RetrogeneDB ID: retro_cfam_545

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 13:26733491..26733929(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HSD17B10
• Ensembl ID: ENSCAFG00000016277
• Aliases: None
• Description: hydroxysteroid (17-beta) dehydrogenase 10 [Source:HGNC Symbol;Acc:4800]

Sequence

>retro_cfam_545
ATGGCTGTGGCATGTCAGAGACATGAAGGGCCTAGTTACTTTAATAACCAGAGGAGTCTCTAGTCTAGGTCTGGTCATGG
CAGAGCGACTGGTGGGGTGAGGGGCCATTGCTGTGCTTCTGGACCTGCGTAACTCTGATGGGGAGGCCCAAGCCAAGAAG
TTAGGGAAGAGCTGTCCCTTTGCCCCAGGAGACATGACCTCAGAGAAGAATGTGCAAGCAGCCCTGACTCTAATAAAAGA
AAAGTTTGGCCAGGTGGATTTGGCAGTCAACTGGACAGACAGTGTAGTGGCCATCTAGACATACAACTTCAAGAAAAATC
AGGCCCCTACCTTGTCAGACTTTCAGCAAGTTCTCAATGTAATCTCATAGACACATTTAATATGTTCCACCTGGTGGTTG
GTGAGATGCGCCAGAATCAACCAGACCAGGGAGGCCAA

Alignment

ORF - retro_cfam_545 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.95 %
• Parental protein coverage: 55.94 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAAAC-RGVKGLVALVTGGASGLGLATAERLVGQGATAVLLDLPNSDGEVQAKKLGKNCTFAAADVTSEK
          MA.AC.R..KGLV.L.T.G.S.LGL..AERLVG.GA.AVLLDL.NSDGE.QAKKLGK.C.FA..D.TSEK
Retrocopy MAVAC>RDMKGLVTLITRGVSSLGLVMAERLVG*GAIAVLLDLRNSDGEAQAKKLGKSCPFAPGDMTSEK

Parental  DVQAALTLAKEKFGRVDVAVNCAGIAVAIKTYNLKKNQAHTLEDFQRVLNV-NLLGTFNVIRLVAGEMGQ
          .VQAALTL.KEKFG.VD.AVN.....VAI.TYN.KKNQA.TL.DFQ.VLNV.NL..TFN...LV.GEM.Q
Retrocopy NVQAALTLIKEKFGQVDLAVNWTDSVVAI*TYNFKKNQAPTLSDFQQVLNV<NLIDTFNMFHLVVGEMRQ

Parental  NEPDQGGQ
          N.PDQGGQ
Retrocopy NQPDQGGQ

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	41.07 RPM
SRP017611_brain	0.00 RPM	23.90 RPM
SRP017611_kidney	0.00 RPM	159.28 RPM
SRP017611_liver	0.00 RPM	39.52 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_545 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_545 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_545 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 15 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005036	1 retrocopy	retro_amel_371,
Canis familiaris	ENSCAFG00000005927	1 retrocopy	retro_cfam_2172,
Canis familiaris	ENSCAFG00000007520	1 retrocopy	retro_cfam_1341,
Canis familiaris	ENSCAFG00000014368	4 retrocopies	retro_cfam_1199, retro_cfam_1212, retro_cfam_1273, retro_cfam_568,
Canis familiaris	ENSCAFG00000016277	1 retrocopy	retro_cfam_545 ,
Choloepus hoffmanni	ENSCHOG00000000939	1 retrocopy	retro_chof_582,
Cavia porcellus	ENSCPOG00000009594	1 retrocopy	retro_cpor_535,
Dipodomys ordii	ENSDORG00000004051	1 retrocopy	retro_dord_532,
Erinaceus europaeus	ENSEEUG00000005080	1 retrocopy	retro_eeur_379,
Felis catus	ENSFCAG00000013899	1 retrocopy	retro_fcat_1827,
Macropus eugenii	ENSMEUG00000008565	1 retrocopy	retro_meug_2184,
Myotis lucifugus	ENSMLUG00000000175	1 retrocopy	retro_mluc_4,
Otolemur garnettii	ENSOGAG00000002951	1 retrocopy	retro_ogar_1823,
Tarsius syrichta	ENSTSYG00000005340	3 retrocopies	retro_tsyr_1000, retro_tsyr_1542, retro_tsyr_2078,
Xenopus tropicalis	ENSXETG00000007721	1 retrocopy	retro_xtro_39,