RetrogeneDB ID: retro_cfam_1561

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 35:668550..669182(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000012568
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NACA
• Ensembl ID: ENSCAFG00000000141
• Aliases: None
• Description: Canis lupus familiaris nascent polypeptide-associated complex alpha subunit (NACA), transcript variant 1, mRNA. [Source:RefSeq mRNA;Acc:NM_001252257]

Sequence

>retro_cfam_1561
ATGCCTGGTGAAGCCACAGAAACCATCCCTGCTACAGAGCAGGAGTTGCCCCAGCTCCAGGCTGAGACAGGGTCTGGAAC
AGAATCTGACGGTAATGAATCAGTATGAGAGCTTGAGGAACAGGATTCCACACCCGCAACCACACAACAAGCCCAGCTGG
CAGCAGCTGGAATCAGTGAAGAACCAGTCGCTAAAGCCGGAGTGAAAAGAAGGCACGAAAGGCTATGTCCAAACTGGGTA
TTTGTCAGGTTACGGGGGTTACGAGAGTCACTGTCCGGAAATCTAAGAATATCCTGTTTGTCATCACAAAACCAGATGTG
TACAAGAGCCCAGCTTCAGATACCTACGTAGCTTTTGGGGAAGCCAAGATTAAGGACTTCTCTCAGCAAGCTCAACTGGC
AGCTGCTGAGAAATTCAAAGTTCAAGGTGGAGCTGTCTCAAACATCCAAGAAAACACACAGACTCCAACTGGACAGGAGG
AGAGTGAAGAGGAAGAGGTTGATGAAACGGGTGTAGAGGTTAAGGGCATAGAACTGGTCACGTCACAAGCAAATGTGTCA
AGAGCAAAGGCAGTCGGAGCCCTGACGGACGACAGTGATGATAGTGTGAATGCTATTATGGAGTTAGCAATG

Alignment

ORF - retro_cfam_1561 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.78 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPGEATETVPATEQELPQPQAETGSGTESDSDESVPELEEQDSTQATTQQAQLAAAAEIDEEPVSKA-KQ
          MPGEATET.PATEQELPQ.QAETGSGTESD..ESV.ELEEQDST.ATTQQAQLAAA..I.EEPV.KA...
Retrocopy MPGEATETIPATEQELPQLQAETGSGTESDGNESV*ELEEQDSTPATTQQAQLAAAG-ISEEPVAKA<RS

Parental  SRSEKKARKAMSKLGLRQVTGVTRVTIRKSKNILFVITKPDVYKSPASDTYIVFGEAKIEDLSQQAQLAA
          .....KA...........VT...RVT.RKSKNILFVITKPDVYKSPASDTY..FGEAKI.D.SQQAQLAA
Retrocopy EKKARKAMSKLGICQVTGVT---RVTVRKSKNILFVITKPDVYKSPASDTYVAFGEAKIKDFSQQAQLAA

Parental  AEKFKVQGEAVSNIQENTQTPTVQEESEEEEVDETGVEVKDIELVMSQANVSRAKAVRALKNNSNDIVNA
          AEKFKVQG.AVSNIQENTQTPT.QEESEEEEVDETGVEVK.IELV.SQANVSRAKAV.AL...S.D.VNA
Retrocopy AEKFKVQGGAVSNIQENTQTPTGQEESEEEEVDETGVEVKGIELVTSQANVSRAKAVGALTDDSDDSVNA

Parental  IMELTM
          IMEL.M
Retrocopy IMELAM

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	186.98 RPM
SRP017611_brain	0.00 RPM	59.46 RPM
SRP017611_kidney	0.07 RPM	400.58 RPM
SRP017611_liver	0.00 RPM	124.00 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1561 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1561 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1561 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 108 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004175	3 retrocopies	retro_amel_1725, retro_amel_1821, retro_amel_643,
Bos taurus	ENSBTAG00000010701	2 retrocopies	retro_btau_1237, retro_btau_1620,
Canis familiaris	ENSCAFG00000000141	8 retrocopies	retro_cfam_1502, retro_cfam_1561 , retro_cfam_1884, retro_cfam_1913, retro_cfam_2096, retro_cfam_2169, retro_cfam_710, retro_cfam_974,
Callithrix jacchus	ENSCJAG00000010701	8 retrocopies	retro_cjac_1063, retro_cjac_1452, retro_cjac_1875, retro_cjac_2202, retro_cjac_2453, retro_cjac_2696, retro_cjac_2975, retro_cjac_3232,
Cavia porcellus	ENSCPOG00000012654	3 retrocopies	retro_cpor_1025, retro_cpor_1365, retro_cpor_617,
Dipodomys ordii	ENSDORG00000014522	2 retrocopies	retro_dord_228, retro_dord_699,
Equus caballus	ENSECAG00000015242	1 retrocopy	retro_ecab_785,
Erinaceus europaeus	ENSEEUG00000010458	5 retrocopies	retro_eeur_170, retro_eeur_207, retro_eeur_242, retro_eeur_334, retro_eeur_520,
Homo sapiens	ENSG00000196531	6 retrocopies	retro_hsap_3006, retro_hsap_3027, retro_hsap_3968, retro_hsap_3992, retro_hsap_737, retro_hsap_77,
Loxodonta africana	ENSLAFG00000004598	6 retrocopies	retro_lafr_1107, retro_lafr_113, retro_lafr_1251, retro_lafr_166, retro_lafr_491, retro_lafr_958,
Macropus eugenii	ENSMEUG00000008412	3 retrocopies	retro_meug_1630, retro_meug_2063, retro_meug_2147,
Microcebus murinus	ENSMICG00000016465	5 retrocopies	retro_mmur_1122, retro_mmur_450, retro_mmur_585, retro_mmur_684, retro_mmur_807,
Myotis lucifugus	ENSMLUG00000001169	16 retrocopies	retro_mluc_1147, retro_mluc_1653, retro_mluc_1668, retro_mluc_1756, retro_mluc_1767, retro_mluc_1851, retro_mluc_1881, retro_mluc_1941, retro_mluc_2587, retro_mluc_2600, retro_mluc_414, retro_mluc_492, retro_mluc_526, retro_mluc_641, retro_mluc_725, retro_mluc_861,
Macaca mulatta	ENSMMUG00000003073	4 retrocopies	retro_mmul_1233, retro_mmul_1933, retro_mmul_2066, retro_mmul_889,
Mus musculus	ENSMUSG00000061315	1 retrocopy	retro_mmus_968,
Nomascus leucogenys	ENSNLEG00000017449	7 retrocopies	retro_nleu_1358, retro_nleu_20, retro_nleu_2522, retro_nleu_478, retro_nleu_754, retro_nleu_839, retro_nleu_941,
Ochotona princeps	ENSOPRG00000001781	3 retrocopies	retro_opri_264, retro_opri_758, retro_opri_961,
Procavia capensis	ENSPCAG00000007067	5 retrocopies	retro_pcap_150, retro_pcap_224, retro_pcap_282, retro_pcap_305, retro_pcap_324,
Pongo abelii	ENSPPYG00000004670	6 retrocopies	retro_pabe_2507, retro_pabe_26, retro_pabe_3279, retro_pabe_633, retro_pabe_656, retro_pabe_764,
Pteropus vampyrus	ENSPVAG00000008015	8 retrocopies	retro_pvam_1007, retro_pvam_1097, retro_pvam_1154, retro_pvam_1173, retro_pvam_1382, retro_pvam_1384, retro_pvam_290, retro_pvam_580,
Sarcophilus harrisii	ENSSHAG00000002175	1 retrocopy	retro_shar_213,
Ictidomys tridecemlineatus	ENSSTOG00000009028	1 retrocopy	retro_itri_367,
Tursiops truncatus	ENSTTRG00000002150	2 retrocopies	retro_ttru_1157, retro_ttru_760,
Vicugna pacos	ENSVPAG00000004028	2 retrocopies	retro_vpac_485, retro_vpac_611,