RetrogeneDB ID: retro_cfam_598

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 14:27742809..27743364(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: MRPS10
• Ensembl ID: ENSCAFG00000001638
• Aliases: None
• Description: mitochondrial ribosomal protein S10 [Source:HGNC Symbol;Acc:14502]

Sequence

>retro_cfam_598
GGTTCAAGGAATTTTTCTATAAATAGTTCTAAGAGCAGTACAGCCAGAAATGGTGGCTTTCTCCTCAGTACCAGCATGAA
ATGGGTACAGTTTTGAAGCCTACATGTTGATATTCCCAAGGATTTGACTAAGCCTACGATAACCATTTCTGATGAACCAG
ATACATGATATAAGCGCCTGTCAGTTTTAGTAAAAGGCCATGATAAGGCTGTATTGGACAGTTATGAATATTTTGCCGTG
CTTGCTGCAAAAGAACTTGGTATCTCTAGTAAAGTACACGAACCTCCAAGGAAAATAGAACGATTCACTCTTCTCAAATC
AGTGCATATTTTCAAGAAGCACAGAGTTCAGTATGAAATGAGAACACTTTACAGATGTTTAGAGTTAGAACATCTAACTG
GAAGTACAGCAGATGTCTATTTGGAAGATATTCATCGAAACTTACCTGAAGGAGTTGCCATGGAAGTGACAAAGACAAAA
TTAGAACGGTTACCAGAACACATCAAGGAGCCAATCTGGGAAATGGTACCAGAAGAAAAAGCAGAAGGCAAGTCC

Alignment

ORF - retro_cfam_598 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.22 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GSRNFSINSSKSSTARNGGFLLSTSMKWVQFSSLHVDIPKDLTKPTITISDEPDTLYKRLSVLVKGHDKA
          GSRNFSINSSKSSTARNGGFLLSTSMKWVQF.SLHVDIPKDLTKPTITISDEPDT.YKRLSVLVKGHDKA
Retrocopy GSRNFSINSSKSSTARNGGFLLSTSMKWVQF*SLHVDIPKDLTKPTITISDEPDT*YKRLSVLVKGHDKA

Parental  VLDSYEYFAVLAAKELGISIKVHEPPRKIERFTLLKSVHIFKKHRVQYEMRTLYRCLELEHLTGSTANVY
          VLDSYEYFAVLAAKELGIS.KVHEPPRKIERFTLLKSVHIFKKHRVQYEMRTLYRCLELEHLTGSTA.VY
Retrocopy VLDSYEYFAVLAAKELGISSKVHEPPRKIERFTLLKSVHIFKKHRVQYEMRTLYRCLELEHLTGSTADVY

Parental  LEYIQRNLPEGVAMEVTKTKLERLPEHIKEPVWEMVPEEKAEGKS
          LE.I.RNLPEGVAMEVTKTKLERLPEHIKEP.WEMVPEEKAEGKS
Retrocopy LEDIHRNLPEGVAMEVTKTKLERLPEHIKEPIWEMVPEEKAEGKS

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	0.08 RPM	7.18 RPM
SRP017611_brain	0.08 RPM	9.77 RPM
SRP017611_kidney	0.73 RPM	36.58 RPM
SRP017611_liver	0.07 RPM	3.70 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_598 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_598 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_598 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001638	1 retrocopy	retro_cfam_598 ,
Choloepus hoffmanni	ENSCHOG00000006109	1 retrocopy	retro_chof_1964,
Dasypus novemcinctus	ENSDNOG00000006067	1 retrocopy	retro_dnov_2007,
Macaca mulatta	ENSMMUG00000014661	1 retrocopy	retro_mmul_48,
Mus musculus	ENSMUSG00000034729	1 retrocopy	retro_mmus_1654,
Nomascus leucogenys	ENSNLEG00000004800	1 retrocopy	retro_nleu_1385,
Rattus norvegicus	ENSRNOG00000022609	1 retrocopy	retro_rnor_2284,
Tursiops truncatus	ENSTTRG00000014063	1 retrocopy	retro_ttru_1203,