RetrogeneDB ID: retro_cfam_1018

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 21:33198392..33198736(+)
• Located in intron of: ENSCAFG00000007500

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000009857
• Aliases: None
• Description: None

Sequence

>retro_cfam_1018
ATGGTCACCAAGATGCAGCAGGAGACTGCCGCTCAGCAAATAATGTCTTAGGCTACTAATGTGAAAAAAAGATATTATTT
TGGAGAAGAGAGATTTTCAGCCCTCAGAGCAGAAAATCAGAAAACAAACCTTGAACTACATCAGTTAGAACAAGTAATGG
ATGAAGTAATCAAAGTCCAAACAGATACCAAATTAGACTTCAATCTAGAAAAGAACATGGTGAAATAACTGCATTTGTTG
AATGAAAGGAAGATGCTAGAAGCAAGGACAGAAAATCATGCCCAGCAAGACTGGGTTTCACCCAGACAGGAAGACAGAAA
GAGGTCACTGGCCTCAAAACCATG

Alignment

ORF - retro_cfam_1018 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68. %
• Parental protein coverage: 53.74 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MVTKMQQEVTVQQIMSQIANVK-KDMIILEKSEF-SALRAENEKINVELHRLKQQIMDEVIKVRTDTKLD
          MVTKMQQE...QQIMS...NVK.KD.IILEK..F.SALRAEN.K.N.ELH.L..Q.MDEVIKV.TDTKLD
Retrocopy MVTKMQQETAAQQIMS*ATNVK>KD-IILEKRDF<SALRAENQKTNLELHQL-EQVMDEVIKVQTDTKLD

Parental  FNLEKSRVKELYSLNERKLLEMRTEMVALHAQQD-RAVTQTDRKIDTEVAGLKTM
          FNLEK..VK.L..LNERK.LE.RTE....HAQQD....TQT.R....EV.GLKTM
Retrocopy FNLEKNMVK*LHLLNERKMLEARTEN---HAQQD<LGFTQTGRQ--KEVTGLKTM

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	12.10 RPM
SRP017611_brain	0.00 RPM	12.15 RPM
SRP017611_kidney	0.00 RPM	63.99 RPM
SRP017611_liver	0.00 RPM	6.60 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1018 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1018 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1018 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000395	2 retrocopies	retro_amel_1628, retro_amel_473,
Canis familiaris	ENSCAFG00000009857	3 retrocopies	retro_cfam_1018 , retro_cfam_1556, retro_cfam_823,
Callithrix jacchus	ENSCJAG00000016050	1 retrocopy	retro_cjac_2522,
Cavia porcellus	ENSCPOG00000014899	1 retrocopy	retro_cpor_934,
Equus caballus	ENSECAG00000009150	2 retrocopies	retro_ecab_273, retro_ecab_469,
Felis catus	ENSFCAG00000005972	3 retrocopies	retro_fcat_1290, retro_fcat_1405, retro_fcat_1538,
Homo sapiens	ENSG00000050393	1 retrocopy	retro_hsap_1795,
Gorilla gorilla	ENSGGOG00000002632	1 retrocopy	retro_ggor_1320,
Loxodonta africana	ENSLAFG00000003287	2 retrocopies	retro_lafr_1252, retro_lafr_870,
Microcebus murinus	ENSMICG00000000183	2 retrocopies	retro_mmur_280, retro_mmur_580,
Myotis lucifugus	ENSMLUG00000010975	1 retrocopy	retro_mluc_1574,
Mustela putorius furo	ENSMPUG00000000698	1 retrocopy	retro_mputfur_640,
Nomascus leucogenys	ENSNLEG00000000914	1 retrocopy	retro_nleu_2768,
Otolemur garnettii	ENSOGAG00000013458	3 retrocopies	retro_ogar_1587, retro_ogar_1819, retro_ogar_3178,
Pan troglodytes	ENSPTRG00000017740	1 retrocopy	retro_ptro_1200,
Tarsius syrichta	ENSTSYG00000012562	1 retrocopy	retro_tsyr_810,
Tursiops truncatus	ENSTTRG00000012874	1 retrocopy	retro_ttru_1597,