RetrogeneDB ID: retro_cfam_162

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 24:815860..816889(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000005159
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: SURF6
• Ensembl ID: ENSCAFG00000019758
• Aliases: None
• Description: None

Sequence

>retro_cfam_162
CTGTCTTCGCTGCTCGCCAAGGACGCCTACCTGCAGGGCCTGGCCAGGAAGACCTGCTCCCAGCCCAGCCTGGAGCCGCA
GAAGCGCGCGTCCGCCAGTAAAGCTCGAAGCTCTGAAGCTGCTGGGCCTCCCAAAAAGAAGAGGCAGACGGCGCAGAAGA
AATCCCAGAGGCGGGCGGAGAAGGCTGTGGAGCCTAAGTCCCAGGCCCTGGAGAAGTCTCCCCCAGCTTCCAGGGCTGGA
AAGCCAGCAGTAGCCGAGGAGGAAGAGGCCTTCGGCTCCACGGGATCCCCAGCAGGTGCCCTGGTTACAGAGCCTGACTC
TCTCTTTGCCTTGGAGGTTGTGCGACAGCGGCTACATGAAGAAGTTCAGGGGGCCCGGCATCAGGGCCGCACCGCCGAGC
TGTCTCCCGCCGCCTTGGAGAAGAGACGGCGGAGGAAACAGGAGCGGGACCGGAAAAAGAGAAAGCGAAAGGAGCTGAGG
GCAAAGGAGAAGGTGGCACGGGCTGCGGAGGTTGCTGAGCCGCCCCATGAGCCCCACGAGCCACCCCCTGAGGAGGCACA
GTCAGGGCTGCTCTTCAACAAGGTGGAGGGGACTGAGGAGCAAGCCAGCAGCAAGGCCCAGCGCCGGAAGGAGAAGAGGC
AGAAGCTGAAGGGGAACCTGACGCCGCTGACGGGCAAGAACTACCGGCGGCCGCTGCAGCGCCTTCAGGCACGGCAGGCT
CGGCTGGACGAGCTGCGGGACCAGGACGAGGGGAAGGCCCGGGAGCTCGAGAGTAAGATGAAGTGGACCAACCTGCTGTA
CAAGGCCCAGGGCGTGCGCATCCGAGACAATGAGCACCTGCTGCAGGAGGCCCTGAAGCGCAAGGAGAAGCGCACCGCCC
ACGTGGTCGAGAGGATGCAGCGGCGGCAGGATAAGCGGCGGCAGAACCTGCGCAAGAAAAAGGCGGCCCGGGCAGAGCAG
CGCCTGGAGAAGGCCCACAGGAAGGGCCGCATCCTTCCCCAGGACCTGGAGCGGGCTGGCCTGGCGTGA

Alignment

ORF - retro_cfam_162 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.06 %
• Parental protein coverage: 91.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSSLLAKDAYLQGLARKICSQPSLEPQKRTSASKARSSEAAGPPKKKRKTAQKKSQRREEKAVEPKSQAL
          .SSLLAKDAYLQGLARK.CSQPSLEPQKR.SASKARSSEAAGPPKKKR.TAQKKSQRR.EKAVEPKSQAL
Retrocopy LSSLLAKDAYLQGLARKTCSQPSLEPQKRASASKARSSEAAGPPKKKRQTAQKKSQRRAEKAVEPKSQAL

Parental  EKSPPASRAGKPAVAKEEEAFSSTGSPADALVTEPDSLFALEVVRQRLHEKIQEARHQGRTTELSPAALE
          EKSPPASRAGKPAVA.EEEAF.STGSPA.ALVTEPDSLFALEVVRQRLHE..Q.ARHQGRT.ELSPAALE
Retrocopy EKSPPASRAGKPAVAEEEEAFGSTGSPAGALVTEPDSLFALEVVRQRLHEEVQGARHQGRTAELSPAALE

Parental  KRRRRKQERDRKKRKRKELRAKEKVAQAAEVAELPHEPHEPPPEEAQSGLLFNKVEVTEEQASSKAQRRK
          KRRRRKQERDRKKRKRKELRAKEKVA.AAEVAE.PHEPHEPPPEEAQSGLLFNKVE.TEEQASSKAQRRK
Retrocopy KRRRRKQERDRKKRKRKELRAKEKVARAAEVAEPPHEPHEPPPEEAQSGLLFNKVEGTEEQASSKAQRRK

Parental  EKRQKLKGNLTPLTGKNYRQLLERLQARQAQLDELRDQDEGKARELESKMKWTNLLYKAEGVRIRDNEHL
          EKRQKLKGNLTPLTGKNYR..L.RLQARQA.LDELRDQDEGKARELESKMKWTNLLYKA.GVRIRDNEHL
Retrocopy EKRQKLKGNLTPLTGKNYRRPLQRLQARQARLDELRDQDEGKARELESKMKWTNLLYKAQGVRIRDNEHL

Parental  LQEALKRKEKRRA----QRKRKWEKRTAHVVEKMQRRQDKRRQNLRKK
          LQEALKRKEKR.A.......R...KR......K...R...R......K
Retrocopy LQEALKRKEKRTAHVVERMQRRQDKRRQNLRKKKAARAEQRLEKAHRK

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
SRP012049_cerebellum	0.00 RPM	17.56 RPM
SRP017611_brain	0.00 RPM	11.43 RPM
SRP017611_kidney	0.00 RPM	5.94 RPM
SRP017611_liver	0.15 RPM	5.44 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_162 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_162 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_162 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000019758	1 retrocopy	retro_cfam_162 ,
Otolemur garnettii	ENSOGAG00000027199	1 retrocopy	retro_ogar_3000,
Rattus norvegicus	ENSRNOG00000005031	1 retrocopy	retro_rnor_1538,