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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcagtgaaacaactttcgaagacttactttgaccttgttttatctgattctgattttgcccttgtttcttatgcagTTTTTCATTGTATTATCGTGCTTGATATCTGTCTCAGTGAACTTCAGCACTTTCCTTGTGATCGGAAAGACTTCTCCTGTCACTTACCAAGTCCTGGGCC

Basic information

species Oryza sativa
transcript LOC_Os05g07670.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g07670.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G063511_T02 (Zea mays), 3'ss of exon 6
gtaagcagtgaaacaactttcgaagacttactttgaccttgttttatctgattctgattttgcccttgtttcttatgcagTTTTTCATTGTATTATCGTGCTTGATATCTGTCTCAGTGAACTTCAGCACTTTCCTTGTGATCGGAAAGACTTCTCCTGTCACTTACCAAGTCCTGGGCC
|| ||  |  ||||| |||| |   || ||     ||  | ||  |||  | ||| | ||| | ||| |||  | |||||||||||||||| || || ||| ||||||| ||||||||||||||||||||||| |||||||| |||||||| |||||||| |||||||||||||||||||
gtgagttgcaaaacatctttggtgcacatatccctacagt-ttccatcacactctaagttttctcttattttgtgtgcagTTTTTCATTGTGTTGTCATGCCTGATATCGGTCTCAGTGAACTTCAGCACTTTTCTTGTGATTGGAAAGACGTCTCCTGTTACTTACCAAGTCCTGGGCC

upper sequence: LOC_Os05g07670.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G063253_T08 (Zea mays), 3'ss of exon 5
gtaagcagtgaaacaactttcgaagacttactttgaccttgttttatctgattctgattttgcccttgtttcttatgcagTTTTTCATTGTATTATCGTGCTTGATATCTGTCTCAGTGAACTTCAGCACTTTCCTTGTGATCGGAAAGACTTCTCCTGTCACTTACCAAGTCCTGGGCC
|| || ||| ||||| |||| |   |||||     ||   |||| | |  ||||| ||||| | ||| ||||  |||||||||||||| ||  | || |||||||||||||| |||||||||||||||||||||||||||||||||||||| |||||||| |||||||||||||||||||
gtgagtagtaaaacatctttggtgcacttatcccaac--agtttcaccatattctaatttttctcttatttcgcatgcagTTTTTCATCGTCCTGTCATGCTTGATATCTGTTTCAGTGAACTTCAGCACTTTCCTTGTGATCGGAAAGACATCTCCTGTTACTTACCAAGTCCTGGGCC

upper sequence: LOC_Os05g07670.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G063253_T09 (Zea mays), 3'ss of exon 4
gtaagcagtgaaacaactttcgaagacttactttgaccttgttttatctgattctgattttgcccttgtttcttatgcagTTTTTCATTGTATT--ATCGTGCTTGATATCTGTCTCAGTGAACTTCAGCACTTTCCTTGTGATCGGAAAGACTTC-TCCTGTCACTTACCAAGTCCTGGGCC-------------------
 | | | |  | ||| ||   |   ||||||   | ||| |       | |  |     |||  |||| || |  |   ||||| | |     |   |   ||| || |    |    |  | | | |   || |  |||  || |    |  ||| | ||    |  |       |   ||                    
-tgatcggaaagacatctcctgtt-acttaccaagtcctgggccatcttaaaacatgccttgttcttgcttttggttatgttttgcttcacgatccgtttagCTGGAGAAACATACTTGGAATCCTAATTGCTGTAGTTGGAATGGTCTTGTATTCATACTTCTGCACAGTGGAGACCCAGCAAAAAAATGTTGAAGTCTCC

upper sequence: LOC_Os05g07670.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT2G30460.1 (Arabidopsis thaliana), 3'ss of exon 7
gtaagcagtgaaacaactttcgaagacttactttgacc-ttgttttatctgattctgattttgcccttgtttcttatgcagTTTTTCATTGTATTATCGTGCTTGATATCTGTCTCAGTGAACTTCAGCACTTTCCTTGTGATCGGAAAGACTTCTCCTGTCACTTACCAAGTCCTGGGCC
|| || | |||| |||  |  |  || |    || |   ||| ||   |  |||   |      ||||||||   |||||||| ||||| || || || ||| | |||||||| ||||| ||||||||||| || || || || |||||||| |||||||||||||| || || || || |
gtgag-aatgaagcaatatatgtggaatggtcttcattattgcttctacatatttacaaacacaccttgtttga-atgcagTTCTTCATCGTCTTGTCCTGCCTCATATCTGTTTCAGTAAACTTCAGCACGTTTCTCGTCATTGGAAAGACATCTCCTGTCACTTATCAGGTTCTAGGAC

upper sequence: LOC_Os05g07670.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv13s0067g02970.t01 (Vitis vinifera), 3'ss of exon 7
gtaagcagtgaaacaactttcgaagacttactttgaccttgttttatctgattctgattttgcccttgtttcttatgcagTTTTTCATTGTATTATCGTGCTTGATATCTGTCTCAGTGAACTTCAGCACTTTCCTTGTGATCGGAAAGACTTCTCCTGTCACTTACCAAGTCCTGGGCC
|| |||| | ||| | |     |   |||  ||   | |  |    | |   ||  || ||   || ||   |  ||||| ||||||||||  |||| |||||||| ||||||||||| || || ||||| || |||||||| || ||||| || || ||||| || || |||||||| |
gtgagcatttaaagatccactaaccgcttttttcttcttcatgaattttcggtcccatcttattct-gtgcat--tgcagGTTTTCATTGTTCTATCCTGCTTGATCTCTGTCTCAGTCAATTTTAGCACCTTTCTTGTGATTGGCAAGACATCGCCCGTCACCTATCAGGTCCTGGGGC

upper sequence: LOC_Os05g07670.1 (Oryza sativa), 3'ss of exon 6
lower sequence: EFJ14247 (Selaginella moellendorffii), 3'ss of exon 5
gtaagcagtgaaacaactttcgaagacttactttgaccttgttttatctgattctgattttgcccttgtttcttatgcagTTTTTCATTGTATTATCGTGCTTGATATCTGTCTCAGTGAACTTCAGCACTTTCCTTGTGATCGGAAAGACTTCTCCTGTCACTTACCAAGTCCTGGGCC
                      |  || | ||||      |  |    |||  |   ||||    |  || | | ||||| | |||||  |  | || |||||||| || || || |||||||||||||| |||||||| || || ||||| || || || |||||||||||| | ||||
-------------------gtaagcacatgctttttatccgccta---tgaaacgcctttttttttctttgcctctgcagCTATTCATCATCCTTTCTTGCTTGATTTCCGTTTCTGTGAACTTCAGCACATTCCTTGTTATAGGGAAGACGTCGCCGGTGACTTACCAAGTCTTAGGCC

upper sequence: LOC_Os05g07670.1 (Oryza sativa), 3'ss of exon 6
lower sequence: EFJ20116 (Selaginella moellendorffii), 3'ss of exon 5
gtaagcagtgaaacaactttcgaagacttactttgaccttgttttatctgattctgattttgcccttgtttcttatgcagTTTTTCATTGTATTATCGTGCTTGATATCTGTCTCAGTGAACTTCAGCACTTTCCTTGTGATCGGAAAGACTTCTCCTGTCACTTACCAAGTCCTGGGCC
                      |  || | ||||      |  |    |||  |   ||||    |  || | | | ||| | |||||  |  | || |||||||| || || || |||||||||||||| |||||||| || || ||||| || || || |||||||||||| | ||||
-------------------gtaagcacatgctttttatccgccta---tgaaacgcctttttttttctttgcctttacagCTATTCATCATCCTTTCTTGCTTGATTTCCGTTTCTGTGAACTTCAGCACATTCCTTGTTATAGGGAAGACGTCGCCGGTGACTTACCAAGTCTTAGGCC

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|33805792|gb|CF328775.1|CF328775
EST:     TTTTGACTAACCAAAATGTATTTGCATTCGACTACACATCCCAAGTTGTG                         TTTTTCGTTGTATTATCGTGCTTGATATCTGTCTCAGTGAACTTCAGCACT
genomic: TTTTGACTAACCAAAATGTATTTGCATTCGACTACACATCCCAAGTTGTGgtaagcagtg ... tcttatgcagTTTTTCATTGTATTATCGTGCTTGATATCTGTCTCAGTGAACTTCAGCACT
EST: gi|86494251|gb|CI136884.1|CI136884
EST:     TCCCAAGTTGTG                         TTTTTCATTGTATTATCGTGCTTGATATCTGTCTCAGTGAACTTCAGCACT
genomic: TCCCAAGTTGTGgtaagcagtg ... tcttatgcagTTTTTCATTGTATTATCGTGCTTGATATCTGTCTCAGTGAACTTCAGCACT
EST: gi|218493898|gb|FG949293.1|FG949293
EST:     TTTTGACTAACCAAAATGTATTTGCATTCGACTACACATCCCAAGTTGTG                         TTTTTCATTGTATTATCGTGCTTGATATCTGTCTCAGTGAACTTCAGCACT
genomic: TTTTGACTAACCAAAATGTATTTGCATTCGACTACACATCCCAAGTTGTGgtaagcagtg ... tcttatgcagTTTTTCATTGTATTATCGTGCTTGATATCTGTCTCAGTGAACTTCAGCACT

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: 72 (upstream exon), 75 (downstream exon)
Score: 31

CCCCTATCAATCACTGACCCTCTTCCTTATTGGTCCATTCCTTGATGGATTTTTGACTAACCAAAATGTATTTGCATTCGACTACACATCCCAAGTTGTGgtaagcagtg ... tcttatgcagTTTTTCATTGTATTATCGTGCTTGATATCTGTCTCAGTGAACTTCAGCACTTTCCTTGTGATCGGAAAGACTTCTCCTGTCACTTACCAAGTCCTGGGCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttactttgaccttgttttatctgattctgattttgcccttgtttcttatgcagTTTTTCATTGTATTATCGTGCTTGATATCTGTCTCAGTGAACTTCAGCACTTTCCTTGTGATCGGAAAGACTTCTCCTGTCACTTACCAAGTCCTGGGCC
                                ttttgcccttgtttct  CT-rich tract
             ttgttttat  TA-rich tract