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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTGGAAATTTGGGGAGGAAGGGAACAAATACTTCCGTCATGCTACTGGGCAGATATACGCGATTTCAAAAGACCTCGCGACCTACATTTCAATCAACCAgtatgtttcctatgccatgccatgcaaaatccttatgaccgaaaaaatactaatgtttccaatgatgttttgtcag

Basic information

species Oryza sativa
transcript LOC_Os02g35870.2
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g35870.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G013079_T01 (Zea mays), 5'ss of exon 9
ACTGGAAATTTGGGGAGGAAGGGAACAAATACTTCCGTCATGCTACTGGGCAGATATACGCGATTTCAAAAGACCTCGCGACCTACATTTCAATCAACCAgtatgttt--cctatgc-catgccatgcaaaa---tccttatgaccgaaaaaatactaatgtttccaatgatgttttgtcag
|||||||||||||||||||||| || ||||||||||||||||| || ||||||||||| || ||||| ||||| ||||| || || ||||||||||||||||||||||     |||  |||| ||| || ||   ||  |    |  ||     ||||||| | ||| |||| |||  ||||
ACTGGAAATTTGGGGAGGAAGGAAATAAATACTTCCGTCATGCCACGGGGCAGATATATGCCATTTCGAAAGATCTCGCTACTTATATTTCAATCAACCAgtatgtttaattcatgttcatgacatacagaagtgtctgttcatctaaaggggaactaatgatgccagtgatattt-atcag

upper sequence: LOC_Os02g35870.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G070708_T02 (Zea mays), 5'ss of exon 9
ACTGGAAATTTGGGGAGGAAGGGAACAAATACTTCCGTCATGCTACTGGGCAGATATACGCGATTTCAAAAGACCTCGCGACCTACATTTCAATCAACCAgtatgtttcctatgc---catgccatgcaaaa---------tccttatgaccgaaaaaatactaatgtttccaatgatgttttgtcag
|||||||||||||||||||||| || || ||||||||||||||||| ||||||||||| || ||||| ||||| || ||||| || || |||||||| | ||||||||  |  |    || | ||| |||||         ||| | | |  | |||   ||| ||| | | |  ||| |||| ||||
ACTGGAAATTTGGGGAGGAAGGAAATAAGTACTTCCGTCATGCTACAGGGCAGATATATGCCATTTCGAAAGATCTGGCGACTTATATCTCAATCAATCGgtatgtttaattcgtgttcacgacatacaaaagggtgcctgtccatctaaagggaaactaactgatgctgcaagcgatatttt-tcag

upper sequence: LOC_Os02g35870.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA04G43340.2 (Glycine max), 5'ss of exon 9
ACTGGAAATTTGGGGAGGAAGGGAACAAATACTTCCGTCATGCTACTGGGCAGATATACGCGATTTCAAAAGACCTCGCGACCTACATTTCAATCAACCAgtatgtttcctatgc--catgccatgcaaaatc------cttatgaccgaaaaaatactaatgtttccaatg---atgttttgtcag-------------
  ||||| ||||| || || ||||||||||||||||| ||||| |||||||||||||| || || ||||| || || || || |||||||| |||||||||||||| |   ||    | ||| |  |  ||        ||| ||| |     |  || | ||| |    ||   | |  ||  |||             
TTTGGAAGTTTGGAGAAGAGGGGAACAAATACTTCCGACATGCAACTGGGCAGATATATGCAATCTCAAAGGATCTGGCCACTTACATTTCCATCAACCAgtatgtatatcatttttcgtgcaacacttaactggctatcttctgatctcggcaccacaactgtgtattttgtacagggattaccagatgagcaattgtt

upper sequence: LOC_Os02g35870.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA13G02420.1 (Glycine max), 5'ss of exon 9
ACTGGAAATTTGGGGAGGAAGGGAACAAATACTTCCGTCATGCTACTGGGCAGATATACGCGATTTCAAAAGACCTCGCGACCTACATTTCAATCAACCAgtatg--tttcctatgccatgccatgcaaaa-tccttatgaccgaaaaaatactaatgtttccaatgatgttttgtcag-----------------------
  ||||||||||| || || ||||||||||||||||| ||||| |||||||||||||| || || || || || || || ||||||||||| |||||||||||||  |   || | |||     | |  |  | | ||||   || |   ||  |  |   | |||| ||       |                        
TTTGGAAATTTGGAGAAGAGGGGAACAAATACTTCCGACATGCAACTGGGCAGATATATGCAATCTCTAAGGATCTGGCCACCTACATTTCCATCAACCAgtatggatacgcttttccaattagtacttagcttcctatggttgagag--tatcagaggggctaatgttgaccccatacaactgtagtgcatgatcaagaat

upper sequence: LOC_Os02g35870.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA14G33700.1 (Glycine max), 5'ss of exon 9
ACTGGAAATTTGGGGAGGAAGGGAACAAATACTTCCGTCATGCTACTGGGCAGATATACGCGATTTCAAAAGACCTCGCGACCTACATTTCAATCAACCAgtatgtttcc--tatgccatgccatgcaaaatcct-tatgaccgaaa----aaatactaatgtt-----tccaatgatgttttgtcag------------
  ||||| ||||| || || ||||||||||| ||||| ||||| |||||||||||||| || || || || || || || ||||||||||| || ||||||||||  | |  | | ||||||  | | || || | ||| |  || |    |    ||||| ||     | |||  || ||   | |             
TTTGGAAGTTTGGAGAAGAGGGGAACAAATATTTCCGACATGCAACTGGGCAGATATATGCAATCTCTAAGGATCTAGCCACCTACATTTCCATTAACCAgtatggatacagttttccatgcactactaagtcatctataattgagaccagaggagctaatcttgaccatacaactatattgcatgaatagatttaagta

upper sequence: LOC_Os02g35870.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA06G11330.1 (Glycine max), 5'ss of exon 9
ACTGGAAATTTGGGGAGGAAGGGAACAAATACTTCCGTCATGCTACTGGGCAGATATACGCGATTTCAAAAGACCTCGCGACCTACATTTCAATCAACCAgtatgt-------ttcctatgccatgccatgcaaaat-ccttatgaccgaaaaaatactaatgt---ttccaatgatgttttgtcag-------------
  ||||| ||||| || || ||||||||||||||||| ||||| |||||||||||||| || || ||||| ||  | || || |||||||| |||||| |||| ||       ||    | |  | |    |   ||  ||| ||| |     |  |  | |||   || |    | |  ||  |||             
TTTGGAAGTTTGGAGAAGAGGGGAACAAATACTTCCGACATGCAACTGGGCAGATATATGCAATCTCAAAGGATTTGGCCACTTACATTTCCATCAACAAgtacgtatatcatttttcgtccactacttaactggatatcttctgatctcggtaccataactgtgtatttcgcacagggattaccagattagcaattgtt

upper sequence: LOC_Os02g35870.1 (Oryza sativa), 5'ss of exon 9
lower sequence: AT1G77810.2 (Arabidopsis thaliana), 5'ss of exon 9
ACTGGAAATTTGGGGAGGAAGGGAACAAATACTTCCGTCATGCTACTGGGCAGATATACGCGATTTCAAAAGACCTCGCGACCTACATTTCAATCAACCAgtatgt-ttcctatgccatgccatgcaaaatccttatgaccgaaaaaatact----aatgtttccaatgatgttttgtcag
| ||||||||||| ||||| || ||||||||||| || |||||||| || ||||| || || || || || || || || |  ||||| || ||||||||||| ||  | ||    | |       |||   | |   | | ||    |       || |||| |||   ||| |   |||
ATTGGAAATTTGGAGAGGATGGTAACAAATACTTTCGACATGCTACAGGACAGATCTATGCCATCTCCAAGGATCTTGCTAATTACATATCCATCAACCAgtacgtacttctgcatcctttt-cataaagagccttccatcaaatgtttgtcctaaaaggtttacaactttgtatg--cag

upper sequence: LOC_Os02g35870.1 (Oryza sativa), 5'ss of exon 9
lower sequence: AT1G22015.1 (Arabidopsis thaliana), 5'ss of exon 9
ACTGGAAATTTGGGGAGGAAGGGAACAAATACTTCCGTCATGCTACTGGGCAGATATACGCGATTTCAAAAGACCTCGCGACCTACATTTCAATCAACCAgtatgtttcctatgccatgccatgcaaaatccttatgaccgaaaaaatact--aatgtttccaatgatgttttgtcag----------------------------
  ||||||||||| || ||||| |||||||| ||||| |||||||| || ||||| || || || ||||| || || || || ||||| || | ||||||||| ||  || |    |||   |    | |    |  |   || | ||  |  |        |||||   |    ||                             
TTTGGAAATTTGGAGAAGAAGGTAACAAATATTTCCGACATGCTACGGGACAGATTTATGCCATATCAAAGGATCTTGCCACATACATATCTAACAACCAgtaagtgaccaactttatggtttttggattttcgacaaggtaagatatgttttaccaagggaaatgagtatcaaccaaacataacatttgatgtttgacttcgcag

upper sequence: LOC_Os02g35870.1 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv18s0001g04150.t01 (Vitis vinifera), 5'ss of exon 9
ACTGGAAATTTGGGGAGGAAGGGAACAAATACTTCCGTCATGCTACTGGGCAGATATACGCGATTTCAAAAGACCTCGCGACCTACATTTCAATCAACCAgtatgtttcctatgccatgccatgcaaaatccttatgaccgaaaaaatactaatgtttccaat---gatgttttgtcag----------------------
||||||| ||||| ||||| |||||||| || ||||| ||||| ||||||||||| || || || |||||||| || || || ||||| || ||||||||||| |  |    |    |   ||    |||     ||   |   |  | || |  |  |  ||    | || |||  |                       
ACTGGAAGTTTGGAGAGGAGGGGAACAAGTATTTCCGGCATGCAACTGGGCAGATTTATGCAATCTCAAAAGATCTGGCCACATACATCTCGATCAACCAgtaagaattgagt-tttttttatatggaattagcctgtttggccattttctgagctaccatatcaaaaggtcttgcaattcatcccctgggcatgattttc

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|58666495|gb|CK055181.1|CK055181
EST:     CAGATATACGCGATTTCAAAAGACCTCGCGACCTACATTTCAATCAACCA                         GCCTATCTTACACAAATTTGCGAACGAAGATGTATCACTTGGTTCATGGTT
genomic: CAGATATACGCGATTTCAAAAGACCTCGCGACCTACATTTCAATCAACCAgtatgtttcc ... gttttgtcagGCCTATCTTACACAAATTTGCGAACGAAGATGTATCACTTGGTTCATGGTT
EST: gi|163922994|gb|EG712767.1|EG712767
EST:     CAGATATACGCGATTTCAAAAGACCTCGCGACCTACATTTCAATCAACCA                         GCCTATCTTACACAAATTTGCGAACGAAGATGTATCACTTGGTTCATGGTT
genomic: CAGATATACGCGATTTCAAAAGACCTCGCGACCTACATTTCAATCAACCAgtatgtttcc ... gttttgtcagGCCTATCTTACACAAATTTGCGAACGAAGATGTATCACTTGGTTCATGGTT
EST: gi|29682555|gb|CB678830.1|CB678830
EST:     CAGATATACGCGATTTCAAAAGACCTCGCGACCTACATTTCAATCAACCA                         GCCTATCTTACACAAATTTGCGAACGAAGATGTATCACTTGGTTCATGGTT
genomic: CAGATATACGCGATTTCAAAAGACCTCGCGACCTACATTTCAATCAACCAgtatgtttcc ... gttttgtcagGCCTATCTTACACAAATTTGCGAACGAAGATGTATCACTTGGTTCATGGTT
EST: gi|58666808|gb|CK055494.1|CK055494
EST:     CAGATATACGCGATTTCAAAAGACCTCGCGACCTACATTTCAATCAACCA                         GCCTATCTTACACAAATTTGCGAACGAAGATGTATCACTTGGTTCATGGTT
genomic: CAGATATACGCGATTTCAAAAGACCTCGCGACCTACATTTCAATCAACCAgtatgtttcc ... gttttgtcagGCCTATCTTACACAAATTTGCGAACGAAGATGTATCACTTGGTTCATGGTT

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: 49 (upstream exon), 73 (downstream exon)
Score: 14

ACTGGAAATTTGGGGAGGAAGGGAACAAATACTTCCGTCATGCTACTGGGCAGATATACGCGATTTCAAAAGACCTCGCGACCTACATTTCAATCAACCAgtatgtttcc ... gttttgtcagGCCTATCTTACACAAATTTGCGAACGAAGATGTATCACTTGGTTCATGGTTTATTGGTTTAGAAGTGAATCATATCGATGAAAGAAACATGTGCTGCGGG




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