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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatattccgtaacacatcttaaagcaagctctttgataacaaaatgtgcatgtcccaaccatcctacaaggagaatgccaaagatttccaatcctaaagtacctttcttaagtagaatttgagctcaaacacaggctgcgaggcccatttattacagtgctaatttttccattttttgttttcacagGATGGAAGAATTAACTACCAGGAGTTTGTCGCCATGATGAGGAACAACAACCCTGAGATTGCTCCCAACCGGCGGCGCATGTTCTAACTTCCTTTACAAT

Basic information

species Oryza sativa
transcript LOC_Os01g43410.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g43410.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM5G856738_T01 (Zea mays), 3'ss of exon 6
gtaagtatattccgtaacacatcttaaagcaagctctttgataacaaaatgtgcatgtcccaaccatcctacaaggagaatgccaaagatttccaatcctaaagtacctttcttaagtagaatttgagctcaaacacaggctgcgaggcccatttattacagtgctaatttttccattttttgttt-tcacagGATGGAAGAATTAACTACCAGGAGTTTGTCGCCATGATGAGGAACAACAACCCTGAGATTGCTCCCAACCGGCGGCGCATGTTCTAACT-TCCTTTACAAT
                                                                                      |   | || ||  |||  |   || ||   | | |  |   | | |         | | |            | |||  | | ||  |  || |||   | |  ||||||||||||||||| |||||||||||||| ||||||||||||||||| | ||||||||||| ||| |||||| | |||||||||||||| || | ||||| 
--------------------------------------------------------------------------------------aacataccgattataatat-ttttgctggtgcatacataatgatgacttttcttttacaaaaa------gacatagtaatgagttcccatttctttacatatggcagGATGGAAGAATTAATTACCAGGAGTTTGTTGCCATGATGAGGAACAATACCCCTGAGATTGTTCCAAACCGGAGACGCATGTTCTAACTGTCATGTACAA-

upper sequence: LOC_Os01g43410.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G025387_T02 (Zea mays), 3'ss of exon 7
gtaagtatattccgtaacacatcttaaagcaagctctttgataacaaaatgtgcatgtcccaaccatcctacaaggagaatgccaaagatttccaatcctaaagtacctttcttaagtagaatttgagctcaaacacaggctgcgaggcccatttattacagtgctaatttttccattttttgttttca----cagGATGGAAGAATTAACTACCAGGAGTTTGTCGCCATGATGAGGAACAACAACCCTGAGATTGCTCCCAACCGGCGGCGCATGTTCTAACT-TCCTTTACAAT
                                                                                             |||||   |   ||||    |  |   ||  ||   |||   | ||  ||| |   | |||||| | |||||||| ||| || || ||| || | |    ||||||||||||||||| |||||||||||||| ||||||||||||||||||| ||||||||||| ||| || ||| |||||||||||||||| || |  |||| 
-------------------------------------------------------------------------------------------cacaatctctacaaacct----tgtgatcaacctgca-tcaggaaaagagtgctaactcaatttatcagagtgctaactttcccgttattttttcttattgccagGATGGAAGAATTAATTACCAGGAGTTTGTTGCCATGATGAGGAACAACAGCCCTGAGATTGTTCCAAATCGGAGGCGCATGTTCTAACTGTCATGGACAA-

upper sequence: LOC_Os01g43410.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA08G02300.1 (Glycine max), 3'ss of exon 8
gtaagtatattccgtaacacatcttaaagcaagctctttgataacaaaatgtgcatgtcccaaccatcctacaaggagaatgccaaagatttccaatcctaaagtacctttcttaagtagaatttgagctcaaacacaggc---tgcgaggcccatttattacagtgc-taatttttccattttttgttttcacagGATGGAAGAATTAACTACCAGGAGTTTGTCGCCATGATGAGGAACAACAACCCTGAGATTGCTCCCAACCGGCGGCGCATGTTCTAACTT-CCTTTACAAT
                                                                                               |||||  ||| |   |  |  ||     | | ||  |     ||     ||    |    || |||| | |    ||| ||     |   | || |  ||||||||||||||||||||  | |||||||| ||||||||||||||   |||||| || ||  ||| ||     |     | ||   || |  ||  | || |
----------------------------------------------------------------------------------------------catcct--agttctcattgttggttatcctagtgccaagttgtagatgtttgtagtgttgtttaattatactttacaatattaattatcaattttcttgcagGATGGAAGAATTAACTATGATGAGTTTGTAGCCATGATGAGGAAAGGCAACCCAGATATAACTCACA-TAACCCATAGACGTCGCAAATAACCCCTGCATT

upper sequence: LOC_Os01g43410.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA05G37260.1 (Glycine max), 3'ss of exon 7
gtaagtatattccgtaacacatcttaaagcaagctctttgataacaaaatgtgcatgtcccaaccatcctacaaggagaatgccaaagatttccaatcctaaagtacctttcttaagtagaatttgagctcaaacacaggctgcgaggcccatttattacagtgctaatttttccattttttgttttcacagGATGGAAGAATTAACTACCAGGAGTTTGTCGCCATGATGAGGAACAACAACCCTGAGATTGCTCCCAACCGGCGGCGCATGTTCTAACTTCCTTTACAAT
                                                                                   |  || | ||  ||  |    |   | || ||     || |||           ||  |   |     ||   || || |  ||||| |   |||| |||      ||||||||||||||||||||  | |||||||| ||||||||||||||   |||||| || ||  | | ||     |   |      | ||    || | |  |
-------------------------------------------------------------------------------tcatcctagttctctcattgt----tggttatcctagtgccaagttgtagatgtttgtagtgtttaa---ttatcctttgcaatattaattctcaaatttcttg------cagGATGGAAGAATTAACTATGATGAGTTTGTAGCCATGATGAGGAAAGGCAACCCAGACATAACGCACATAACCCAAAGACGTCGCAAATAAGCTATGCTTT

upper sequence: LOC_Os01g43410.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA11G02260.1 (Glycine max), 3'ss of exon 7
gtaagtatattccgtaacacatcttaaagcaagctctttgataacaaaatgtgcatgtcccaaccatcctacaaggagaatgccaaagatttccaatcctaaagtacctttcttaagtagaatttgagctcaaacacaggctgcgaggcccatttattacagtgctaatttttccattttttgttt-tcacagGATGGAAGAATTAACTACCAGGAGTTTGTCGCCATGATGAGGAACAACAACCCTGAGATTGCTCCCAACCGGCGGCGCATGTTCTAACTTCCTTTACAAT
                                                    | | |   |   | | | | |       |  |   | |    | ||||| | |  | || |||  |    ||||     | |  |   |||         || |||    |  |||   | |  |      ||| |  ||||||||||||||||||||  | |||||||| ||||||||||||||   ||| || ||  | |    |||| | || ||||  |  | |  |   | | || 
----------------------------------------------------gtacgctgctttc-ttccatatccttgttctcgttggtgctta-tcctagaatgacatt-ttagat---gtttg----tatattctctctgt--------ttaattgttattttaaccatccattcccaaatttgttgcagGATGGAAGAATTAACTATGACGAGTTTGTAGCCATGATGAGGAAAGGCAATCCAGATTTAGTAAACAACAGACGTCGCAAATAATCAAGTTGATCATAAA

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|396941516|gb|HO188725.1|HO188725
EST:     GGGACGATAAAACGATTAAGGAAATCATCGCTGAAGTAGATACTGATCAT                         GATGGAAGAATTAACTACCAGGAGTTTGTCGCCATGATGAGGAACAACAAC
genomic: GGGACGATAAAACGATTAAGGAAATCATCGCTGAAGTAGATACTGATCATgtaagtatat ... gttttcacagGATGGAAGAATTAACTACCAGGAGTTTGTCGCCATGATGAGGAACAACAAC
EST: gi|29639095|gb|CB644104.1|CB644104
EST:     GGGACGATAAAACGATTAAGGAAATCATCGCTGAAGTAGATACTGATCAT                         GATGGAAGAATTAACTACCAGGAGTTTGTCGCCATGATGAGGAACAACAAC
genomic: GGGACGATAAAACGATTAAGGAAATCATCGCTGAAGTAGATACTGATCATgtaagtatat ... gttttcacagGATGGAAGAATTAACTACCAGGAGTTTGTCGCCATGATGAGGAACAACAAC
EST: gi|29657260|gb|CB653535.1|CB653535
EST:     GGGACGATAAAACGATTAAGGAAATCATCGCTGAAGTAGATACTGATCAT                         GATGGAAGAATTAACTACCAGGAGTTTGTCGCCATGATGAGGAACAACAAC
genomic: GGGACGATAAAACGATTAAGGAAATCATCGCTGAAGTAGATACTGATCATgtaagtatat ... gttttcacagGATGGAAGAATTAACTACCAGGAGTTTGTCGCCATGATGAGGAACAACAAC
EST: gi|86896428|gb|CI328842.1|CI328842
EST:     ATACTGATCAT                         GATGGAAGAATTAACTACCAGGAGTTTGTCGCCATGATGAGGAACAACAAC
genomic: ATACTGATCATgtaagtatat ... gttttcacagGATGGAAGAATTAACTACCAGGAGTTTGTCGCCATGATGAGGAACAACAAC
EST: gi|29681100|gb|CB677375.1|CB677375
EST:     GGGACGATAAAACGATTAAGGAAATCATCGCTGAAGTAGATACTGATCAT                         GATGGAAGAATTAACTACCAGGAGTTTGTCGCCATGATGAGGAACAACAAC
genomic: GGGACGATAAAACGATTAAGGAAATCATCGCTGAAGTAGATACTGATCATgtaagtatat ... gttttcacagGATGGAAGAATTAACTACCAGGAGTTTGTCGCCATGATGAGGAACAACAAC
EST: gi|112787230|gb|EE592302.1|EE592302
EST:     GGGACGATAAAACGATTAAGGAAATCATCGCTGAAGTAGATACTGATCGT                         GATGGAAGAATTAACTACCAGGAGTTTGTCGCCATGATGAGGAACAACAAC
genomic: GGGACGATAAAACGATTAAGGAAATCATCGCTGAAGTAGATACTGATCATgtaagtatat ... gttttcacagGATGGAAGAATTAACTACCAGGAGTTTGTCGCCATGATGAGGAACAACAAC
EST: gi|29637711|gb|CB642720.1|CB642720
EST:     GGGACGATAAAACGATTAAGGAAATCATCGCTGAAGTAGATACTGATCAT                         GATGGAAGAATTAACTACCAGGAGTTTGTCGCCATGATGAGGAACAACAAC
genomic: GGGACGATAAAACGATTAAGGAAATCATCGCTGAAGTAGATACTGATCATgtaagtatat ... gttttcacagGATGGAAGAATTAACTACCAGGAGTTTGTCGCCATGATGAGGAACAACAAC
EST: gi|29678242|gb|CB674517.1|CB674517
EST:     GGGACGATAAAACGATTAAGGAAATCATCGCTGAAGTAGATACTGATCAT                         GATGGAAGAATTAACTACCAGGAGTTTGTCGCCATGATGAGGAACAACAAC
genomic: GGGACGATAAAACGATTAAGGAAATCATCGCTGAAGTAGATACTGATCATgtaagtatat ... gttttcacagGATGGAAGAATTAACTACCAGGAGTTTGTCGCCATGATGAGGAACAACAAC
EST: gi|86260437|gb|CI066310.1|CI066310
EST:     GGGACGATAAAACGATTAAGGAAATCATCGCTGAAGTAGATACTGATCAT                         GATGGAAGAATTAACTACCAGGAGTTTGTCGCCATGATGAGGAACAACAAC
genomic: GGGACGATAAAACGATTAAGGAAATCATCGCTGAAGTAGATACTGATCATgtaagtatat ... gttttcacagGATGGAAGAATTAACTACCAGGAGTTTGTCGCCATGATGAGGAACAACAAC
EST: gi|29633567|gb|CB638576.1|CB638576
EST:     GGGACGATAAAACGATTAAGGAAATCATCGCTGAAGTAGATACTGATCAT                         GATGGAAGAATTAACTACCAGGAGTTTGTCGCCATGATGAGGAACAACAAC
genomic: GGGACGATAAAACGATTAAGGAAATCATCGCTGAAGTAGATACTGATCATgtaagtatat ... gttttcacagGATGGAAGAATTAACTACCAGGAGTTTGTCGCCATGATGAGGAACAACAAC
EST: gi|29633531|gb|CB638540.1|CB638540
EST:     GGGACGATAAAACGATTAAGGAAATCATCGCTGAAGTAGATACTGATCAT                         GATGGAAGAATTAACTACCAGGAGTTTGTCGCCATGATGAGGAACAACAAC
genomic: GGGACGATAAAACGATTAAGGAAATCATCGCTGAAGTAGATACTGATCATgtaagtatat ... gttttcacagGATGGAAGAATTAACTACCAGGAGTTTGTCGCCATGATGAGGAACAACAAC

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: 70 (upstream exon), 70 (downstream exon)
Score: 62

ATACATAACAGTAGATGAGTTGGAAGAAGCTCTGAAGAAGTATGATATGGGGGACGATAAAACGATTAAGGAAATCATCGCTGAAGTAGATACTGATCATgtaagtatat ... gttttcacagGATGGAAGAATTAACTACCAGGAGTTTGTCGCCATGATGAGGAACAACAACCCTGAGATTGCTCCCAACCGGCGGCGCATGTTCTAACTTCCTTTACAAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggctgcgaggcccatttattacagtgctaatttttccattttttgttttcacagGATGGAAGAATTAACTACCAGGAGTTTGTCGCCATGATGAGGAACAACAACCCTGAGATTGCTCCCAACCGGCGGCGCATGTTCTAACTTCCTTTACAAT
                         tgctaat  putative branch site (score: 62)
                               tttttccattttttgt  CT-rich tract
                            taatttttccattttt  TA-rich tract