RetrogeneDB ID: retro_cfam_2014

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 9:57844086..57844740(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000020192
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HPRT
• Ensembl ID: ENSCAFG00000018870
• Aliases: HPRT1, HPRT
• Description: Canis lupus familiaris hypoxanthine phosphoribosyltransferase 1 (HPRT1), mRNA. [Source:RefSeq mRNA;Acc:NM_001003357]

Sequence

>retro_cfam_2014
ATGGCAAGCCGAAGCCCCAGCATTGTGATTAGTGATGATGAACCAGGTTATGACCTAGATTTGTTTTGTATACCTAATCA
TTATGCTCAGGATTTGGAAAAGGTATTTATTCCTCATGGATTAATTATGGACAGGACAGAACGGCTTGCACGAGATGTGA
TGAAGGAGATGGGAAGCCATCACATTGTAGCCCTATGTGTACTCAAGGGGGGCTATACATTCTTTGCTGACCTGCTGGAT
TACATTAAAGCACTGAACAGAAATAGTGATAGGTCCATTCCTATGACTGTGGACTTCATTAGACTGAAAAGCAACTGTAG
TGACCAGTCAACAGGGGACATAAAAGTAATTGGTGGAGATGACCTCTCAACTTTAACTGAAAAGAATGTCTTGATTGTTG
AAGATCTCATTGACACAGGCAAAACAATGCAAACCTTGCTTTCCTTGGTCGCGCAGTATAATCCAAAAATGGTCAAGGTT
GCAAGCTTGCTGGTGAAAAGGACTCCTCGAAGTACTGGTTATAGACCAGACTTTGTTGGATTTGAAATTCCAGACAAGTT
TGTTGTAGGATATGCCCTTGACTATAATGAATATTTTAGAGATTTGAATCATGTTTGTGTCATTAGTGAAACTGGAAAAG
CAAAATACAAAGCC

Alignment

ORF - retro_cfam_2014 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.66 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MATRSPSVVISDDEPGYDLDLFCIPHHYAEDLEKVFIPHGLIMDRTERLARDVMKEMGGHHIVALCVLKG
          MA.RSPS.VISDDEPGYDLDLFCIP.HYA.DLEKVFIPHGLIMDRTERLARDVMKEMG.HHIVALCVLKG
Retrocopy MASRSPSIVISDDEPGYDLDLFCIPNHYAQDLEKVFIPHGLIMDRTERLARDVMKEMGSHHIVALCVLKG

Parental  GYKFFADLLDYIKALNRNSDGSIPMTVDFIRLKSYCNDQSTGDIKVIGGDDLSTLTGKNVLIVEDIIDTG
          GY.FFADLLDYIKALNRNSD.SIPMTVDFIRLKS.C.DQSTGDIKVIGGDDLSTLT.KNVLIVED.IDTG
Retrocopy GYTFFADLLDYIKALNRNSDRSIPMTVDFIRLKSNCSDQSTGDIKVIGGDDLSTLTEKNVLIVEDLIDTG

Parental  KTMQTLLSLVKEHNPKMVKVASLLVKRTPRSVGYKPDFVGFEIPDKFVVGYALDYNEYFRDLNHVCVISE
          KTMQTLLSLV...NPKMVKVASLLVKRTPRS.GY.PDFVGFEIPDKFVVGYALDYNEYFRDLNHVCVISE
Retrocopy KTMQTLLSLVAQYNPKMVKVASLLVKRTPRSTGYRPDFVGFEIPDKFVVGYALDYNEYFRDLNHVCVISE

Parental  TGKAKYKA
          TGKAKYKA
Retrocopy TGKAKYKA

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	1.34 RPM	38.43 RPM
SRP017611_brain	2.46 RPM	92.65 RPM
SRP017611_kidney	0.86 RPM	68.68 RPM
SRP017611_liver	0.15 RPM	13.49 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2014 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2014 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2014 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 51 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001339	1 retrocopy	retro_amel_129,
Bos taurus	ENSBTAG00000014685	3 retrocopies	retro_btau_162, retro_btau_179, retro_btau_721,
Canis familiaris	ENSCAFG00000018870	1 retrocopy	retro_cfam_2014 ,
Cavia porcellus	ENSCPOG00000002512	1 retrocopy	retro_cpor_1299,
Dasypus novemcinctus	ENSDNOG00000008495	5 retrocopies	retro_dnov_1480, retro_dnov_1908, retro_dnov_2057, retro_dnov_255, retro_dnov_763,
Felis catus	ENSFCAG00000004575	2 retrocopies	retro_fcat_104, retro_fcat_1608,
Homo sapiens	ENSG00000165704	1 retrocopy	retro_hsap_917,
Gorilla gorilla	ENSGGOG00000008050	1 retrocopy	retro_ggor_740,
Loxodonta africana	ENSLAFG00000009892	2 retrocopies	retro_lafr_1042, retro_lafr_475,
Microcebus murinus	ENSMICG00000006547	1 retrocopy	retro_mmur_1186,
Myotis lucifugus	ENSMLUG00000003591	1 retrocopy	retro_mluc_2107,
Macaca mulatta	ENSMMUG00000008303	1 retrocopy	retro_mmul_1118,
Mustela putorius furo	ENSMPUG00000012699	3 retrocopies	retro_mputfur_1317, retro_mputfur_1638, retro_mputfur_836,
Oryctolagus cuniculus	ENSOCUG00000003186	1 retrocopy	retro_ocun_1082,
Otolemur garnettii	ENSOGAG00000003881	3 retrocopies	retro_ogar_1886, retro_ogar_3298, retro_ogar_3463,
Pongo abelii	ENSPPYG00000020733	2 retrocopies	retro_pabe_3601, retro_pabe_791,
Pan troglodytes	ENSPTRG00000022287	2 retrocopies	retro_ptro_2042, retro_ptro_636,
Rattus norvegicus	ENSRNOG00000031367	2 retrocopies	retro_rnor_1208, retro_rnor_2491,
Sarcophilus harrisii	ENSSHAG00000007965	3 retrocopies	retro_shar_470, retro_shar_513, retro_shar_661,
Tupaia belangeri	ENSTBEG00000000859	5 retrocopies	retro_tbel_1607, retro_tbel_2234, retro_tbel_3627, retro_tbel_4320, retro_tbel_729,
Tarsius syrichta	ENSTSYG00000009579	1 retrocopy	retro_tsyr_2050,
Tursiops truncatus	ENSTTRG00000009954	9 retrocopies	retro_ttru_1007, retro_ttru_1272, retro_ttru_1523, retro_ttru_1598, retro_ttru_1620, retro_ttru_276, retro_ttru_641, retro_ttru_732, retro_ttru_829,