RetrogeneDB ID: retro_cfam_1493

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 32:7137836..7138987(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000009085
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000008683
• Aliases: None
• Description: None

Sequence

>retro_cfam_1493
GTCGTCTCCTACCTGGTGATCTGCACACGGTCCTCAGAGGCCTCCGCTGCTGTGCGGGCCGGCCTGATAAGTACCATGGG
AAAACCATTCCTATTGATGGGGACCTTTTCAGTTATACCTGCCATGAACCTGTCGGGGTGTGCGGGCAGATCGTTCCGTG
GACCGTCCCCCTCCTGATGCAAGCCTGGAAACTGGTCCAGCCCTGGCGACCGGAAATGTGATTGCGATGAGGGTAGCTGA
GCAGACTCCGCTCGCCGCCCTCTATGTGGCCAACCTGATTAAGGAGGCTGGCTTTCCTCCTGGCTGGTCAATACTATTCC
TGGATTTGGCCCCACAGCTGGGGCTGCCATCGCCTCCCATGAGGATGGGGACAAAGTGGCAGGCTCCACCAAGGTTGGCC
ACCTAGTCCAGGTTGCTGCAGGGAACAGTAACCTCAAGAGAGTGACCCTGGAGCTGGGAGGAAAGAGCCCCCACTATCAT
CATGTCAGATACAGACATGAACTGGGCCGTAGAGCAGGCCCACTTTGCCCTGTTCTTCCAACGAGGGCCAGTGCTGCTGT
GCAGGCTACCGGACCTTTGTGCAAGAAGATGTTTACGCTGAGTTTGTGGAGCAGAGTGTTGCCAGGACCAAGTCACGTGT
AGTTGGGAACCCCTTTGACAACCAGACTGAGCAGGGGCCGCAGGTGGATGAAACTCAGTTTAAGAAGATCCTTGGTTATA
TCAAATCTGGGAAGGAGGAGGGGGCAAAACTATTGTGTGGTGGAGGGGCACCTGCTGACCTTGGCTACTTTATCCAGCCC
ACCGAGTTTGGAGATGTGCAAGACAGCATGACTATCGCCAAGGAGGAGATCTTTGAGACAATGATGCAGATCCTGAAGTT
CAAGACCATAGAGGAAGTTGTTGGGAGAGCCAACAATTCCAAGTATGGGCTGGCTGCAGCTGTCTTCACCAAGGACTTGG
ACAAGGCCAATTATCTGTCCCAAGCCTTCCAAGCTGGCACTGTGTGGATCAACTGCTGTGATGTATTTGGGGCCCAGTCA
CTATTCAGTGGCTACAAGATGTCTGGGAGTGGCCGGGAGCTGGGAGAGTATGGGTTACAGGCATACACAGAAGTGAAAAC
TGTCATGATCAAAGTGCCTCAGAAGAACTCC

Alignment

ORF - retro_cfam_1493 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.98 %
• Parental protein coverage: 74.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  VISYLV-DLDMVLRCLRYYAGWADKYHGKTIPIDGDFFSYTRHEPVGVCGQIIPWNFPLLMQAWKL-GPA
          V.SYLV.DL..VLR.LR..AG..DKYHGKTIPIDGD.FSYT.HEPVGVCGQI.PW..PLLMQAWKL.GPA
Retrocopy VVSYLV<DLHTVLRGLRCCAGRPDKYHGKTIPIDGDLFSYTCHEPVGVCGQIVPWTVPLLMQAWKL<GPA

Parental  LATGNVIVMKVAEQTPLTALYVANLIKEAGFPPG-VVNIIPGFGPTAGAAIASHEDVDKVAFTGSTEVGH
          LATGNVI.M.VAEQTPL.ALYVANLIKEAGFPPG..VN.IPGFGPTAGAAIASHED.DKVA..GST.VGH
Retrocopy LATGNVIAMRVAEQTPLAALYVANLIKEAGFPPG<LVNTIPGFGPTAGAAIASHEDGDKVA--GSTKVGH

Parental  LVQVAAGNSNLKRVTLELGGKSPN-IIMSDADMNWAVEQAHFALFF-NQGQCCCAGSRTFVQEDVYAEFV
          LVQVAAGNSNLKRVTLELGGKSP..IIMSD.DMNWAVEQAHFALFF.N.GQCCCAG.RTFVQEDVYAEFV
Retrocopy LVQVAAGNSNLKRVTLELGGKSPH>IIMSDTDMNWAVEQAHFALFF>NEGQCCCAGYRTFVQEDVYAEFV

Parental  ERSVARAKSRVVGNPFDSQTEQGPQVDETQFKKILGYIKSGKEEGAKLLCGGGAAADRGYFIQPTVFGDV
          E.SVAR.KSRVVGNPFD.QTEQGPQVDETQFKKILGYIKSGKEEGAKLLCGGGA.AD.GYFIQPT.FGDV
Retrocopy EQSVARTKSRVVGNPFDNQTEQGPQVDETQFKKILGYIKSGKEEGAKLLCGGGAPADLGYFIQPTEFGDV

Parental  QDTMTIAKEEIFGPVMQILKFKTIEEVIGRANNSKYGLAAAVFTKDLDKANYLSQALQAGTVWINCYDVF
          QD.MTIAKEEIF...MQILKFKTIEEV.GRANNSKYGLAAAVFTKDLDKANYLSQA.QAGTVWINC.DVF
Retrocopy QDSMTIAKEEIFETMMQILKFKTIEEVVGRANNSKYGLAAAVFTKDLDKANYLSQAFQAGTVWINCCDVF

Parental  GAQSPFGGYKMSGSGRELGEYGLQAYTEVKTVTIKVPQKNS
          GAQS.F.GYKMSGSGRELGEYGLQAYTEVKTV.IKVPQKNS
Retrocopy GAQSLFSGYKMSGSGRELGEYGLQAYTEVKTVMIKVPQKNS

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	0.71 RPM	229.82 RPM
SRP017611_brain	0.79 RPM	167.28 RPM
SRP017611_kidney	0.26 RPM	622.00 RPM
SRP017611_liver	0.15 RPM	326.75 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1493 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1493 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1493 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013664	1 retrocopy	retro_amel_51,
Bos taurus	ENSBTAG00000008743	1 retrocopy	retro_btau_48,
Canis familiaris	ENSCAFG00000008683	1 retrocopy	retro_cfam_1493 ,
Equus caballus	ENSECAG00000017673	2 retrocopies	retro_ecab_1054, retro_ecab_1061,
Felis catus	ENSFCAG00000022000	1 retrocopy	retro_fcat_1590,
Homo sapiens	ENSG00000111275	1 retrocopy	retro_hsap_19,
Gorilla gorilla	ENSGGOG00000007108	1 retrocopy	retro_ggor_33,
Latimeria chalumnae	ENSLACG00000011798	1 retrocopy	retro_lcha_108,
Microcebus murinus	ENSMICG00000003487	1 retrocopy	retro_mmur_19,
Myotis lucifugus	ENSMLUG00000017084	1 retrocopy	retro_mluc_1918,
Macaca mulatta	ENSMMUG00000008336	1 retrocopy	retro_mmul_247,
Mustela putorius furo	ENSMPUG00000002282	1 retrocopy	retro_mputfur_27,
Mus musculus	ENSMUSG00000029455	1 retrocopy	retro_mmus_222,
Nomascus leucogenys	ENSNLEG00000000016	1 retrocopy	retro_nleu_22,
Otolemur garnettii	ENSOGAG00000033093	1 retrocopy	retro_ogar_203,
Pongo abelii	ENSPPYG00000004966	1 retrocopy	retro_pabe_32,
Pteropus vampyrus	ENSPVAG00000013189	1 retrocopy	retro_pvam_163,
Rattus norvegicus	ENSRNOG00000001344	1 retrocopy	retro_rnor_307,
Sus scrofa	ENSSSCG00000009889	1 retrocopy	retro_sscr_9,
Ictidomys tridecemlineatus	ENSSTOG00000015009	1 retrocopy	retro_itri_33,
Xenopus tropicalis	ENSXETG00000020930	1 retrocopy	retro_xtro_12,