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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcaaattgtttttattcttcatacttttaattttatttcttctgaatctttaaatccatcgattgattgcttacatagaaatcgatttgaattgccagGTATGTGGTTGAAAGAATGGATGGTGATCTGTGGGATAAAGTTCTACAGCCTGAAAATGAATATAGAAGGCAACTCATTGACCAAGTGGTTTCTACGGCT

Basic information

species Oryza sativa
transcript LOC_Os11g01380.1
intron # 23
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 23
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 21
gtatgcaaattgtttttattcttcatacttttaa-ttttatttcttctgaatctttaaatcc--atcgattgattgctta--catagaa-atcgatttgaattgccagGTATGTGGTTGAAAGAATGGATGGTGATCTGTGGGATAAAGTTCTACAGCCTGAAAATGAATATAGAAGGCAACTCATTGACCAAGTGGTTTCTACGGCT
||||  || || ||||| ||| |  ||||  |   |||| ||| |||     || || ||    | | || | | ||||   |||   | ||  |||| || |  ||| ||||||||||| |||||||||||||||||||||||||||||||| |||||||| |||||||||||||||||||||||||||||||||||||| || || 
gtatataa-ttatttttgttcctgttactgatgccttttgtttgttccagtcctctatatattgagcaatggctcgcttggtcatgtcacataaatttaaaatttcagATATGTGGTTGAGAGAATGGATGGTGATCTGTGGGATAAAGTTCTTCAGCCTGAGAATGAATATAGAAGGCAACTCATTGACCAAGTGGTTTCGACCGCA

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 23
lower sequence: GRMZM2G111355_T01 (Zea mays), 3'ss of exon 3
gtatgcaaattgtttttattcttcatacttttaattttatttcttctgaatctttaaatccatcgattgattgcttacatag-------aaatcgatttgaattgccagGTATGTGGTTGAAAGAATGGATGGTGATCTGTGGGATAAAGTTCTACAGCCTGAAAATGAATATAGAAGGCAACTCATTGACCAAGTGGTTTCTACGGCT
||||| || |  |||||||| ||   |||| | |      |  |||   || |  | ||| || |  |||   |||||||           ||  |||| || || ||||||||||||||| ||||||||||||||||| |||||||||||||| ||||| || |||||||||||||||||||||||||||||||||||||| || || 
gtatgtaa-taatttttattgttgtgacttgtgacacc--tgtttcaagatgtccacatcaattgtctgacgacttacatgttcatattgcatttatttaaaatgacagGTATGTGGTTGAGAGAATGGATGGTGATCTATGGGATAAAGTTCTTCAGCCCGAGAATGAATATAGAAGGCAACTCATTGACCAAGTGGTTTCGACTGCA

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 23
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 23
---gtatgcaaattgtttttattcttcatacttttaattttatttcttctgaatctttaaatccatcgattgattgcttacatagaaatcgatttgaattgccagGTATGTGGTTGAAAGAATGGATGGTGATCTGTGGGATAAAGTTCTACAGCCTGAAAATGAATATAGAAGGCAACTCATTGACCAAGTGGTTTCTACGGCT
     |  |      |||  |       || || |  |  |   ||  |  ||||  |   | | |  ||| |    | |||||   ||  ||||  || | ||| ||||| ||||| ||||||||||||||| |||||| |||||||||  | ||||| |||||||||||||||||||| ||||| || || || ||||| |||
agtacactccgtcactttagaggagctctatttgtggtccttaatccaccaaatcaatt--ttctttaattcaacattcacatacttat--attttgat-gacagATATGTTGTTGAGAGAATGGATGGTGATTTGTGGGCTAAAGTTCTTGATCCTGATAATGAATATAGAAGGCAACTTATTGATCAGGTTGTATCTACTGCT

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 23
lower sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 23
--gtatgcaaattgttttt-attcttcatacttttaattttatttcttctgaatctttaaatccatcgattgattgcttacatagaaatcgatttgaattgccagGTATGTGGTTGAAAGAATGGATGGTGATCTGTGGGATAAAGTTCTACAGCCTGAAAATGAATATAGAAGGCAACTCATTGACCAAGTGGTTTCTACGGCT
  | |      |   |||  |      ||| || | ||  |   |   |  ||||  |   | | |  ||  | || | ||||     |    |||   || ||| ||||| ||||| ||||||||||||||| |||||| |||||||||  | ||||| |||||||||||||||||||| ||||| || || || ||||| |||
ctgcacctccgtcactttagaggagctatatttgtgatccttaatacaccaaatcaatt--ttctttaatacaatgttcacatg---cttatattgtgatgacagATATGTTGTTGAGAGAATGGATGGTGATTTGTGGGCTAAAGTTCTTGATCCTGATAATGAATATAGAAGGCAACTTATTGATCAGGTTGTATCTACTGCT

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 23
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 22
gtatgcaaattgtttttattcttcatacttttaattttatttcttctgaatctttaaatccatcgattgattgcttacatagaaatcgatttgaattgccagGTATGTGGTTGAAAGAATGGATGGTGATCTGTGGGATAAAGTTCTACAGCCTGAAAATGAATATAGAAGGCAACTCATTGACCAAGTGGTTTCTACGGCT
              ||| |  |  ||| || || |||   ||  ||| | |  |||  ||| | |||| | |||||||||    ||  ||| | ||| | || ||||| ||||| || |||||||||||||| ||||| ||||||||  | ||||| ||||  || ||||||||||| ||||| || || || ||||| |||
-------------gtttgtggtgtatatttatatttt---tttctctaagtaatta--tccttggattcaatgcttacatgcttat--attgggattac-agATATGTTGTTGAGAGGATGGATGGTGATCTTTGGGAGAAAGTTCTTAACCCTGATAATGCCTACAGAAGGCAACTTATTGATCAGGTTGTATCTACAGCT

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 23
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 23
gtatgcaaattgtttttattcttcatacttttaattttatttcttctgaatctttaaatccatcgattgattgcttacatagaaatcgatttgaattgccagGTATGTGGTTGAAAGAATGGATGGTGATCTGTGGGATAAAGTTCTACAGCCTGAAAATGAATATAGAAGGCAACTCATTGACCAAGTGGTTTCTACGGCT
          | ||||     | | |||    | | || || ||     |    | | |   | | |||     | | | | || |   ||| |||||  |||||||| || || || ||||||||||||||||||||||| |||||  |     | ||||| |||||||| || || ||||||||||| || ||||| |||
---------gtattttatcattacttacgaaaattcttgttactctcacaatggtgactttgtagtttg----ttaatacacaagt---tttcaattgt-agGTATGTAGTGGAGAGGATGGATGGTGATCTGTGGGATAAGGTTCTCGATGAAAACAATGATTATAGAAGACAGCTTATTGACCAAGTTGTGTCTACTGCT

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|58652712|gb|CK041392.1|CK041392
EST:     GAACTTATTAATGTCACCAATAAAAACTCACTGTTCAAGCTGCAAGCTAC                         GTATGTGGTTGAAAGAATGGATGGTGATCTGTGGGATAAAGTTCTACAGCC
genomic: GAACTTATTAATGTCACCAATAAAAACTCACTGTTCAAGCTGCAAGCTAGgtatgcaaat ... gaattgccagGTATGTGGTTGAAAGAATGGATGGTGATCTGTGGGATAAAGTTCTACAGCC
EST: gi|29627716|gb|CB632727.1|CB632727
EST:     GAACTTATTAATGTCACCAATAAAAACTCACTGTTCAAGCTGCAAGCTAG                         GTATGTGGTTGAAAGAATGGATGGTGATCTGTGGGATAAAGTTCTACAGCC
genomic: GAACTTATTAATGTCACCAATAAAAACTCACTGTTCAAGCTGCAAGCTAGgtatgcaaat ... gaattgccagGTATGTGGTTGAAAGAATGGATGGTGATCTGTGGGATAAAGTTCTACAGCC

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: 75 (upstream exon), 74 (downstream exon)
Score: 144

GGGATCCTACCCTTGCTGTTGTTGCTTACAGACGTGGACAGTGTGATGATGAACTTATTAATGTCACCAATAAAAACTCACTGTTCAAGCTGCAAGCTAGgtatgcaaat ... gaattgccagGTATGTGGTTGAAAGAATGGATGGTGATCTGTGGGATAAAGTTCTACAGCCTGAAAATGAATATAGAAGGCAACTCATTGACCAAGTGGTTTCTACGGCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaatctttaaatccatcgattgattgcttacatagaaatcgatttgaattgccagGTATGTGGTTGAAAGAATGGATGGTGATCTGTGGGATAAAGTTCTACAGCCTGAAAATGAATATAGAAGGCAACTCATTGACCAAGTGGTTTCTACGGCT
                        tgcttac  putative branch site (score: 144)
                                         atttgaatt  TA-rich tract