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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaaacaattaagataaatctatatttcttcatttcattccttcatccatcataaccgtagtttccttgtctcttcagCAAATAGAGTTCGGCTTTGGAACAAAGGTGTTGATTCTGAAAGTTTCCATCCTAAATTTCGGAAGCATGAAATGCGCATTAAATTGAG

Basic information

species Oryza sativa
transcript LOC_Os03g15840.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g15840.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G117153_T01 (Zea mays), 3'ss of exon 7
gttaaacaattaagataa-atctatatttcttcatttc-attccttcatccatcataaccgtagt-ttccttgtctcttcagCAAATAGAGTTCGGCTTTGGAACAAAGGTGTTGATTCTGAAAGTTTCCATCCTAAATTTCGGAAGCATGAAATGCGCATTAAATTGAG
|||||  | | |  |||  ||  || ||| ||  |||  || |||  ||||||  ||| | |    |||| ||  ||||||||||| ||| | ||||||||||| || ||||| ||||||||||| || ||| |||||| ||||| ||| ||||||||  | | ||||||
gttaagtagtgacaatattattaatgttttttatttttgatccctctatccatgctaaacatgaccttccatgcttcttcagCAAACAGAATACGGCTTTGGAATAAGGGTGTAGATTCTGAAAGCTTTCATACTAAATATCGGAGGCACGAAATGCGTGTCAGATTGAG

upper sequence: LOC_Os03g15840.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G049190_T02 (Zea mays), 3'ss of exon 7
gttaaacaattaagataa-atctatatttctt-----catttcattccttcatccatcataaccgtagttt-ccttgtctcttcagCAAATAGAGTTCGGCTTTGGAACAAAGGTGTTGATTCTGAAAGTTTCCATCCTAAATTTCGGAAGCATGAAATGCGCATTAAATTGAG
||| |  | | || |||  ||  || ||| ||       ||| || |||  ||||||  ||| | ||   | || |||| |||||||||| ||| | ||||||||||| || ||||| ||||||||||| || ||| |||||| ||||| ||||||||||||  | | ||||||
gtttagtagtgaaaatattattaatgttttttgtagtttttttatccctctatccatgctaaacataacctaccatgtcccttcagCAAACAGAATACGGCTTTGGAATAAGGGTGTAGATTCTGAAAGCTTTCATACTAAATATCGGAGGCATGAAATGCGTGTCAGATTGAG

upper sequence: LOC_Os03g15840.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA18G42540.1 (Glycine max), 3'ss of exon 7
------------------------------------------------------gttaaacaattaagataaatctatatttcttcatttcattccttcatccatcataaccgtagtttccttgtc--tcttcagCAAATAGAGTTCGGCTTTGGAACAAAGGTGTTGATTCTGAAAGTTTCCATCCTAAATTTCGGAAGCATGAAATGCGCATTAAATTGAG
                                                       ||  | |||    ||   ||  |||  || | |   || |    |    |       ||  ||  | |||   | | |||| || |   |||| ||||||||||| ||||||||||||||||  |||||||| ||||  ||    |||||||||||  | | | | ||
gtgaacataaaatccgcttatctagacttttagctattcttaattggtgacagcatttgaaaatacgcatttctcggtatgcctac-tactatgctgcgaatttttgagtaagtttttctcctgttggtatccagCTAACAAGATTCGTCTTTGGAACAAGGGTGTTGATTCTGAAAAATTCCATCCCAAATACCGCTCCCATGAAATGCGATTAAGACTAAG

upper sequence: LOC_Os03g15840.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA07G17680.1 (Glycine max), 3'ss of exon 6
---------------------------------------------gttaaacaattaagataaatctatatttcttcatttcattccttc-atccatca------taaccgtagtttccttgtctc----ttcagCAAATAGAGTTCGGCTTTGGAACAAAGGTGTTGATTCTGAAAGTTTCCATCCTAAATTTCGGAAGCATGAAATGCGCATTAAATTGAG
                                             | |||     | |||  ||| | | |||| |  | |   | || | || || ||      | ||||   ||| ||  | |     | |||| || |   |||| ||||||||||| ||||||||||||||||  |||||||| ||||  ||    |||||||||||  | | | | ||
gtgaacatagaatccccttatctagtcttttagctatgcttaattggtaatagcatcaga-gaatatgtgtttcctggtatgcctactactatgcagcaaaattttgaccgagtttttctcctgttggtatccagCTAACAAGATTCGTCTTTGGAACAAGGGTGTTGATTCTGAAAAATTCCATCCCAAATACCGCTCCCATGAAATGCGATTAAGACTAAG

upper sequence: LOC_Os03g15840.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA01G27840.1 (Glycine max), 3'ss of exon 7
---------------------------------------------------gttaaacaattaagataaatctatatttcttcatttcattcc---ttcatccatcata-----accgtagtttccttgtc--tcttcagCAAATAGAGTTCGGCTTTGGAACAAAGGTGTTGATTCTGAAAGTTTCCATCCTAAATTTCGGAAGCATGAAATGCGCATTAAATTGAG
                                                    | | |  ||    | | |  ||| ||| |  | | ||||     | || | ||  |      | |  | ||    |||   | | |||| || |   || | ||||||||||| ||||||||||||||||||||||||||   |||   |   |||||||||||  | | | ||||
gtgaactcaaacaccccttatgaagtgatttcatagctcttcgctgagttgataatagcatctgaacataagtatttttttatactacattgtcaatgcagcaattttttgtctaactcaattctactgttgatgtccagCGAACAAGATTTGTCTTTGGAACAAGGGTGTTGATTCTGAAAGTTTCCATCCGCGATTCAAGTCCCATGAAATGCGATTAAGACTGAG

upper sequence: LOC_Os03g15840.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA03G14200.1 (Glycine max), 3'ss of exon 7
-------------------gttaaacaattaagataaatctatatttcttcatttcattccttcatccatcata-accgtagtttccttgtc--tcttcagCAAATAGAGTTCGGCTTTGGAACAAAGGTGTTGATTCTGAAAGTTTCCATCCTAAATTTCGGAAGCATGAAATGCGCATTAAATTGAG
                     |||||| | ||  |||    | |  |      |  || |    ||   |  |  | |  | ||  | |||   | | |||| || |   || | ||||||||||| ||||| ||||||||||||||||||||   |||   |   |||||||||||  | |   ||||
aataataaatacaagataacataaaca-taaatgtaatctaacaactacattgtcaatgcagcaattttttgtctaactcaattctcctgttgatgtccagCGAACAAGATTTGTCTTTGGAACAAGGGTGTCGATTCTGAAAGTTTCCATCCACGATTCAAGTCCCATGAAATGCGATTAAGGCTGAG

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|29682379|gb|CB678654.1|CB678654
EST:     CTTTGAAACTGCGAAAGTAGTATCAG                         CAAATAGAGTTCGGCTTGGGAACAAAGGTGTTGATTCTGAAAGTTTCCATC
genomic: CTTTGAAACTGCGAAAGTAGTATCAGgttaaacaat ... gtctcttcagCAAATAGAGTTCGGCTTTGGAACAAAGGTGTTGATTCTGAAAGTTTCCATC
EST: gi|58691923|gb|CK080610.1|CK080610
EST:     TCCGTCAGTAGCTATTGCCGAGGACTTTGAAACTGCGAAAGTAGTATCAG                         CAAACAGAGTTCGGCTTTGGAACAAAGGTGTTGATTCTGAAAGTTTCCATC
genomic: TCCGTCAGTAGCTATTGCCGAGGACTTTGAAACTGCGAAAGTAGTATCAGgttaaacaat ... gtctcttcagCAAATAGAGTTCGGCTTTGGAACAAAGGTGTTGATTCTGAAAGTTTCCATC

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: 68 (upstream exon), 66 (downstream exon)
Score: 16

GATGTCTTCATAGGTCTGCAGATCTTACTCTAGTTCCGTCAGTAGCTATTGCCGAGGACTTTGAAACTGCGAAAGTAGTATCAGgttaaacaat ... gtctcttcagCAAATAGAGTTCGGCTTTGGAACAAAGGTGTTGATTCTGAAAGTTTCCATCCTAAATTTCGGAAGCATGAAATGCGCATTAAATTGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttcttcatttcattccttcatccatcataaccgtagtttccttgtctcttcagCAAATAGAGTTCGGCTTTGGAACAAAGGTGTTGATTCTGAAAGTTTCCATCCTAAATTTCGGAAGCATGAAATGCGCATTAAATTGAG
                          tcataac  putative branch site (score: 16)
                                      tttccttgtctcttc  putative PPT
        atttcatt  TA-rich tract