RetrogeneDB ID: retro_cfam_2178

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:67191519..67192254(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZDHHC6
• Ensembl ID: ENSCAFG00000010960
• Aliases: None
• Description: zinc finger, DHHC-type containing 6 [Source:HGNC Symbol;Acc:19160]

Sequence

>retro_cfam_2178
ATGGATACATTCTGCTCAGTTATCAAGTTTGAAAATCTCCAAGAACTAAAGAGACTGTGTCACTGGGGTCCCATCATAGC
CCTCGGTGTTATAGCAGTATGTTCCACAATGGCCATGATTGACTCTGTGTTGTGGTATTGGCCTTTACATACAACTGGAG
GAAGCGTGAATTTCATTATGTTGATAAACTGGACTGTCATGATTCTTTATAACTACTTCAATGCCATGTTTATTGGTCCT
GGCTTTGTCCCTTTGGGGTGGAAACCGGAAAATTCTCAGGATAGAGAGGATGTACCTCTCTGGAGGATGTACCTCCAGTA
TTGTAAAGTCTGCCAAGCATACAAGGCACCACGGTCACATCACTGCATAAAGTGTAACAGATGTGTGATGAAGATGGACC
ATCACTGTCCTTGGATCAGCAACTCTTGTGGTTACCAAAATCATGCTTCCTTCACACTGTTTCTCCTTTTAGCACCACTG
GGTTGTATTCATTCTGCCTTCATTTTTGTTATGACTATGTATACACAGCTTCATAATCGGCTCTCCTTTGGGTGGAACAC
GGTAAAGATTGATATGAGTGCATCCCGGAGAGATCCCCTTCCAATTATTCCCTTTGGATTAGCAGCATTTGCGGCCACCT
TGTTTGCCTTGGGATTAGCTTTAGGAACAACCATAGCTGTTGGGATGTTGTTTTTTATCCAGATGAAAATAATTCTCAGA
AACAATATAAGCTTA

Alignment

ORF - retro_cfam_2178 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.8 %
• Parental protein coverage: 57.63 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDTFCSVIKFENLQELKRLCHWGPIIALGVIAICSTMAMIDSVLWYWPLHTTGGSVNFIMLINWTVMILY
          MDTFCSVIKFENLQELKRLCHWGPIIALGVIA.CSTMAMIDSVLWYWPLHTTGGSVNFIMLINWTVMILY
Retrocopy MDTFCSVIKFENLQELKRLCHWGPIIALGVIAVCSTMAMIDSVLWYWPLHTTGGSVNFIMLINWTVMILY

Parental  NYFNAMFIGPGFVPLGWKPENSQD----SMYLQYCKVC---QAYKAPRSHHCRKCNRCVMKMDHHCPWIN
          NYFNAMFIGPGFVPLGWKPENSQD.........Y...C...QAYKAPRSHHC.KCNRCVMKMDHHCPWI.
Retrocopy NYFNAMFIGPGFVPLGWKPENSQDREDVPLWRMYLQYCKVCQAYKAPRSHHCIKCNRCVMKMDHHCPWIS

Parental  NCCGYQNHASFTLFLLLAPLGCIHAAFIFVMTMYTQLYNRLSFGWNTVKIDMSAARRDPLPIIPFGLAAF
          N.CGYQNHASFTLFLLLAPLGCIH.AFIFVMTMYTQL.NRLSFGWNTVKIDMSA.RRDPLPIIPFGLAAF
Retrocopy NSCGYQNHASFTLFLLLAPLGCIHSAFIFVMTMYTQLHNRLSFGWNTVKIDMSASRRDPLPIIPFGLAAF

Parental  AATLFALGLALGTTIAVGMLFFIQMKIILRNKTSI
          AATLFALGLALGTTIAVGMLFFIQMKIILRN..S.
Retrocopy AATLFALGLALGTTIAVGMLFFIQMKIILRNNISL

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	26.04 RPM
SRP017611_brain	0.00 RPM	17.15 RPM
SRP017611_kidney	0.00 RPM	36.19 RPM
SRP017611_liver	0.00 RPM	9.86 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2178 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2178 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2178 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015401	1 retrocopy	retro_amel_1120,
Canis familiaris	ENSCAFG00000010960	1 retrocopy	retro_cfam_2178 ,
Choloepus hoffmanni	ENSCHOG00000012828	1 retrocopy	retro_chof_1480,
Felis catus	ENSFCAG00000030784	1 retrocopy	retro_fcat_1193,
Loxodonta africana	ENSLAFG00000008129	1 retrocopy	retro_lafr_304,
Mustela putorius furo	ENSMPUG00000002043	1 retrocopy	retro_mputfur_668,
Mus musculus	ENSMUSG00000024982	1 retrocopy	retro_mmus_1740,
Otolemur garnettii	ENSOGAG00000030535	1 retrocopy	retro_ogar_1652,
Ictidomys tridecemlineatus	ENSSTOG00000013840	1 retrocopy	retro_itri_308,
Tarsius syrichta	ENSTSYG00000009673	2 retrocopies	retro_tsyr_1653, retro_tsyr_1771,