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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgatgttgccaatgatcaatatcaatgtataccatattcatttgtattgttcgtgcaatatattttattatgtttcatttaatgtgtttgctttatgcagTATATCTTCATCAGACCTTGTTTCAAAATGGATGGGAGAGAGTGAAAAACTTGTTGCAAACCTTTTCCAAATGGCTCGAGAAAACGCTCCTTCCATTATC

Basic information

species Oryza sativa
transcript LOC_Os01g04814.4
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g04814.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G088834_T01 (Zea mays), 3'ss of exon 2
tgatgttgccaatgatcaat--atcaatgtataccatattcat-ttgtattgttcgtgcaatatattttat-tatgtttcatttaatgtgtttgcttta-tgcagTATATCTTCATCAGACCTTGTTTCAAAATGGATGGGAGAGAGTGAAAAACTTGTTGCAAACCTTTTCCAAATGGCTCGAGAAAACGCTCCTTCCATTATC
     || |   ||||   |  ||  ||||   | ||| | || |  ||   || ||    |||    ||| | | |   |||| |     |||||||| |||||||||||||| ||||| || |||||||| |||||||| || ||||| ||| | |||||||| || |||||||||||||| ||||| || ||||||||||||
-----tttcacttgattggtcaatggatgttagcaatactaatatcctaccatttgttttctatgccgtatctttatgatatttcacactgttgctttactgcagTATATCTTCTTCAGATCTGGTTTCAAAGTGGATGGGTGAAAGTGAGAAATTAGTTGCAAATCTGTTCCAAATGGCTCGGGAAAATGCCCCTTCCATTATC

upper sequence: LOC_Os01g04814.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G126860_T01 (Zea mays), 3'ss of exon 2
tgatgttgccaatgatcaatatcaatgtataccatattcatttgtattgttcgtgcaa-tatattttattatgtttcatttaatgtgtttgctttat-gcagTATATCTTCATCAGACCTTGTTTCAAAATGGATGGGAGAGAGTGAAAAACTTGTTGCAAACCTTTTCCAAATGGCTCGAGAAAACGCTCCTTCCATTATC
  || |  |     ||   |     |  ||||   |||  |   | |        | | |||| ||| ||   |   |||| |     ||||||||| ||||||||||||| ||||| || |||||||| |||||||| || || || ||| | || ||||| ||||||||||||||||| ||||| || ||||||||||||
--atctaacttgcaattttttagtttacatacttgattggtcaatgtaagataccctactatactttttttcatgatatttcacaatgttgctttattgcagTATATCTTCTTCAGATCTGGTTTCAAAGTGGATGGGTGAAAGCGAGAAATTAGTCGCAAATCTTTTCCAAATGGCTCGTGAAAATGCCCCTTCCATTATC

upper sequence: LOC_Os01g04814.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA11G19120.1 (Glycine max), 3'ss of exon 2
---tgatgttgccaatgatcaatatcaatgtataccatattcatttgtattgtt-cgtgcaatatattttattatgtttcatttaatgtgtttgctttatgcagTATATCTTCATCAGACCTTGTTTCAAAATGGATGGGAGAGAGTGAAAAACTTGTTGCAAACCTTTTCCAAATGGCTCGAGAAAACGCTCCTTCCATTATC
   |||   ||    || |  | || ||   |     |     |  ||  | |   | ||| | | ||  |  |||||| |  |  ||  ||  ||| |  |||| | |||||||||||||| |||||||| ||||||||||| |||||||| || ||  |||| ||||||||||||||||| ||||  || ||||| || || 
ccttgacagtgattttgtttgaaataaa-aaaggttgtgaatgtgagtgctttggtgggcattttcttgcagcatgttttaacttttgaatt--cttcac-cagTGTTTCTTCATCAGACCTGGTTTCAAAGTGGATGGGAGAAAGTGAAAAGCTGGTCTCAAATCTTTTCCAAATGGCTCGCGAAAGTGCACCTTCTATAATA

upper sequence: LOC_Os01g04814.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA12G09300.1 (Glycine max), 3'ss of exon 2
------tgatgttgccaatgatcaatatcaatgtataccatattcatttgtattgttcgtgcaatatattttattatgtttcatttaatgtgtttgctttatgcagTATATCTTCATCAGACCTTGTTTCAAAATGGATGGGAGAGAGTGAAAAACTTGTTGCAAACCTTTTCCAAATGGCTCGAGAAAACGCTCCTTCCATTATC
      |||| |||    |||  ||||     | | |   ||     ||   ||    | ||| | | ||     |||||| |  |  |   ||  ||| |  |||| | ||||| |||||||| |||||||| ||||||||||| |||||||| || ||  |||| |||||||||||||| || ||||  || ||||| || || 
tgtcagtgattttgtt--tgaaaaataaggtcgcaaat-gtaagtgcttaggttaggtgggcatttttttgctacatgttttaactttttaatt--cttcac-cagTGTTTCTTCGTCAGACCTGGTTTCAAAGTGGATGGGAGAAAGTGAAAAGCTGGTCTCAAATCTTTTCCAAATGGCACGCGAAAGTGCACCTTCTATCATA

upper sequence: LOC_Os01g04814.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA13G39410.1 (Glycine max), 3'ss of exon 2
--tgatgttgccaatgatcaatatcaatgtataccatattcatttgtattgttcgtgcaatatattttattatgtttcatttaatgt-gtttgctttatgcagTATATCTTCATCAGACCTTGTTTCAAAATGGATGGGAGAGAGTGAAAAACTTGTTGCAAACCTTTTCCAAATGGCTCGAGAAAACGCTCCTTCCATTATC
  | |  |     |   |||   || ||  ||   ||     |  ||    |  |||  | || || |   | |  |  || | | | |  | ||| || |||| | ||||||||||||||||||||||| |||||||| || |||||||| || ||| ||||||||||| |||||||||||||||  || ||||| || || 
ccttaaatcaggtaaattcatattccataaatgttatgaatgtaggt-ccataagtg-gacatgttcttgcaagcatttttaacttttgaattcttcat-cagTGTTTCTTCATCAGACCTTGTTTCAAAGTGGATGGGTGAAAGTGAAAAGCTGGTTTCAAACCTTTTCGAAATGGCTCGAGAAAGTGCCCCTTCTATCATA

upper sequence: LOC_Os01g04814.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA12G30910.1 (Glycine max), 3'ss of exon 2
tgatgttgccaatgatcaatatcaatgtataccat-attcatttgtattgttcgtgcaatatattttattatgtttcatttaatgt-gtttgctttatgcagTATATCTTCATCAGACCTTGTTTCAAAATGGATGGGAGAGAGTGAAAAACTTGTTGCAAACCTTTTCCAAATGGCTCGAGAAAACGCTCCTTCCATTATC
   || |  | || |  ||      | | ||   | ||  || |   |   |      | || || |   | |  |  || | | | |  | ||| || |||| | ||||||||||||||||||||||| |||||||| || |||||||| || ||| ||||||||||| |||||||||||||||  || ||||| || || 
-cttgatatctattaaaaaaggtcttttgtattgttatgaatgtaggtccataagtggacatgttcttgcaagcatttttaacttttgaattcttcat-cagTGTTTCTTCATCAGACCTTGTTTCAAAGTGGATGGGTGAAAGTGAAAAGCTGGTTTCAAACCTTTTCGAAATGGCTCGAGAAAGTGCCCCTTCTATCATA

upper sequence: LOC_Os01g04814.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv13s0106g00490.t01 (Vitis vinifera), 3'ss of exon 2
tgatgttgccaatgatcaatatcaatgtataccatattcatttgtattgttcg-tgcaatatattttattatgtttcattta--atgtgtttgctttatgcagTATATCTTCATCAGACCTTGTTTCAAAATGGATGGGAGAGAGTGAAAAACTTGTTGCAAACCTTTTCCAAATGGCTCGAGAAAACGCTCCTTCCATTATC
   |     | |         |   |  ||| ||||   |   || |  || | |  | |  |   ||  | ||  ||  |   |  | ||  ||||   |||| | |||||||| || || ||||||||||||||||| || |||||||| || ||  |||| || || ||||||||||| ||||  ||||||||||| || 
---tacaaacgaaagaagggttggcttaatatcatagatacaggtttattttgatagacttgagcctacaaagtcacaaatgccaaatattgtctttccacagTGTGTCTTCATCTGATCTAGTTTCAAAATGGATGGGTGAAAGTGAAAAGCTAGTCTCAAATCTGTTTCAAATGGCTCGTGAAAGTGCTCCTTCCATCATT

upper sequence: LOC_Os01g04814.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv06s0080g00160.t01 (Vitis vinifera), 3'ss of exon 2
-----tgatgttgccaatgatcaatatcaatgtataccatattcatttgtatt-gttcgtgcaatatattttattatgtttcatttaatgtgtttgctttatgcagTATATCTTCATCAGACCTTGTTTCAAAATGGATGGGAGAGAGTGAAAAACTTGTTGCAAACCTTTTCCAAATGGCTCGAGAAAACGCTCCTTCCATTATC
     || |  ||    || | |   |   | | | |    || || |  ||  | |   || | |||  ||   | ||  ||  |  |||       || |||||| | ||||| |||||||| |||||||| |||||||| || ||||||||  | ||| |||| ||||| ||||||||||| || |  ||||||||||| |||
aagtctgtttctgtttctggttatcgtatttttctcctccttttatgttcatgagcttaggcca-ataagttggcaagtgccaactgctgt-----tcttttgcagTGTCTCTTCTTCAGACCTGGTTTCAAAGTGGATGGGTGAAAGTGAAAAGTTAGTTTCAAATCTTTTTCAAATGGCTCGGGAGAGTGCTCCTTCCATCATC

upper sequence: LOC_Os01g04814.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S200_72V6.1 (Physcomitrella patens), 3'ss of exon 2
--------------------------------------------------------------------------------------------tgatgttgccaatgatc-aatatcaatgtataccatattcatttgtattgttcgtgcaatatattttatta-tgtttcatttaatgtgtttgctttat--gcagTATATCTTCATCAGACCTTGTTTCAAAATGGATGGGAGAGAGTGAAAAACTTGTTGCAAACCTTTTCCAAATGGCTCGAGAAAACGCTCCTTCCATTATC
                                                                                            | |  |    ||| |||  | |  | ||  ||  |   || |      | |  |     | |   |  |   ||  | | | | | | |   |||| |  ||||||| || || || ||| | || ||||| |||||||||||||| || |||||||||||||| || || |||||||| |  |||   ||||| |||||||| 
gtaactggagaagcatatatgcaaacaacaatgattttgttggatgcattttctttttgttttgttgcaataatcactattccagacttgggtcaaatgaagaataatctgagaagagtgggtaataaggtcttccaagct-tcaggatgttgtgaatggtggctgcgtgactgattttttaaactttctctgcagTATTTCCTCTTCTGACTTGGTGTCAAAGTGGATGGGAGAGAGCGAGAAACTTGTTGCAAATCTGTTTCAAATGGCCCATGAAGCTGCTCCATCCATTATT

upper sequence: LOC_Os01g04814.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S76_197V6.1 (Physcomitrella patens), 3'ss of exon 2
-------------------------------------------tgatgttgcc--aatgatcaatat--caatgtataccatattcatttgtattgttcgtgcaatatatttta--ttatgtttc----atttaatgtgtttgctttatgcagTATATCTTCATCAGACCTTGTTTCAAAATGGATGGGAGAGAGTGAAAAACTTGTTGCAAACCTTTTCCAAATGGCTCGAGAAAACGCTCCTTCCATTATC
                                             |  ||| |  |||||  |||    |        | | |        | ||   | |  | |||| ||    |  || |||    | | | | |   |    | |||||||| || || |||||| | || ||||| ||||||||||||||||| || ||||||||||| || || |||||||| || |||   ||||| ||||| |||
gtaactgtcgaagcataatttggacacgatcatcttgtattaccaactttggctaaatgaagaattctccgggacgagcgagaaatgaggttgttaaacctttagtatacttggactggtggttctgggactgattattactttcctctgcagTATTTCCTCTTCAGACTTGGTGTCAAAGTGGATGGGAGAGAGTGAGAAGCTTGTTGCAAATCTGTTTCAAATGGCCCGTGAAGCTGCTCCATCCATCATC

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|300215967|gb|HO088593.1|HO088593
EST:     TCTTATTTGGCTAAAGCTGTTGCAACTGAGGCTGATTCTACATTTTTCAG                         TATATCTTCATCAGACCTTGTTTCAAAATGGATGGGAGAGAGTGAAAAACT
genomic: TCTTATTTGGCTAAAGCTGTTGCAACTGAGGCTGATTCTACATTTTTCAGgtagttatac ... ctttatgcagTATATCTTCATCAGACCTTGTTTCAAAATGGATGGGAGAGAGTGAAAAACT
EST: gi|33381146|gb|CF196489.1|CF196489
EST:     TCTTATTTGGCTAAAGCTGTTGCAACTGAGGCTGATTCTACATTTTTCAG                         TATATCTTCATCAGACCTTGTTTCAAAATGGATGGGAGAGAGTGAAAAACT
genomic: TCTTATTTGGCTAAAGCTGTTGCAACTGAGGCTGATTCTACATTTTTCAGgtagttatac ... ctttatgcagTATATCTTCATCAGACCTTGTTTCAAAATGGATGGGAGAGAGTGAAAAACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgttcgtgcaatatattttattatgtttcatttaatgtgtttgctttatgcagTATATCTTCATCAGACCTTGTTTCAAAATGGATGGGAGAGAGTGAAAAACTTGTTGCAAACCTTTTCCAAATGGCTCGAGAAAACGCTCCTTCCATTATC
                               atttaat  putative branch site (score: 4)
                                         tttgcttt  putative PPT
           aatatattttattatg  TA-rich tract