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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtatcttcatttgtatcttgtctgaatatttttgtccctgttatccatctgtgtggctaactgctcacaaaacctgcagTGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAG

Basic information

species Oryza sativa
transcript LOC_Os07g43470.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g43470.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G158021_T01 (Zea mays), 3'ss of exon 8
---------------------------------------gtgagtatcttcatttgtatcttgtctgaatatttttgtccctgttatcc--atctgtgtggctaactgctcacaaaacctgcagTGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAG
                                        ||      ||   | |  | |   |   ||| |||| | | |||| |      |   ||  |||||||||| |||||  ||||| ||  |||| |||||||| || ||||| ||||||||||||||||||||||||
gtgagtgccatataattatgttattattgtctcacttgaatggaatcttttgatcggctatgtaccagataattttttacttgtttttttggccctcgtctctaactgctc-caaaaattgcagCGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAG

upper sequence: LOC_Os07g43470.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA06G15180.2 (Glycine max), 3'ss of exon 8
----------------gtgagtatcttcatttgtatcttgtctgaatatttttgtccctgttatc-catctgtgtggctaactgctcacaaaacctgcagTGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAG
                 | | | |||       || |   ||  || |  | | |  || |  |  |||   | |   | ||   |  ||||   |||||||| ||||| |||||||| || | ||| || |||||||| ||||||||||||
aaaaaagtttgagtcaataaatctctctccccttagcccttcaaaaaaaatgtttttctttcctgacattcatttaattcacatttaccaaatgatgcagTGCTTTGGTCTGGGGTTCAAGTGCGAAACACAAGCCTCAAAGAGTTGGCAAG

upper sequence: LOC_Os07g43470.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA06G15180.1 (Glycine max), 3'ss of exon 8
----------------gtgagtatcttcatttgtatcttgtctgaatatttttgtccctgttatc-catctgtgtggctaactgctcacaaaacctgcagTGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAG------------------------------------------------
                 | | | |||       || |   ||  || |  | | |  || |  |  |||   | |   | ||   |  ||||   |||||||| ||||| |||||||| || | ||| || |||||||| ||||||||||||                                                
aaaaaagtttgagtcaataaatctctctccccttagcccttcaaaaaaaatgtttttctttcctgacattcatttaattcacatttaccaaatgatgcagTGCTTTGGTCTGGGGTTCAAGTGCGAAACACAAGCCTCAAAGAGTTGGCAAGGTTGATACTGTACTTAATTTACATTATTTTTTGCTTCATCCTCTTTTC

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|88831549|gb|CI369231.1|CI369231
EST:     GAAGACTTCTGCAACAGAATCCACAAGGACATGGTGAAACAATTTAAATA                         TGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAA
genomic: GAAGACTTCTGCAACAGAATCCACAAGGACATGGTGAAACAATTTAAATAgtgagtatct ... aaacctgcagTGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAA
EST: gi|88845150|gb|CI084075.1|CI084075
EST:     GAAGACTTCTGCAACAGAATCCACAAGGACATGGTGAAACAATTNAAATA                         TGCATTGGTGTGGAGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCTA
genomic: GAAGACTTCTGCAACAGAATCCACAAGGACATGGTGAAACAATTTAAATAgtgagtatct ... aaacctgcagTGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAA
EST: gi|86498576|gb|CI141209.1|CI141209
EST:     TGCAACAGAATCCACAAGGACATGGTGAAACAATTTAAATA                         TGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAA
genomic: TGCAACAGAATCCACAAGGACATGGTGAAACAATTTAAATAgtgagtatct ... aaacctgcagTGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAA
EST: gi|86887194|gb|CI326009.1|CI326009
EST:     GAAGACTTCTGCAACAGAATCCACAAGGACATGGTGAAACAATTTAAATA                         TGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAA
genomic: GAAGACTTCTGCAACAGAATCCACAAGGACATGGTGAAACAATTTAAATAgtgagtatct ... aaacctgcagTGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAA
EST: gi|88831194|gb|CI082004.1|CI082004
EST:     GAAGACTTCTGCAACAGAATCCACAAGGACATGGTGAAACAATTNAAATA                         TGCATTGGTGTGGAGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTNGGCTA
genomic: GAAGACTTCTGCAACAGAATCCACAAGGACATGGTGAAACAATTTAAATAgtgagtatct ... aaacctgcagTGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAA
EST: gi|86887208|gb|CI326023.1|CI326023
EST:     GAAGACTTCTGCAACAGAATCCACAAGGACATGGTGAAACAATTTAAATA                         TGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAA
genomic: GAAGACTTCTGCAACAGAATCCACAAGGACATGGTGAAACAATTTAAATAgtgagtatct ... aaacctgcagTGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAA
EST: gi|86852710|gb|CI321830.1|CI321830
EST:     GAAGACTTCTGCAACA-AATCCACAA-GACAT-GTGAAACAATTTAAATA                         TCCAGTTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCA
genomic: GAAGACTTCTGCAACAGAATCCACAAGGACATGGTGAAACAATTTAAATAgtgagtatct ... aaacctgcagTGCA-TTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCA
EST: gi|88381165|gb|CI525935.1|CI525935
EST:     GAAGACTTCTGCAACAGAATCCACAAGGACATGGTGAAACAATTTAAATA                         TGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAA
genomic: GAAGACTTCTGCAACAGAATCCACAAGGACATGGTGAAACAATTTAAATAgtgagtatct ... aaacctgcagTGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAA
EST: gi|88294527|gb|CI530067.1|CI530067
EST:     GAAGACTTCTGCAACAGAATCCACAAGGACATGGTGAAACAATTTAAATA                         TGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAA
genomic: GAAGACTTCTGCAACAGAATCCACAAGGACATGGTGAAACAATTTAAATAgtgagtatct ... aaacctgcagTGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAA
EST: gi|13807087|gb|AU181805.1|AU181805
EST:     GGTGAAACAATTTAAATA                         TGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAA
genomic: GGTGAAACAATTTAAATAgtgagtatct ... aaacctgcagTGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAA
EST: gi|88250102|gb|CI249951.1|CI249951
EST:     GAAGACTTCTGCAACAGAATCCACAAGGACATGGTGAAACAATTTAAATA                         TGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAA
genomic: GAAGACTTCTGCAACAGAATCCACAAGGACATGGTGAAACAATTTAAATAgtgagtatct ... aaacctgcagTGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAA
EST: gi|88840330|gb|CI079784.1|CI079784
EST:     GAAGACTTCTGCAACAGAATCCACAAGGACATGGTGAAACAATTTAAATA                         TGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAA
genomic: GAAGACTTCTGCAACAGAATCCACAAGGACATGGTGAAACAATTTAAATAgtgagtatct ... aaacctgcagTGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAA
EST: gi|88246122|gb|CI245971.1|CI245971
EST:     GAAGACTTCTGCAACAGAATCCACAAGGACATGGTGAAACAATTTAAATA                         TGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAA
genomic: GAAGACTTCTGCAACAGAATCCACAAGGACATGGTGAAACAATTTAAATAgtgagtatct ... aaacctgcagTGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAA
EST: gi|86428361|gb|CI075042.1|CI075042
EST:     GAAGACTTCTGCAACAGAATCCACAAGGACATGGTGAAACAATTNAAATA                         TGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAA
genomic: GAAGACTTCTGCAACAGAATCCACAAGGACATGGTGAAACAATTTAAATAgtgagtatct ... aaacctgcagTGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAA
EST: gi|86488429|gb|CI131062.1|CI131062
EST:     GAAGACTTCTGCAACAGAATCCACAAGGACATGGTGAAACAATTTAAATA                         TGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAA
genomic: GAAGACTTCTGCAACAGAATCCACAAGGACATGGTGAAACAATTTAAATAgtgagtatct ... aaacctgcagTGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAA
EST: gi|5003286|gb|AU068435.1|AU068435
EST:     GAAGACTTCTGCAACAGAATCCACAAGGACATGGTGAAACAATTTAAATA                         TGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAA
genomic: GAAGACTTCTGCAACAGAATCCACAAGGACATGGTGAAACAATTTAAATAgtgagtatct ... aaacctgcagTGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAA
EST: gi|88842869|gb|CI371769.1|CI371769
EST:     GAAGACTTCTGCAACAGAATCCACAAGGACATGGTGAAACAATTTAAATA                         TGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAA
genomic: GAAGACTTCTGCAACAGAATCCACAAGGACATGGTGAAACAATTTAAATAgtgagtatct ... aaacctgcagTGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAA
EST: gi|88250137|gb|CI249986.1|CI249986
EST:     GAAGACTTCTGCAACAGAATCCACAAGGACATGGTGAAACAATTTAAATA                         TGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAA
genomic: GAAGACTTCTGCAACAGAATCCACAAGGACATGGTGAAACAATTTAAATAgtgagtatct ... aaacctgcagTGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAA
EST: gi|12622128|gb|AU172341.1|AU172341
EST:     GAAGACTTCTGCAACAGAATCCNCAAGGACATGGTGAAACAATTTAAATA                         TGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAA
genomic: GAAGACTTCTGCAACAGAATCCACAAGGACATGGTGAAACAATTTAAATAgtgagtatct ... aaacctgcagTGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAA
EST: gi|58679794|gb|CK068481.1|CK068481
EST:     GAAGACTTCTGCAACAGAATCCACAAGGACATGGTGAAACAATTTAAATA                         TGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCT
genomic: GAAGACTTCTGCAACAGAATCCACAAGGACATGGTGAAACAATTTAAATAgtgagtatct ... aaacctgcagTGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCT
EST: gi|86858867|gb|CI275094.1|CI275094
EST:     GAAGACTTCTGCAACAGAATCCACAAGGACATGGTGAAACAATTTAAATA                         TGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAA
genomic: GAAGACTTCTGCAACAGAATCCACAAGGACATGGTGAAACAATTTAAATAgtgagtatct ... aaacctgcagTGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAA
EST: gi|88830896|gb|CI079330.1|CI079330
EST:     GAAGACTTCTGCAACAGAATCCACAAGGACATGGTGAAACAATTTAAATA                         TGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAA
genomic: GAAGACTTCTGCAACAGAATCCACAAGGACATGGTGAAACAATTTAAATAgtgagtatct ... aaacctgcagTGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAA
EST: gi|88845195|gb|CI084120.1|CI084120
EST:     GAAGACTTCTGCAACAGAATCCACAAGGACATGGTGAAACAATTGAAATA                         TGCATTGGTGTGGAGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTNGGCTA
genomic: GAAGACTTCTGCAACAGAATCCACAAGGACATGGTGAAACAATTTAAATAgtgagtatct ... aaacctgcagTGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAA
EST: gi|86487602|gb|CI130235.1|CI130235
EST:     GAAGACTTCTGCAACAGAATCCACAAGGACATGGTGAAACAATTTAAATA                         TGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAA
genomic: GAAGACTTCTGCAACAGAATCCACAAGGACATGGTGAAACAATTTAAATAgtgagtatct ... aaacctgcagTGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAA
EST: gi|88245533|gb|CI245382.1|CI245382
EST:     GAAGACTTCTGCAACAGAATCCACAAGGACATGGTGAAACAATTTAAATA                         TGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAA
genomic: GAAGACTTCTGCAACAGAATCCACAAGGACATGGTGAAACAATTTAAATAgtgagtatct ... aaacctgcagTGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAA
EST: gi|86525484|gb|CI165690.1|CI165690
EST:     GAAGACTTCTGCAACAGAATCCACAAGGACATGGTGAAACAATTTAAATA                         TGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAA
genomic: GAAGACTTCTGCAACAGAATCCACAAGGACATGGTGAAACAATTTAAATAgtgagtatct ... aaacctgcagTGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAA
EST: gi|88830576|gb|CI078020.1|CI078020
EST:     AAGACTTCTGCAACAGAATCCACAAGGACATGGTGAAACAA-TTAGAATA                         TGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCA
genomic: AAGACTTCTGCAACAGAATCCACAAGGACATGGTGAAACAATTTA-AATAgtgagtatct ... aaacctgcagTGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCA
EST: gi|86887193|gb|CI326008.1|CI326008
EST:     GAAGACTTCTGCAACAGAATCCACAAGGACATGGTGAAACAATTTAAATA                         TGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAA
genomic: GAAGACTTCTGCAACAGAATCCACAAGGACATGGTGAAACAATTTAAATAgtgagtatct ... aaacctgcagTGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAA
EST: gi|86823697|gb|CI258751.1|CI258751
EST:     GAAGACTTCTGCAACAGAATCCACAAGGACATGGTGAAACAATTTAAATA                         TGCATTGGTGTGGGGTTCTAGCGCGAAGCATAAGCCTCAGAGAGTTGGCAA
genomic: GAAGACTTCTGCAACAGAATCCACAAGGACATGGTGAAACAATTTAAATAgtgagtatct ... aaacctgcagTGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAA
EST: gi|88228618|gb|CI228098.1|CI228098
EST:     GAAGACTTCTGCAACAGAATCCACAAGGACATGGTGAAACAATTTAAATA                         TGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAA
genomic: GAAGACTTCTGCAACAGAATCCACAAGGACATGGTGAAACAATTTAAATAgtgagtatct ... aaacctgcagTGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAA
EST: gi|86887118|gb|CI325933.1|CI325933
EST:     GAAGACTTCTGCAACAGAATCCACAAGGACATGGTGAAACAATTTAAATA                         TGCATT-GTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAA
genomic: GAAGACTTCTGCAACAGAATCCACAAGGACATGGTGAAACAATTTAAATAgtgagtatct ... aaacctgcagTGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAA

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: 73 (upstream exon), 54 (downstream exon)
Score: 56

ACCCAGATTATGAGGACCCTGTAATCGTATCCTCTAAGAAGAAAACAGTGGAAGACTTCTGCAACAGAATCCACAAGGACATGGTGAAACAATTTAAATAgtgagtatct ... aaacctgcagTGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatatttttgtccctgttatccatctgtgtggctaactgctcacaaaacctgcagTGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAG
                                     tgctcac  putative branch site (score: 56)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtatcttcatttgtatcttgtctgaatatttttgtccctgttatccatctgtgtggctaactgctcacaaaacctgcagTGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC