RetrogeneDB ID: retro_cfam_213

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 21:29997524..29998802(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000006595
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000007705
• Aliases: None
• Description: None

Sequence

>retro_cfam_213
ATGGCGCTCCGGGTCACCAGGAACACAAAAGTGAATGTTGAAAACAAGGCGAAGATCGGTATGGCAGGGGCAAAGCGGGT
GCCTCTGGCCTCTGCTGCAGCCTCCAAGCCCGGCCTGAGGCCAAGAACTGCTCTGGGAGACATTGGTAACAAAGTCAGTG
AACAACCACAAGCCAAACTGCCTCTGAAAAAGGAAGCAAAAACTGCGGTTCCTGGAAAAGTCATTGCTAAAAAAATACCA
AAGCCTCTAGAGAAGGCACCTGAGCCTGTCCCTGTCCCGGAACCAGAGCTGGAACCTGAGCCGGTTAAAGAAGAAAAACT
TTCGCCCGAGCCTATTTTGGTTGATACTCCCTCTCCAAGCCCGATGGAAACATCTGGATGTGCTCCTGCAGAAGAATATC
TGTGTCAGGCTTTCTCTGATGTAATTCTTGCAGTGAATGATGTAGATGCAGAAGATGGAGCTGATCCAAACCTTTGTAGT
GAATACGTGAAAGATATTTATGCTTATCTGAGACAACTTGAGGAAGAACAAGCAGTCAAACCAAAATACCTACTGGGTCG
TGAAGTCACTGGAAACATGAGAGCCATCCTAATTGACTGGCTAGTACAGGTTCAAATGAAATTCAGGTTACTGCAGGAGA
CCATGTACATGACTGTTTCCATTATTGATCGGTTCATGCAGAATAACTGTGTGCCCAAGAAGATGCTGCAGCTGGTTGGT
GTCACTGCCATGTTTATTGCAAGCAAATATGAGGAAATGTACCCTCCAGAAATTGGTGACTTTGCCTTTGTGACTGACAA
TACTTACACTAAACACCAAATCAGACAGATGGAAATGAAGATTCTAAGATCTTTAAATTTTGGTCTGGGCCGCCCTCTAC
CCCTGCATTTCCTTCGGAGAGCATCTAAGATTGGAGAGGTTGATGTTGAGCAACATACTTTGGCCAAATACCTGATGGAG
CTATCTATGTTGGACTACGATATGGTACACTTTCCTCCTTCTCAGATTGCAGCAGGAGCTTTTTGCTTAGCGCTGAAAAT
TCTCGATAATGGTGAATGGACACCAACTCTACAGCATTATCTGTCCTACACTGAAGAATCCCTTCTAAATGTTATGCAAC
ACCTGGCTAAGAATATAGTCATGGTGAATCGTGGGCTTACAAAGCACATGACTATCAAGAACAAGTATGCCGCCTCTAAG
CATGCTAAGATCAGCACTCTGGCACAGCTAAATTCTGCACTAGTTCAAGATTTAGCCAAGGCTGTGGCAAAGGTGTAA

Alignment

ORF - retro_cfam_213 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100.0 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MALRVTRNTKVNVENKAKIGMAGAKRVPLASAAASKPGLRPRTALGDIGNKVSEQPQAKLPLKKEAKTAV
          MALRVTRNTKVNVENKAKIGMAGAKRVPLASAAASKPGLRPRTALGDIGNKVSEQPQAKLPLKKEAKTAV
Retrocopy MALRVTRNTKVNVENKAKIGMAGAKRVPLASAAASKPGLRPRTALGDIGNKVSEQPQAKLPLKKEAKTAV

Parental  PGKVIAKKIPKPLEKAPEPVPVPEPELEPEPVKEEKLSPEPILVDTPSPSPMETSGCAPAEEYLCQAFSD
          PGKVIAKKIPKPLEKAPEPVPVPEPELEPEPVKEEKLSPEPILVDTPSPSPMETSGCAPAEEYLCQAFSD
Retrocopy PGKVIAKKIPKPLEKAPEPVPVPEPELEPEPVKEEKLSPEPILVDTPSPSPMETSGCAPAEEYLCQAFSD

Parental  VILAVNDVDAEDGADPNLCSEYVKDIYAYLRQLEEEQAVKPKYLLGREVTGNMRAILIDWLVQVQMKFRL
          VILAVNDVDAEDGADPNLCSEYVKDIYAYLRQLEEEQAVKPKYLLGREVTGNMRAILIDWLVQVQMKFRL
Retrocopy VILAVNDVDAEDGADPNLCSEYVKDIYAYLRQLEEEQAVKPKYLLGREVTGNMRAILIDWLVQVQMKFRL

Parental  LQETMYMTVSIIDRFMQNNCVPKKMLQLVGVTAMFIASKYEEMYPPEIGDFAFVTDNTYTKHQIRQMEMK
          LQETMYMTVSIIDRFMQNNCVPKKMLQLVGVTAMFIASKYEEMYPPEIGDFAFVTDNTYTKHQIRQMEMK
Retrocopy LQETMYMTVSIIDRFMQNNCVPKKMLQLVGVTAMFIASKYEEMYPPEIGDFAFVTDNTYTKHQIRQMEMK

Parental  ILRSLNFGLGRPLPLHFLRRASKIGEVDVEQHTLAKYLMELSMLDYDMVHFPPSQIAAGAFCLALKILDN
          ILRSLNFGLGRPLPLHFLRRASKIGEVDVEQHTLAKYLMELSMLDYDMVHFPPSQIAAGAFCLALKILDN
Retrocopy ILRSLNFGLGRPLPLHFLRRASKIGEVDVEQHTLAKYLMELSMLDYDMVHFPPSQIAAGAFCLALKILDN

Parental  GEWTPTLQHYLSYTEESLLNVMQHLAKNIVMVNRGLTKHMTIKNKYAASKHAKISTLAQLNSALVQDLAK
          GEWTPTLQHYLSYTEESLLNVMQHLAKNIVMVNRGLTKHMTIKNKYAASKHAKISTLAQLNSALVQDLAK
Retrocopy GEWTPTLQHYLSYTEESLLNVMQHLAKNIVMVNRGLTKHMTIKNKYAASKHAKISTLAQLNSALVQDLAK

Parental  AVAKV
          AVAKV
Retrocopy AVAKV

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	4.58 RPM
SRP017611_brain	0.00 RPM	1.83 RPM
SRP017611_kidney	0.00 RPM	1.65 RPM
SRP017611_liver	0.00 RPM	0.51 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_213 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_213 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_213 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014239	2 retrocopies	retro_btau_1317, retro_btau_600,
Canis familiaris	ENSCAFG00000007705	1 retrocopy	retro_cfam_213 ,
Callithrix jacchus	ENSCJAG00000016075	1 retrocopy	retro_cjac_4137,
Cavia porcellus	ENSCPOG00000014629	1 retrocopy	retro_cpor_13,
Erinaceus europaeus	ENSEEUG00000005724	2 retrocopies	retro_eeur_386, retro_eeur_548,
Felis catus	ENSFCAG00000001572	1 retrocopy	retro_fcat_840,
Myotis lucifugus	ENSMLUG00000012856	1 retrocopy	retro_mluc_1020,
Mustela putorius furo	ENSMPUG00000014648	1 retrocopy	retro_mputfur_58,
Mus musculus	ENSMUSG00000041431	5 retrocopies	retro_mmus_1170, retro_mmus_1550, retro_mmus_2508, retro_mmus_2615, retro_mmus_3023,
Procavia capensis	ENSPCAG00000002451	1 retrocopy	retro_pcap_176,
Rattus norvegicus	ENSRNOG00000018635	2 retrocopies	retro_rnor_568, retro_rnor_814,
Sarcophilus harrisii	ENSSHAG00000007685	1 retrocopy	retro_shar_290,
Tupaia belangeri	ENSTBEG00000011817	4 retrocopies	retro_tbel_1185, retro_tbel_3200, retro_tbel_4185, retro_tbel_4531,
Tarsius syrichta	ENSTSYG00000008928	1 retrocopy	retro_tsyr_232,
Tursiops truncatus	ENSTTRG00000002874	2 retrocopies	retro_ttru_524, retro_ttru_59,