |||    | |||| || |||         ||||  ||        |       || | |   |||  |||||||| || || ||||| || || || ||| |||| || ||||| || || |||||||||||||| ||||| ||||||||||| |||||||| ||| | || || 
----------gtaacgatgattcatttcatttagtgttctaatgttcttatatcta-tgttacgtctttt---------ctgatcaa--------aatgttctatctttttctttt-tgtttcagCCGGTTTATGAACCAGTACTTTTTGTTGATTGCTTGCCTTCAGCTATGGTCACTTATCACCCCTGTGAATCCTGCAAGTACATGGGGTCCGTTAATATTC
















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|88394093|gb|CI684763.1|CI684763
EST:     AGTACACCCTACTAAATTTCCTGCCCAAAAAATCTATGGGAGCAATTCAG                         GCGTTTCATGAATCAATATTTCTTGCTGATAGCATGCCTCCAACTGTGGTC
genomic: AGTACACCCTACTAAATTTCCTGCC-AAAAAATCTATGGGAGCAATTCAGgtttgtactt ... catgtttcagGCGTTTCATGAATCAATATTTCTTGCTGATAGCATGCCTCCAACTGTGGTC
EST: gi|88364266|gb|CI612215.1|CI612215
EST:     AAGTACACCCTACTAAATTTCCTGCCAAAAAATCTATGGGAGCAATTCAG                         GCGTTTCATGAATCAAGTATTTGTTGCTGATAGCATGCCTCCAACTGTGGT
genomic: AAGTACACCCTACTAAATTTCCTGCCAAAAAATCTATGGGAGCAATTCAGgtttgtactt ... catgtttcagGCGTTTCATGAATCAA-TATTTCTTGCTGATAGCATGCCTCCAACTGTGGT
EST: gi|88396610|gb|CI601093.1|CI601093
EST:     AAGTACACCCTACTAAATTTCCTGCCAAAAAATCTATGGGAGCAATTCAG                         GCGTTTCATGAATCAATATTTCTTGCTGATAGCATGCCTC-AACTGTGGTC
genomic: AAGTACACCCTACTAAATTTCCTGCCAAAAAATCTATGGGAGCAATTCAGgtttgtactt ... catgtttcagGCGTTTCATGAATCAATATTTCTTGCTGATAGCATGCCTCCAACTGTGGTC
EST: gi|88463600|gb|CI696068.1|CI696068
EST:     AAGTACACCCTACTAAATTTCCTGCCAAAAAATCTATGGGAGCAATTCAG                         GCGTTTCATGAATCAATATTTCTTGCTGATAGCATGCCTCCAACTGTGGTC
genomic: AAGTACACCCTACTAAATTTCCTGCCAAAAAATCTATGGGAGCAATTCAGgtttgtactt ... catgtttcagGCGTTTCATGAATCAATATTTCTTGCTGATAGCATGCCTCCAACTGTGGTC
EST: gi|88592052|gb|CI710129.1|CI710129
EST:     AAGTACACCCTACTAAATTCCCTGCCAAAAAATCTATGGGAGCAATTCAG                         GCGTCCCATGAATCAATATTTCTTGCTGATAGCATGCCTCCAA
genomic: AAGTACACCCTACTAAATTTCCTGCCAAAAAATCTATGGGAGCAATTCAGgtttgtactt ... catgtttcagGCGTTTCATGAATCAATATTTCTTGCTGATAGCATGCCTCCAA
EST: gi|88313652|gb|CI671784.1|CI671784
EST:     AAGTACACCCTACTAAATTTCCTGCCAAAAAATCTATGGGAGCAATTCAG                         GCGTTTCATGAATCAATATTTCTTGCTGATAGCATGCCTCCAACTGTGGTC
genomic: AAGTACACCCTACTAAATTTCCTGCCAAAAAATCTATGGGAGCAATTCAGgtttgtactt ... catgtttcagGCGTTTCATGAATCAATATTTCTTGCTGATAGCATGCCTCCAACTGTGGTC
EST: gi|88589387|gb|CI707258.1|CI707258
EST:     AGTACACCCTACTAAATTTCCTGCCCAAAAAATCTATGGGAGCAATTCAG                         GCGTTTCATGAATCAATATTTCTTGCTGATAGCATGCCTCCAACTGTGGTC
genomic: AGTACACCCTACTAAATTTCCTGCC-AAAAAATCTATGGGAGCAATTCAGgtttgtactt ... catgtttcagGCGTTTCATGAATCAATATTTCTTGCTGATAGCATGCCTCCAACTGTGGTC
EST: gi|88760044|gb|CI769600.1|CI769600
EST:     AAGTACACCCTACTAAATTTCCTGCCAAAAAATCTATGGGAGCAATTCAG                         GCGTTTCATGAATCAATATTTCTTGCTGAT
genomic: AAGTACACCCTACTAAATTTCCTGCCAAAAAATCTATGGGAGCAATTCAGgtttgtactt ... catgtttcagGCGTTTCATGAATCAATATTTCTTGCTGAT
EST: gi|88578687|gb|CI687633.1|CI687633
EST:     AAGTACACCCTACTAAATTTCCTGCCAAAAAATCTATGGGAGCAATTCAG                         GCGTTTCATGAATCAATATTTCTTGCTGATAGCATGCCTCCAACTGTGGTC
genomic: AAGTACACCCTACTAAATTTCCTGCCAAAAAATCTATGGGAGCAATTCAGgtttgtactt ... catgtttcagGCGTTTCATGAATCAATATTTCTTGCTGATAGCATGCCTCCAACTGTGGTC
EST: gi|88761179|gb|CI770735.1|CI770735
EST:     AAGTACACCCTACTAAATTTCCTGCCAAAAAATCTATGGGAGCAATTCAG                         GCGTTTCATGAATCAATATTTCTTGCTGATAGCATG
genomic: AAGTACACCCTACTAAATTTCCTGCCAAAAAATCTATGGGAGCAATTCAGgtttgtactt ... catgtttcagGCGTTTCATGAATCAATATTTCTTGCTGATAGCATG
EST: gi|88591834|gb|CI709889.1|CI709889
EST:     AAGTACACCCTACTAAATTTCCTGCCAAAAAATCTATGGGAGCAATTCAG                         GCGTTTCATGAATCAATATTTCTTGCTGATAG
genomic: AAGTACACCCTACTAAATTTCCTGCCAAAAAATCTATGGGAGCAATTCAGgtttgtactt ... catgtttcagGCGTTTCATGAATCAATATTTCTTGCTGATAG
EST: gi|88388380|gb|CI683151.1|CI683151
EST:     AAGTACACCCTACTAAATTTCCTGCCAAAAAATCTATGGGAGCAATTCAG                         GCGTTTCATGAATCAATATTTCTTGCTGATAGCATGCCTCCAACTGTGGTC
genomic: AAGTACACCCTACTAAATTTCCTGCCAAAAAATCTATGGGAGCAATTCAGgtttgtactt ... catgtttcagGCGTTTCATGAATCAATATTTCTTGCTGATAGCATGCCTCCAACTGTGGTC
EST: gi|88342386|gb|CI645908.1|CI645908
EST:     AAGTACACCCTACTAAATTTCCTGCCAAAAAATCTATGGGAGCAATTCAG                         GCGTTTCATGAATCAATATTTCTTGCTGATAGCATGCCTCCAACTGTGGTC
genomic: AAGTACACCCTACTAAATTTCCTGCCAAAAAATCTATGGGAGCAATTCAGgtttgtactt ... catgtttcagGCGTTTCATGAATCAATATTTCTTGCTGATAGCATGCCTCCAACTGTGGTC
EST: gi|88410576|gb|CI686913.1|CI686913
EST:     AAGTACACCCTACTAAATTTCCTGCCAAAAAATCTATGGGAGCAATTCAG                         GCGTTTCATGAATCAATATTTCTTGCTGATAGCATGCCTCCAACTGTGGTC
genomic: AAGTACACCCTACTAAATTTCCTGCCAAAAAATCTATGGGAGCAATTCAGgtttgtactt ... catgtttcagGCGTTTCATGAATCAATATTTCTTGCTGATAGCATGCCTCCAACTGTGGTC
EST: gi|88576841|gb|CI673370.1|CI673370
EST:     AAGTACACCCTACTAAATTTCCTGCCAAAAAATCTATGGGAGCAATTCAG                         GCGTTTCATGAATCAATATTTCTTGCTGATAGCATGCCTCCAACTGTGGTC
genomic: AAGTACACCCTACTAAATTTCCTGCCAAAAAATCTATGGGAGCAATTCAGgtttgtactt ... catgtttcagGCGTTTCATGAATCAATATTTCTTGCTGATAGCATGCCTCCAACTGTGGTC
EST: gi|88419783|gb|CI686549.1|CI686549
EST:     AAGTACACCCTACTAAATTTCCTGCCAAAAAATCTATGGGAGCAATTCAG                         GCGTTTCATGAATCAATATTTCTTGCTGATAGCATGCCTCCAACTGTGGTC
genomic: AAGTACACCCTACTAAATTTCCTGCCAAAAAATCTATGGGAGCAATTCAGgtttgtactt ... catgtttcagGCGTTTCATGAATCAATATTTCTTGCTGATAGCATGCCTCCAACTGTGGTC
EST: gi|88578151|gb|CI674788.1|CI674788
EST:     AAGTACACCCTACTAAATTTCCTGCCAAAAAATCTATGGGAGCAATTCAG                         GCGTTTCATGAATCAATATTTCTTGCTGATAGCATGCCTCCAACTGTGGTC
genomic: AAGTACACCCTACTAAATTTCCTGCCAAAAAATCTATGGGAGCAATTCAGgtttgtactt ... catgtttcagGCGTTTCATGAATCAATATTTCTTGCTGATAGCATGCCTCCAACTGTGGTC
EST: gi|88729512|gb|CI753022.1|CI753022
EST:     AAGTACACCCTACTAAATTTCCTGCCAAAAAATCTATGGGAGCAATTCAG                         GCGTTTCATGAATCAATATTTCTTGCTGATAGCATGCCTCCAACTGTGGTC
genomic: AAGTACACCCTACTAAATTTCCTGCCAAAAAATCTATGGGAGCAATTCAGgtttgtactt ... catgtttcagGCGTTTCATGAATCAATATTTCTTGCTGATAGCATGCCTCCAACTGTGGTC
EST: gi|88589646|gb|CI708444.1|CI708444
EST:     AAGTACACCCTACTAAATTTCCTGCCAAAAAATCTATGGGAGCAATTCAG                         GCGTTTCATGAATCAATATTTCTTGCT
genomic: AAGTACACCCTACTAAATTTCCTGCCAAAAAATCTATGGGAGCAATTCAGgtttgtactt ... catgtttcagGCGTTTCATGAATCAATATTTCTTGCT
EST: gi|88590118|gb|CI708947.1|CI708947
EST:     AAGTACACCCTACTAAATTTCCTGCCAAAAAATCTATGGGAGCAATTCAG                         GCGTTTCATGAATCAATATTTCTTGCTGATAG
genomic: AAGTACACCCTACTAAATTTCCTGCCAAAAAATCTATGGGAGCAATTCAGgtttgtactt ... catgtttcagGCGTTTCATGAATCAATATTTCTTGCTGATAG
EST: gi|88581955|gb|CI699174.1|CI699174
EST:     AAGTACACCCTACTAAATTTCCTGCCAAAAAATCTATGGGAGCAATTCAG                         GCGTTTCATGAATCAATATTTCTTGCTGATAGCATGCCTCCAACTGTGGTC
genomic: AAGTACACCCTACTAAATTTCCTGCCAAAAAATCTATGGGAGCAATTCAGgtttgtactt ... catgtttcagGCGTTTCATGAATCAATATTTCTTGCTGATAGCATGCCTCCAACTGTGGTC
EST: gi|88591715|gb|CI709768.1|CI709768
EST:     AAGTACACCCTACTAAATTTCCTGCCAAAAAATCTATGGGAGCAATTCAG                         GCGTTTCATGAATCAATATTTCTTGCTGATAGCATGCCT
genomic: AAGTACACCCTACTAAATTTCCTGCCAAAAAATCTATGGGAGCAATTCAGgtttgtactt ... catgtttcagGCGTTTCATGAATCAATATTTCTTGCTGATAGCATGCCT
EST: gi|88763055|gb|CI772611.1|CI772611
EST:     AAGTACACCCTACTAAATTTCCTGCCAAAAAATCTATGGGAGCAATTCAG                         GCGTTTCATGAATCAATATTTCTTGCTGATAGCATGCCTCCAACTG
genomic: AAGTACACCCTACTAAATTTCCTGCCAAAAAATCTATGGGAGCAATTCAGgtttgtactt ... catgtttcagGCGTTTCATGAATCAATATTTCTTGCTGATAGCATGCCTCCAACTG
EST: gi|88391194|gb|CI595448.1|CI595448
EST:     AAGTACACCCTACTAAATTTCCTGCCAAAAAATCTATGGGAGCAATTCAG                         GCGTTTCATGAATCAATATTTCTTGCTGATAGCATGCCTCCAACTGTGGTC
genomic: AAGTACACCCTACTAAATTTCCTGCCAAAAAATCTATGGGAGCAATTCAGgtttgtactt ... catgtttcagGCGTTTCATGAATCAATATTTCTTGCTGATAGCATGCCTCCAACTGTGGTC
EST: gi|88581178|gb|CI698152.1|CI698152
EST:     AAGTACACCCTACTAAATTTCCTGCCAAAAAATCTATGGGAGCAATTCAG                         GCGTTTCATGAATCAATATTTCTTGCTGATAGCATGCCTCCAACTGTGGTC
genomic: AAGTACACCCTACTAAATTTCCTGCCAAAAAATCTATGGGAGCAATTCAGgtttgtactt ... catgtttcagGCGTTTCATGAATCAATATTTCTTGCTGATAGCATGCCTCCAACTGTGGTC
EST: gi|88335567|gb|CI642791.1|CI642791
EST:     AAGTACACCCTACTAAATTTCCTGCCAAAAAATCTATGGGAGCAATTCAG                         GCGTTTCATGAATCAATATTTCTTGCTGATAGCATGCCTCCAACTGTGGTC
genomic: AAGTACACCCTACTAAATTTCCTGCCAAAAAATCTATGGGAGCAATTCAGgtttgtactt ... catgtttcagGCGTTTCATGAATCAATATTTCTTGCTGATAGCATGCCTCCAACTGTGGTC
EST: gi|88579169|gb|CI688145.1|CI688145
EST:     AAGTACACCCTACTAAATTTCCTGCCAAAAAATCTATGGGAGCAATTCAG                         GCGTTTCATGAATCAATA
genomic: AAGTACACCCTACTAAATTTCCTGCCAAAAAATCTATGGGAGCAATTCAGgtttgtactt ... catgtttcagGCGTTTCATGAATCAATA
EST: gi|88349321|gb|CI678299.1|CI678299
EST:     AAGTACACCCTACTAAATTTCCTGCCAAAAAATCTATGGGAGCAATTCAG                         GCGTTTCATGAATCAATATTTCTTGCTGATAGCATGCCTCCAACTGTGGTC
genomic: AAGTACACCCTACTAAATTTCCTGCCAAAAAATCTATGGGAGCAATTCAGgtttgtactt ... catgtttcagGCGTTTCATGAATCAATATTTCTTGCTGATAGCATGCCTCCAACTGTGGTC
EST: gi|88458060|gb|CI695011.1|CI695011
EST:     AAGTACACCCTACTAAATTTCCTGCCAAAAAATCTATGGGAGCAATTCAG                         GCGTTTCATGAATCAATATTTCTTGCTGATAGCATGCCTCCAACTGTGGTC
genomic: AAGTACACCCTACTAAATTTCCTGCCAAAAAATCTATGGGAGCAATTCAGgtttgtactt ... catgtttcagGCGTTTCATGAATCAATATTTCTTGCTGATAGCATGCCTCCAACTGTGGTC
EST: gi|88344390|gb|CI677432.1|CI677432
EST:     AAGTACACCCTACTAAATTTCCTGCCAAAAAATCTATGGGAGCAATTCAG                         GCGTTTCATGAATCAATATTTCTTGCTGATAGCATGCCTCCAACTGTGGTC
genomic: AAGTACACCCTACTAAATTTCCTGCCAAAAAATCTATGGGAGCAATTCAGgtttgtactt ... catgtttcagGCGTTTCATGAATCAATATTTCTTGCTGATAGCATGCCTCCAACTGTGGTC
EST: gi|88381490|gb|CI682146.1|CI682146
EST:     AAGTACACCCTACTAAATTTCCTGCCAAAAAATCTATGGGAGCAATTCAG                         GCGTTTCATGAATCAATATTTCTTGCTGATAGCATGCCTCCAACTGTGGTC
genomic: AAGTACACCCTACTAAATTTCCTGCCAAAAAATCTATGGGAGCAATTCAGgtttgtactt ... catgtttcagGCGTTTCATGAATCAATATTTCTTGCTGATAGCATGCCTCCAACTGTGGTC
EST: gi|88588861|gb|CI706703.1|CI706703
EST:     AAGTACACCCTACTAAATTTCCTGCCAAAAAATCTATGGGAGCAATTCAG                         GCGTTTCATGAATCAATATTTCTTG
genomic: AAGTACACCCTACTAAATTTCCTGCCAAAAAATCTATGGGAGCAATTCAGgtttgtactt ... catgtttcagGCGTTTCATGAATCAATATTTCTTG

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: 66 (upstream exon), 72 (downstream exon)
Score: 11

ATGATGAATCTTACCAGAATGACTATTGTGATAACCGGATTTCTAACACAAAGTACACCCTACTAAATTTCCTGCCAAAAAATCTATGGGAGCAATTCAGgtttgtactt ... catgtttcagGCGTTTCATGAATCAATATTTCTTGCTGATAGCATGCCTCCAACTGTGGTCACTTATCACTCCTGTAAATCCTGCAAGCACATGGGGCCCGCTTATTTTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggagaagcactgactaatagttagtagaagctgatatctccatttcatgtttcagGCGTTTCATGAATCAATATTTCTTGCTGATAGCATGCCTCCAACTGTGGTCACTTATCACTCCTGTAAATCCTGCAAGCACATGGGGCCCGCTTATTTTT
                                    tctccatttc  CT-rich tract
              taatagtta  TA-rich tract