RetrogeneDB ID: retro_cfam_181

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 1:88586044..88586908(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000001926
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: FAM122B
• Ensembl ID: ENSCAFG00000018882
• Aliases: None
• Description: None

Sequence

>retro_cfam_181
ATGGCTCAGGAGAAGATGGAGCTAGACCTGGAGTTGCCTCCGGGTGCTGGCGGGAGCCCGGCGGAGGGCGGCGGCAGCGG
CGCGGGCGGGGGCCTCCGGAGGTCTAACAGCGCCCCCCTGATCCACGGCCTCAGTGACACTTCGCCGGTGTTCCAGGCCG
AGGCGCCGAGCGCCCGGCGGAACAGCACGACGTTCCCGAACCGCCACGGCCTGCTGCTGCCGGCCTCCCCGGTCCGCATG
CACAGCAGCCGCTTGCACCAGATCAAGCAGGAGGAGGGCATGGACCTCATCAACCGAGAGACCGTCCACGAGCGCGAGGT
GCAGAACGCCATGCAGATAAGCCACTCCTGGGAGGAAAGTTTCAGCCTGAGTGACAACGACGCGGAGAAGTCCGCCTCCC
CGAAGCGCATCGATTTCATTCCGGTGTCACCAGCGCCGTCACCCACCCGGGGGATCGGGAAGCAGTGCTTTTCACCATCC
TTGCAAAGTTTTGTGAGTAGCAATGGATTGCCTCCGAGCCCTATTCCCAGCCCAACGACTCGGTTTACTACCCGGAGAAG
CCAGAGTCCCATCAATTGCATTAGACCAAGTGTTCTTGGACCACTGAAAAGAAAATGTGAAATGGAAACTGAGTATCAGC
CAAAGAGATTTTTCCAGGGCATCACCAACATGCTTTCTTCTGACGTTGCACAGCTGTCAGATCCTGGCGTGTGCGTATCG
TCTGATACCCTTGACGGAAACAGCAGCAGCGCCGGATCTTCTTGTAACTCACCAGCGAAAGTCAGCACTACCACCGACTC
TCCTGTGTCGCCTGCCCAAGCGGCCTCTCCATTTATTCCAGTAGATGAACTTTCATCTAAGTGA

Alignment

ORF - retro_cfam_181 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.7 %
• Parental protein coverage: 93.26 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GGTLRRSSSAPLIHGLSDLSQVFQPYTFRTRRNSTTVMSRHNLLLSSSPNRVPSSRLHQIKREEGMDMMN
          GG.LRRS.SAPLIHGLSD.S.VFQ......RRNSTT...RH.LLL..SP.R..SSRLHQIK.EEGMD..N
Retrocopy GGGLRRSNSAPLIHGLSDTSPVFQAEAPSARRNSTTFPNRHGLLLPASPVRMHSSRLHQIKQEEGMDLIN

Parental  RETAHEREVQTAMQISQSWDESLSLSDSDFEKPEKLYSPKRIDFTPVSPAPSPTRGFGKQCFSPSLQMFV
          RET.HEREVQ.AMQIS.SW.ES.SLSD.D.EK.....SPKRIDF.PVSPAPSPTRG.GKQCFSPSLQ.FV
Retrocopy RETVHEREVQNAMQISHSWEESFSLSDNDAEKSA---SPKRIDFIPVSPAPSPTRGIGKQCFSPSLQSFV

Parental  SSSGLPPSPVPSP-RRFANKRSQSPVKCIRPSVLGPLKRKGEMETESQPKRLFQGTTSMLSPEAAQLSDL
          SS.GLPPSP.PSP..RF...RSQSP..CIRPSVLGPLKRK.EMETE.QPKR.FQG.T.MLS...AQLSD.
Retrocopy SSNGLPPSPIPSPTTRFTTRRSQSPINCIRPSVLGPLKRKCEMETEYQPKRFFQGITNMLSSDVAQLSDP

Parental  SSCFVLSSDILDGSSSSSGLSSDSLAKGSTTAESPVACSNSCSPFILMDDLSPK
          ..C...SSD.LDG.SSS.G.S..S.AK.STT..SPV......SPFI..D.LS.K
Retrocopy GVC--VSSDTLDGNSSSAGSSCNSPAKVSTTTDSPVSPAQAASPFIPVDELSSK

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	7.69 RPM	23.65 RPM
SRP017611_brain	6.27 RPM	28.18 RPM
SRP017611_kidney	3.96 RPM	10.37 RPM
SRP017611_liver	0.87 RPM	3.99 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_181 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_181 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_181 has 6 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_35
Mus musculus	retro_mmus_22
Rattus norvegicus	retro_rnor_651
Oryctolagus cuniculus	retro_ocun_205
Bos taurus	retro_btau_103
Equus caballus	retro_ecab_91

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001311	1 retrocopy	retro_amel_105,
Bos taurus	ENSBTAG00000001886	1 retrocopy	retro_btau_103,
Canis familiaris	ENSCAFG00000018882	1 retrocopy	retro_cfam_181 ,
Callithrix jacchus	ENSCJAG00000004313	1 retrocopy	retro_cjac_594,
Cavia porcellus	ENSCPOG00000011218	1 retrocopy	retro_cpor_80,
Equus caballus	ENSECAG00000018643	1 retrocopy	retro_ecab_91,
Felis catus	ENSFCAG00000024842	1 retrocopy	retro_fcat_1575,
Myotis lucifugus	ENSMLUG00000007988	1 retrocopy	retro_mluc_382,
Macaca mulatta	ENSMMUG00000016948	1 retrocopy	retro_mmul_185,
Mustela putorius furo	ENSMPUG00000012690	1 retrocopy	retro_mputfur_64,
Mus musculus	ENSMUSG00000036022	1 retrocopy	retro_mmus_22,
Rattus norvegicus	ENSRNOG00000050146	1 retrocopy	retro_rnor_651,
Sus scrofa	ENSSSCG00000012685	1 retrocopy	retro_sscr_60,
Ictidomys tridecemlineatus	ENSSTOG00000006261	1 retrocopy	retro_itri_61,