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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtatttttacttggcatcatcattgttaatccatgtcgatgtacaaacactgttgtatcctgctttgtatgccacttataattcagttagtgtatggtttaaattgtaacatcttttctgctattgtagtctcatgtctttatcatctttctttcttctgcagTTCTTTTCAGAATTCAACACTAGGTTGCTATCATCAACCAACTACATAACAAAAAGGCAGGCTATCAAG

Basic information

species Oryza sativa
transcript LOC_Os07g39630.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g39630.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G351417_T03 (Zea mays), 3'ss of exon 2
gtgagtatttttacttggcatcatcattgttaatccatgtcgatgtacaaacactgttgtatcctgctttgtatgccacttataattcagttagtgtatggtttaaattgtaacatcttttctgctattgtagtctcatgtctttatcatctttctttcttctgcagTTCTTTTCAGAATTCAACACTAGGTTGCTATCATCAACCAACTACATAACAAAAAGGCAGGCTATCAAG
                                                           ||| || || |   ||     |||  |  | ||||      | || | ||||    ||  |||| || || || | | |   || |  ||| ||  || |||    |||| |||  |||||||||| |||||||||| |||||||||||||| |||||||||||||| |||||||||
---------------------------------------------------------catattctactctacttga----tatgttgtaattagcaccatgatttatttgtg--ttcaattctacttttctaatgttaaccctcttgcattttcattcctt----agTTTTTTGAAGAATTCAACTCTAGGTTGCTGTCATCAACCAACTATATAACAAAAAGGCAAGCTATCAAG

upper sequence: LOC_Os07g39630.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G066051_T01 (Zea mays), 3'ss of exon 6
gtgagtatttttacttggcatcatcattgttaatccatgtcgatgtacaaacactgttgtatcctgctttgtatgccacttataattcagttagtgtatggtttaaattgtaacatcttttctgctattgtagtctcatgtctttatcatctttctttcttctgcagTTCTTTTCAGAATTCAACACTAGGTTGCTATCATCAACCAACTACATAACAAAAAGGCAGGCTATCAAG
                                                     || || ||  || |||  ||||    || |||||       ||  |  |||   | | ||      |||| || || || ||| |   || | |||| ||  || |||    ||||||||  |||||| ||| |||||||||| ||||||||||||||||||||||||||||| |||||||||
----------------------------------------------------cctattctagtctacttgatatg----ttgtaattagcaccatgatttatttgtgt-gcaa------ttctacttttctaatcttaaccctctttcattttcattcctt----agTTCTTTGAAGAATTTAACTCTAGGTTGCTGTCATCAACCAACTACATAACAAAAAGGCAAGCTATCAAG
















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|38473913|gb|CF958045.1|CF958045
EST:     GGCAGAATTTCTGTCAAAGAATTATGACTGG                         TGCTGTTCAGAATTCAACACTAGGTTGCTATCATCAACCAACTACATAACA
genomic: GGCAGAATTTCTGTCAAAGAATTATGACTGGgtgagtattt ... tcttctgcagTTCTTTTCAGAATTCAACACTAGGTTGCTATCATCAACCAACTACATAACA
EST: gi|29675062|gb|CB671337.1|CB671337
EST:     CAAGGCATAAAGCTACCGTGGCAGAATTTCTGTCAAAGAATTATGACTGG                         TTCTTTTCAGAATTCAACACTAGGTTGCTATCATCAACCAACTACATAACA
genomic: CAAGGCATAAAGCTACCGTGGCAGAATTTCTGTCAAAGAATTATGACTGGgtgagtattt ... tcttctgcagTTCTTTTCAGAATTCAACACTAGGTTGCTATCATCAACCAACTACATAACA
EST: gi|29673566|gb|CB669841.1|CB669841
EST:     CAAGGCATAAAGCTACCGTGGCAGAATTTCTGTCAAAGAATTATGACTGG                         TTCTTTTCAGAATTCAACACTAGGTTGCTATCATCAACCAACTACATAACA
genomic: CAAGGCATAAAGCTACCGTGGCAGAATTTCTGTCAAAGAATTATGACTGGgtgagtattt ... tcttctgcagTTCTTTTCAGAATTCAACACTAGGTTGCTATCATCAACCAACTACATAACA
EST: gi|38481075|gb|CF965164.1|CF965164
EST:     AGAA-TTCTGTCGAAGAATTATGACTGG                         TTCTTTTCAGAATTCAACACTAGGTTGCTATCATCAACCAACTACATAACA
genomic: AGAATTTCTGTCAAAGAATTATGACTGGgtgagtattt ... tcttctgcagTTCTTTTCAGAATTCAACACTAGGTTGCTATCATCAACCAACTACATAACA
EST: gi|29673647|gb|CB669922.1|CB669922
EST:     CAAGGCATAAAGCTACCGTGGCAGAATTTCTGTCAAAGAATTATGACTGG                         TTCTTTTCAGAATTCAACACTAGGTTGCTATCATCAACCAACTACATAACA
genomic: CAAGGCATAAAGCTACCGTGGCAGAATTTCTGTCAAAGAATTATGACTGGgtgagtattt ... tcttctgcagTTCTTTTCAGAATTCAACACTAGGTTGCTATCATCAACCAACTACATAACA
EST: gi|58695257|gb|CK083944.1|CK083944
EST:     CAAGGCATAAAGCAACCGTGGCAGAATTTCTGTCGAAGAATTATGACTGG                         TTCTTTTCAGAA
genomic: CAAGGCATAAAGCTACCGTGGCAGAATTTCTGTCAAAGAATTATGACTGGgtgagtattt ... tcttctgcagTTCTTTTCAGAA
EST: gi|29679531|gb|CB675806.1|CB675806
EST:     CAAGGCATAAAGCTCCCGTGGCAGAATTTCTGTCAAAGAATTATGACTGG                         TTCTTTTCAGAATTCAACACTAGGTTGCTATCATCAACCAACTACATAACA
genomic: CAAGGCATAAAGCTACCGTGGCAGAATTTCTGTCAAAGAATTATGACTGGgtgagtattt ... tcttctgcagTTCTTTTCAGAATTCAACACTAGGTTGCTATCATCAACCAACTACATAACA
EST: gi|29664684|gb|CB660959.1|CB660959
EST:     CAAGGCATAAAGCTACCGTGGCAGAATTTCTGTCAAAGAATTATGACTGG                         TTCTTTTCAGAATTCAACACTAGGTTGCTATCATCAACCAACTACATAACA
genomic: CAAGGCATAAAGCTACCGTGGCAGAATTTCTGTCAAAGAATTATGACTGGgtgagtattt ... tcttctgcagTTCTTTTCAGAATTCAACACTAGGTTGCTATCATCAACCAACTACATAACA
EST: gi|58663168|gb|CK051854.1|CK051854
EST:     CAAGGCATAAAGCTACCGTGGCAGAATTTCTGTCAAAGAATTATGACTGG                         TTCTTTTCAGAATTCAACACTAGGTTGCTATCATCAACCAACTACATAACA
genomic: CAAGGCATAAAGCTACCGTGGCAGAATTTCTGTCAAAGAATTATGACTGGgtgagtattt ... tcttctgcagTTCTTTTCAGAATTCAACACTAGGTTGCTATCATCAACCAACTACATAACA
EST: gi|25799534|gb|CA755495.1|CA755495
EST:     CAAGGCATAAAGCTACCGTGGCAGAATTTCTGTCAAAGAATTATGACTGG                         TTCTTTTCAGAATTCAACACTAGGTTGCTATCATCAACCAACTACATAACA
genomic: CAAGGCATAAAGCTACCGTGGCAGAATTTCTGTCAAAGAATTATGACTGGgtgagtattt ... tcttctgcagTTCTTTTCAGAATTCAACACTAGGTTGCTATCATCAACCAACTACATAACA
EST: gi|29656023|gb|CB652298.1|CB652298
EST:     CAAGGCATAAAGCTACCGTGGCAGAATTTCTGTCAAAGAATTATGACTGG                         TTCTTTTCAGAATTCAACACTAGGTTGCTATCATCAACCAACTACATAACA
genomic: CAAGGCATAAAGCTACCGTGGCAGAATTTCTGTCAAAGAATTATGACTGGgtgagtattt ... tcttctgcagTTCTTTTCAGAATTCAACACTAGGTTGCTATCATCAACCAACTACATAACA
EST: gi|66915714|gb|CX102562.1|CX102562
EST:     CAAGGCATAAAGCAACCGTGGCAGAATTTCTGTCGAAGAATTATGACTGG                         TTCTTTTCAGAATTCAACACTAGGTTGCTATCATCAACCAACTACATAACA
genomic: CAAGGCATAAAGCTACCGTGGCAGAATTTCTGTCAAAGAATTATGACTGGgtgagtattt ... tcttctgcagTTCTTTTCAGAATTCAACACTAGGTTGCTATCATCAACCAACTACATAACA
EST: gi|58688748|gb|CK077435.1|CK077435
EST:     CAAGGCATAAAGCTACCGTGGCAGAATTTCTGTCAAAGAATTATGACTGG                         TTCTTTTCAGAATTCAACACTAGGTTGCTATCATCAACCAACTACATAACA
genomic: CAAGGCATAAAGCTACCGTGGCAGAATTTCTGTCAAAGAATTATGACTGGgtgagtattt ... tcttctgcagTTCTTTTCAGAATTCAACACTAGGTTGCTATCATCAACCAACTACATAACA
EST: gi|29660229|gb|CB656504.1|CB656504
EST:     CAAGGCATAAAGCTACCGTGGCAGAATTTCTGTCAAAGAATTATGACTGG                         TTCTTTTCAGAATTCAACACTAGGTTGCTATCATCAACCAACTACATAACA
genomic: CAAGGCATAAAGCTACCGTGGCAGAATTTCTGTCAAAGAATTATGACTGGgtgagtattt ... tcttctgcagTTCTTTTCAGAATTCAACACTAGGTTGCTATCATCAACCAACTACATAACA
EST: gi|58674983|gb|CK063670.1|CK063670
EST:     CAAGGCATAAAGCTACCGTGGCAGAATTTCTGTCAAAGAATTATGACTGG                         TTCTTTTCAGAATTCAACACTAGGTTGCTATCATCAACCAACTACATAACA
genomic: CAAGGCATAAAGCTACCGTGGCAGAATTTCTGTCAAAGAATTATGACTGGgtgagtattt ... tcttctgcagTTCTTTTCAGAATTCAACACTAGGTTGCTATCATCAACCAACTACATAACA
EST: gi|29629034|gb|CB634045.1|CB634045
EST:     CAAGGCATAAAGCAACCGTGGCAGAATTTCTGTCGAAGAATTATGACTGG                         TTCTTTTCAGAATTCAACACTAGGTTGCTATCATCAACCAACTACATAACA
genomic: CAAGGCATAAAGCTACCGTGGCAGAATTTCTGTCAAAGAATTATGACTGGgtgagtattt ... tcttctgcagTTCTTTTCAGAATTCAACACTAGGTTGCTATCATCAACCAACTACATAACA

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: 60 (upstream exon), 69 (downstream exon)
Score: 79

GAACTTCTGACAAGGCATAAAGCTACCGTGGCAGAATTTCTGTCAAAGAATTATGACTGGgtgagtattt ... tcttctgcagTTCTTTTCAGAATTCAACACTAGGTTGCTATCATCAACCAACTACATAACAAAAAGGCAGGCTATCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatcttttctgctattgtagtctcatgtctttatcatctttctttcttctgcagTTCTTTTCAGAATTCAACACTAGGTTGCTATCATCAACCAACTACATAACAAAAAGGCAGGCTATCAAG
 ttgtaac  putative branch site (score: 79)
                     tctcatgtctttatca  putative PPT
                              tttatcat  TA-rich tract