RetrogeneDB ID: retro_cfam_1304

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 29:12702931..12703280(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHMP4B
• Ensembl ID: ENSCAFG00000007478
• Aliases: None
• Description: charged multivesicular body protein 4B [Source:HGNC Symbol;Acc:16171]

Sequence

>retro_cfam_1304
GCAACCATGGAATTTCAGTGAGAGGCCCTGGAGAATGCCAATACTGACACCGAGGTGCTCTAGAATATGGGCTATTCCTC
CAAGGCCATGAAGGTTGCCCAGGACAACATGGACACTGATCAAGATGAAGAGTTAATGCAGGCCATGGCTGACCAACAGG
CACGAAGCAGAGGAGATTTCAACAGGTATTTCAAACCCTGTAGGATTTGGAGAAGAGTTTGACCAGGATGAGCTCCTGGC
AGAATGAGAACTACAATAGGAGGAACTGGACAGGAATTTGCTGCAAATAAGTGGACCCGAACCAGTCCCTCTTCCAAATG
TTCCCTTTCTAACCTTACCATCAAACCCA

Alignment

ORF - retro_cfam_1304 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.88 %
• Parental protein coverage: 52.23 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  STIEFQREALENANTNTEVLKNMGYAAKAMKAAHDNMDIDKVDELMQDIADQQ-ELAEEISTAISKPVGF
          .T.EFQ.EALENANT.TEVL.NMGY..KAMK.A.DNMD.D...ELMQ..ADQQ...AEEIST.IS.PVGF
Retrocopy ATMEFQ*EALENANTDTEVL*NMGYSSKAMKVAQDNMDTDQDEELMQAMADQQ>HEAEEISTGISNPVGF

Parental  GEEFDEDELMAELEELEQEELDKNLLEISGPETVPLPNVPSITLPSKP
          GEEFD.DEL.AE..EL..EELD.NLL.ISGPE.VPLPNVP..TLPS.P
Retrocopy GEEFDQDELLAE-*ELQ*EELDRNLLQISGPEPVPLPNVPFLTLPSNP

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	121.17 RPM
SRP017611_brain	0.00 RPM	122.58 RPM
SRP017611_kidney	0.00 RPM	80.17 RPM
SRP017611_liver	0.00 RPM	20.59 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1304 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1304 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1304 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009038	1 retrocopy	retro_amel_1612,
Canis familiaris	ENSCAFG00000007478	1 retrocopy	retro_cfam_1304 ,
Choloepus hoffmanni	ENSCHOG00000007288	1 retrocopy	retro_chof_2518,
Equus caballus	ENSECAG00000008311	1 retrocopy	retro_ecab_496,
Felis catus	ENSFCAG00000025893	1 retrocopy	retro_fcat_1835,
Homo sapiens	ENSG00000101421	1 retrocopy	retro_hsap_1339,
Gorilla gorilla	ENSGGOG00000007775	1 retrocopy	retro_ggor_29,
Macaca mulatta	ENSMMUG00000008084	1 retrocopy	retro_mmul_2178,
Mustela putorius furo	ENSMPUG00000017821	2 retrocopies	retro_mputfur_1302, retro_mputfur_697,
Nomascus leucogenys	ENSNLEG00000010020	1 retrocopy	retro_nleu_1822,
Pongo abelii	ENSPPYG00000010931	1 retrocopy	retro_pabe_1111,
Pan troglodytes	ENSPTRG00000013408	1 retrocopy	retro_ptro_915,
Pteropus vampyrus	ENSPVAG00000010293	1 retrocopy	retro_pvam_973,
Rattus norvegicus	ENSRNOG00000046585	1 retrocopy	retro_rnor_61,
Tarsius syrichta	ENSTSYG00000013212	1 retrocopy	retro_tsyr_1453,