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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaaactgtttgcttttatttccatattgtgccatagaaacattcttcccagaggttaaattctttattgttttgcttctgtcaaaaaacatttttgtttatttgcagGAAGTAGCTGTCAAGAAATTCTTGGATCAAGATTTCTATGGTGATGCTTTGGATGAATTCCGGAGTGAA

Basic information

species Oryza sativa
transcript LOC_Os03g06410.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g06410.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G044180_T02 (Zea mays), 3'ss of exon 6
gtaagaaact-gtttgcttttatttccatattgtgccataga----aacattcttcccagaggtt-----aaattctttattgttttgctt--------------ctgtcaaaaaac----atttttgtttatttgcagGAAGTAGCTGTCAAGAAATTCTTGGATCAAGATTTCTATGGTGATGCTTTGGATGAATTCCGGAGTGAA
||||| |  |  ||  |   | ||    | ||||  | |         ||||  | | ||| |||      ||  | | |  |  |    |                |||||   ||     ||||  ||||||| |||||||||||||| || |||||||||||||||||||| ||||| |||||| ||||||| ||  ||||||||
gtaagtagttcattcacccattttagttttttgtatcttgagcttggccatttgttcaagatgttctgtggaagccataaaagaatcagatgagaaaccaaatcatggtcaatgcactgaagttttcatttattttcagGAAGTAGCTGTAAAAAAATTCTTGGATCAAGATTTTTATGGCGATGCTCTGGATGAGTTTAGGAGTGAA

upper sequence: LOC_Os03g06410.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G044180_T01 (Zea mays), 3'ss of exon 6
gtaagaaact-gtttgcttttatttccatattgtgccataga----aacattcttcccagaggtt-----aaattctttattgttttgctt--------------ctgtcaaaaaac----atttttgtttatttgcagGAAGTAGCTGTCAAGAAATTCTTGGATCAAGATTTCTATGGTGATGCTTTGGATGAATTCCGGAGTGAA-------------------------------
||||| |  |  ||  |   | ||    | ||||  | |         ||||  | | ||| |||      ||  | | |  |  |    |                |||||   ||     ||||  ||||||| |||||||||||||| || |||||||||||||||||||| ||||| |||||| ||||||| ||  ||||||||                               
gtaagtagttcattcacccattttagttttttgtatcttgagcttggccatttgttcaagatgttctgtggaagccataaaagaatcagatgagaaaccaaatcatggtcaatgcactgaagttttcatttattttcagGAAGTAGCTGTAAAAAAATTCTTGGATCAAGATTTTTATGGCGATGCTCTGGATGAGTTTAGGAGTGAAGTAGGTGAACTTTTATCTGTTTCTATCTTGG

upper sequence: LOC_Os03g06410.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G175563_T01 (Zea mays), 3'ss of exon 5
gtaagaaact-gtttgcttttatttccatattgtgccataga----aacattcttcccagaggtt-----aaattctttattgttttgctt--------------ctgtcaaaaaac----atttttgtttatttgcagGAAGTAGCTGTCAAGAAATTCTTGGATCAAGATTTCTATGGTGATGCTTTGGATGAATTCCGGAGTGAA
||||| |  |  ||  ||  | ||    | ||||  | |         ||||  | | ||| |||      ||  | | |  |  |    |                |||||   ||     |||| |||||||| |||||||||||||| || |||||||||||||||||||| ||||| |||||| ||||||| ||  ||||||||
gtaagtagttcattcactcattttagttttttgtatcttgagcttggccatttgttcaagatgttctgtggaagccataaaagaatcagatgagaaaccaaatcatggtcaatgcactgaagttttcgtttattttcagGAAGTAGCTGTAAAAAAATTCTTGGATCAAGATTTTTATGGCGATGCTCTGGATGAGTTTAGGAGTGAA

upper sequence: LOC_Os03g06410.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G038982_T01 (Zea mays), 3'ss of exon 5
-----------------------------------gtaagaaact---gtttgcttttatttccatattgtgccatagaaacattcttcccagaggttaaattctttattgttttgcttctg-tcaaaaaac----atttttgtttatttgcagGAAGTAGCTGTCAAGAAATTCTTGGATCAAGATTTCTATGGTGATGCTTTGGATGAATTCCGGAGTGAA
                                    |  | | ||   | ||     | | | ||   ||| |    |||    |      |     | |  || | |         || || ||||   ||     |||| ||||||||||||||||||||||| || ||||||||||||||||||||||||||||||||| ||||||| ||  ||||||||
gtaagtagttcatcccccccccctaaaattctattttttgtatcttgagcttagccatttgttcaagatgttctgcggaagtcataaaagaatcaactgagatcatgagaaaccaaattatggtcaatgcactgaagttttcgtttatttgcagGAAGTAGCTGTAAAAAAATTCTTGGATCAAGATTTCTATGGTGATGCTCTGGATGAGTTTAGGAGTGAA

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|88571349|gb|CI662722.1|CI662722
EST:     GTTCATATGGAGAGGTGTACCGTGCTGATTGGAATGGAACA                         GAAGTAGCTGTCAAGAAATTCTTGGATCAAGATTTCTATGGTGATGCTTTG
genomic: GTTCATATGGAGAGGTGTACCGTGCTGATTGGAATGGAACAgtaagaaact ... ttatttgcagGAAGTAGCTGTCAAGAAATTCTTGGATCAAGATTTCTATGGTGATGCTTTG
EST: gi|569642|gb|D40491.1|D40491
EST:     GTTCATATGGAGAGGTGTACCGTGCTGATTGGAATGGAACA                         GAAGTAGCTGTCAAGAAATTCTTGGATCAAGATTTCTATGGTGATGCTTTG
genomic: GTTCATATGGAGAGGTGTACCGTGCTGATTGGAATGGAACAgtaagaaact ... ttatttgcagGAAGTAGCTGTCAAGAAATTCTTGGATCAAGATTTCTATGGTGATGCTTTG
EST: gi|58596848|gb|CK007376.1|CK007376
EST:     GTTCATATGGAGAGGTGTACCGTGCTGATTGGAATGGAACA                         GAAGTAGCTGTCAAGAAATTCTTGGATCAAGATTTCTATGGTGATGCTTTG
genomic: GTTCATATGGAGAGGTGTACCGTGCTGATTGGAATGGAACAgtaagaaact ... ttatttgcagGAAGTAGCTGTCAAGAAATTCTTGGATCAAGATTTCTATGGTGATGCTTTG
EST: gi|569641|gb|D40490.1|D40490
EST:     GTTCATATGGAGAGGTGTACCGTGCTGATTGGAATGGAACA                         GAAGTAGCTGTCAAGAAATTCTTGGATCAAGATTTCTATGGTGATGCTTTG
genomic: GTTCATATGGAGAGGTGTACCGTGCTGATTGGAATGGAACAgtaagaaact ... ttatttgcagGAAGTAGCTGTCAAGAAATTCTTGGATCAAGATTTCTATGGTGATGCTTTG
EST: gi|38475096|gb|CF959229.1|CF959229
EST:     GTTCATATGGAGAGGTGTACCGTGCTGATTGGGGTGGAACA                         GAAGTAGCTGTCAAGAAATTCTTGGATCAATATTTCTATGGTGATGCTTTG
genomic: GTTCATATGGAGAGGTGTACCGTGCTGATTGGAATGGAACAgtaagaaact ... ttatttgcagGAAGTAGCTGTCAAGAAATTCTTGGATCAAGATTTCTATGGTGATGCTTTG
EST: gi|571627|gb|D41138.1|D41138
EST:     GTTCATATGGAGAGGTGTACCGTGCTGATTGGAATGGAACA                         GAAGTAGCTGTCAAGAAATTCTTGGATCAAGATTTCTATGGTGATGCTTTG
genomic: GTTCATATGGAGAGGTGTACCGTGCTGATTGGAATGGAACAgtaagaaact ... ttatttgcagGAAGTAGCTGTCAAGAAATTCTTGGATCAAGATTTCTATGGTGATGCTTTG
EST: gi|58688165|gb|CK076852.1|CK076852
EST:     GTTCATATGGAGAGGTGTACCGTGCTGATTGGAATGGAACA                         GAAGTAGCTGTCAAGAAATTCTTGGATCAAGATTTCTATGGTGATGCTTTG
genomic: GTTCATATGGAGAGGTGTACCGTGCTGATTGGAATGGAACAgtaagaaact ... ttatttgcagGAAGTAGCTGTCAAGAAATTCTTGGATCAAGATTTCTATGGTGATGCTTTG

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), 69 (downstream exon)
Score: 16

GTTCATATGGAGAGGTGTACCGTGCTGATTGGAATGGAACAgtaagaaact ... ttatttgcagGAAGTAGCTGTCAAGAAATTCTTGGATCAAGATTTCTATGGTGATGCTTTGGATGAATTCCGGAGTGAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggttaaattctttattgttttgcttctgtcaaaaaacatttttgtttatttgcagGAAGTAGCTGTCAAGAAATTCTTGGATCAAGATTTCTATGGTGATGCTTTGGATGAATTCCGGAGTGAA
                                      tttttgttt  CT-rich tract
                            tcaaaaaacatttttg  TA-rich tract