RetrogeneDB ID: retro_rnor_679

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 10:31601761..31602681(+)
• Located in intron of: ENSRNOG00000021345

Retrocopy information

• Ensembl ID: ENSRNOG00000021333
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Setd8
• Ensembl ID: ENSRNOG00000001062
• Aliases: Setd8, Pr-set7, RGD1305893
• Description: histone-lysine N-methyltransferase SETD8 [Source:RefSeq peptide;Acc:NP_001233594]

Sequence

>retro_rnor_679
AACGTGTTTGCTGGGCAGTCAAAGATCTATGCCTACAGGAGTCCGAACAAATGCTCTGGAATGCGCTCTCCACTGCAGGA
AGAGAACTCGGTCGCACAACATGAGGTCAAATGCCTGGGGAAACCATTGGCCGGAATCTACAGGAAGCGAGAAGAGAAAA
GGAACGCTGGGAATGTTATCCGAAGCGCTGTGAAGTCAGAAGAAGGAAGAGCAAAGATACCAGGAGAGGTCCCCTGGCGC
CTTTTCCAAACCAAAAATCTGAAGCAACAGAACCTCCAAAAACTCCACCCCCGTCATGTGATTCTACCAGTGTAGCAGTT
GCTAAGCAAGCCCTGAAAAAGCCCCTCAAGGGCAAGCAGGCCCCTCGGGAGAAGTCTCAAGGGAAGACACAGCAGAATAG
AAAACTCACAGATTTCTACCCCGTGCGAAGGAGCTCCAGGAAGAGCAAAGCTGAGCTGCGGTCTGAAGAAAGGAAGAAGA
CAGATGAGCTAATTGAGAGCGGGAAGGAAGAAGGCATCAAGATTGACCTAATCGATGGCAAAGGCAGGGGTGTGATTGCT
ACCAAGCGATTCTCCCGGGGAGACTTTGTGGTAGAATACCATGGAGACCTCATTGAAATCACCGATGCCAGGAAGCGGGA
GGCTCTGTACGCACAGGACCCCTCCACGGGCTGCTACATGTACTATTTTCAATATCTGAGCAAAACCTACTGCGTGGATG
CCACTCAAGAAACGAACCTCCTGGGGAGACTGATCAATCACAGTAAGTGTGGGAATTGCCAGACCAAACTGCATGACATC
GACGGTGTGCCTCACCTCATCCTCATAGCCTCTGGAGACATCGCGGCAGGGGAGGAGCTCCTGTACGATTATGGAGACTG
GAGCAAGGCCTCCATCGAAGCCTACCCTTGGCTGAAGCAC

Alignment

ORF - retro_rnor_679 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.45 %
• Parental protein coverage: 95.34 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NVFAGQSKIYAYMSPNKCSGMRSPLQEENSVAHHEVKCPGKPLAGIYRKREEKRNAGNVIRSAVKSEE-Q
          NVFAGQSKIYAY.SPNKCSGMRSPLQEENSVA.HEVKC.GKPLAGIYRKREEKRNAGNVIRSAVKSEE..
Retrocopy NVFAGQSKIYAYRSPNKCSGMRSPLQEENSVAQHEVKCLGKPLAGIYRKREEKRNAGNVIRSAVKSEE<R

Parental  KSKDTRRGPLAPFPNQKPEATEPPKTPPPSCDSTSVAVAKQALKKPLKGKQAPRKKSQGKTQQNRKLTDF
          KSKDTRRGPLAPFPNQK.EATEPPKTPPPSCDSTSVAVAKQALKKPLKGKQAPR.KSQGKTQQNRKLTDF
Retrocopy KSKDTRRGPLAPFPNQKSEATEPPKTPPPSCDSTSVAVAKQALKKPLKGKQAPREKSQGKTQQNRKLTDF

Parental  YPVRRSSRKSKAELQSEERKKIDELIESGKEEGMKIDLIDGKGRGVIATKRFSRGDFVVEYHGDLIEITD
          YPVRRSSRKSKAEL.SEERKK.DELIESGKEEG.KIDLIDGKGRGVIATKRFSRGDFVVEYHGDLIEITD
Retrocopy YPVRRSSRKSKAELRSEERKKTDELIESGKEEGIKIDLIDGKGRGVIATKRFSRGDFVVEYHGDLIEITD

Parental  AKKREALYAQDPSTGCYMYYFQYLSKTYCVDATQETNRLGRLINHSKCGNCQTKLHDIDGVPHLILIASR
          A.KREALYAQDPSTGCYMYYFQYLSKTYCVDATQETN.LGRLINHSKCGNCQTKLHDIDGVPHLILIAS.
Retrocopy ARKREALYAQDPSTGCYMYYFQYLSKTYCVDATQETNLLGRLINHSKCGNCQTKLHDIDGVPHLILIASG

Parental  DIAAGEELLYDYGDRSKASIEAYPWLKH
          DIAAGEELLYDYGD.SKASIEAYPWLKH
Retrocopy DIAAGEELLYDYGDWSKASIEAYPWLKH

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.07 RPM	11.43 RPM
SRP017611_kidney	0.07 RPM	16.54 RPM
SRP017611_liver	0.40 RPM	4.10 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_679 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_679 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_679 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000010371	1 retrocopy	retro_dnov_258,
Homo sapiens	ENSG00000183955	2 retrocopies	retro_hsap_2294, retro_hsap_4320,
Macaca mulatta	ENSMMUG00000013514	1 retrocopy	retro_mmul_1579,
Mus musculus	ENSMUSG00000049327	2 retrocopies	retro_mmus_1459, retro_mmus_3478,
Otolemur garnettii	ENSOGAG00000031093	1 retrocopy	retro_ogar_1217,
Pongo abelii	ENSPPYG00000005085	2 retrocopies	retro_pabe_1347, retro_pabe_1381,
Pan troglodytes	ENSPTRG00000005598	1 retrocopy	retro_ptro_1622,
Rattus norvegicus	ENSRNOG00000001062	4 retrocopies	retro_rnor_1551, retro_rnor_2837, retro_rnor_38, retro_rnor_679 ,
Sarcophilus harrisii	ENSSHAG00000015376	2 retrocopies	retro_shar_110, retro_shar_115,
Tursiops truncatus	ENSTTRG00000015884	1 retrocopy	retro_ttru_1301,