RetrogeneDB ID: retro_cfam_1238

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 27:5992021..5992715(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: PSMC1
• Ensembl ID: ENSCAFG00000017510
• Aliases: None
• Description: Canis lupus familiaris proteasome (prosome, macropain) 26S subunit, ATPase, 1 (PSMC1), mRNA. [Source:RefSeq mRNA;Acc:NM_001251951]

Sequence

>retro_cfam_1238
AAGAATGACAAGGACAAGAAAAAGAAATATGAACCTCCTGTACCAACTAGACTGGGGAAAAAGAAGAAAACAAAGGGACC
AGATGGTGTCCGTTAAGCCACCAATAGTGACACCTCACATTTAGTGCCCCTTAAAATTACTGAAGTTAGAATTAAAGACT
ATCTTCTCATGGAGGAAGAATTCACTAGAAATCAGGAACAAAAAAAGCCTTTAGAAGAAAAGCAAAAGGAGGAAAGAACA
AAGGTGGATGATCTGAGGGGACCCCAATGTCAGTGCGAAACATGGAAAAGATCATTGATGAAAATCACACCATCACGCCT
ATATCAGTGGGTTCAGAACACTACACAGCATTCTTTCCTATGTAGACAAGGATCTGCTGAAACCAGGCTGCTCCACCCTG
CTCAACCACAAGGTGCATGCTCTCGCACAGGTGCTCATGAGTGACACAGATCCCTTGGCCACAGTGATGAAGGTAGAAAA
GGATTCCCAGGAAACCTATGCTGATACTGGGGAGTTGGACAACTAAATTCAGGACACTAAGGTATCTGTGGAGCTTCCTC
TCACTCATCCTGAGTATTATGAAGAGATGGGTATAAAGCCCCCAAAGAGGGTCATTCTCTATGGTCCACCTGGCACAGGG
AAAACCTTATTAACCAAAGCAGTAGCAAACCAAACCTCAGCCACTTTCCTGAGA

Alignment

ORF - retro_cfam_1238 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.15 %
• Parental protein coverage: 53.18 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KDDKDKKKKYEPPVPTRVGKKKKKTKGPDAAS-KLPLVTPHTQCRL-KLLKLERIKDYLLMEEEFIRNQE
          K.DKDKKKKYEPPVPTR.GKKKK.TKGPD....K.P.VTPH..C.L.K.....RIKDYLLMEEEF.RNQE
Retrocopy KNDKDKKKKYEPPVPTRLGKKKK-TKGPDGVR>KPPIVTPHI*CPL<KITEV-RIKDYLLMEEEFTRNQE

Parental  QMKPLEEKQEEERSKVDDLRG-TPMSVGTLEEIIDDNHAIVSTSVGSEHYV-SILSFVDKDLLEPGCSVL
          Q.KPLEEKQ.EER.KVDDLRG.TPMSV...E.IID.NH.I...SVGSEHY..SILS.VDKDLL.PGCS.L
Retrocopy QKKPLEEKQKEERTKVDDLRG<TPMSVRNMEKIIDENHTITPISVGSEHYT<SILSYVDKDLLKPGCSTL

Parental  LNHKVHAVIGVLMDDTDPLVTVMKVEKAPQETYADIGGLDNQIQEIKESVELPLTHPEYYEEMGIKPPKG
          LNHKVHA...VLM.DTDPL.TVMKVEK..QETYAD.G.LDN.IQ..K.SVELPLTHPEYYEEMGIKPPK.
Retrocopy LNHKVHALAQVLMSDTDPLATVMKVEKDSQETYADTGELDN*IQDTKVSVELPLTHPEYYEEMGIKPPKR

Parental  VILYGPPGTGKTLLAKAVANQTSATFLR
          VILYGPPGTGKTLL.KAVANQTSATFLR
Retrocopy VILYGPPGTGKTLLTKAVANQTSATFLR

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	60.56 RPM
SRP017611_brain	0.00 RPM	50.49 RPM
SRP017611_kidney	0.00 RPM	69.67 RPM
SRP017611_liver	0.00 RPM	29.95 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1238 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1238 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1238 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 25 parental genes, and 101 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001839	4 retrocopies	retro_amel_1536, retro_amel_1886, retro_amel_405, retro_amel_962,
Canis familiaris	ENSCAFG00000017510	2 retrocopies	retro_cfam_1238 , retro_cfam_1562,
Choloepus hoffmanni	ENSCHOG00000013595	1 retrocopy	retro_chof_1954,
Callithrix jacchus	ENSCJAG00000017701	7 retrocopies	retro_cjac_1152, retro_cjac_1537, retro_cjac_2417, retro_cjac_2433, retro_cjac_4219, retro_cjac_661, retro_cjac_678,
Cavia porcellus	ENSCPOG00000002424	1 retrocopy	retro_cpor_144,
Dasypus novemcinctus	ENSDNOG00000006458	1 retrocopy	retro_dnov_2162,
Equus caballus	ENSECAG00000003601	1 retrocopy	retro_ecab_355,
Echinops telfairi	ENSETEG00000002661	1 retrocopy	retro_etel_580,
Felis catus	ENSFCAG00000011310	8 retrocopies	retro_fcat_1444, retro_fcat_1559, retro_fcat_2015, retro_fcat_344, retro_fcat_614, retro_fcat_691, retro_fcat_713, retro_fcat_924,
Homo sapiens	ENSG00000100764	10 retrocopies	retro_hsap_1090, retro_hsap_1278, retro_hsap_2080, retro_hsap_2658, retro_hsap_2810, retro_hsap_2873, retro_hsap_3323, retro_hsap_3416, retro_hsap_3793, retro_hsap_975,
Gorilla gorilla	ENSGGOG00000010620	8 retrocopies	retro_ggor_1004, retro_ggor_1298, retro_ggor_1629, retro_ggor_1954, retro_ggor_1993, retro_ggor_2309, retro_ggor_780, retro_ggor_858,
Macropus eugenii	ENSMEUG00000001526	1 retrocopy	retro_meug_623,
Microcebus murinus	ENSMICG00000016733	7 retrocopies	retro_mmur_1039, retro_mmur_1063, retro_mmur_1245, retro_mmur_1577, retro_mmur_216, retro_mmur_839, retro_mmur_983,
Myotis lucifugus	ENSMLUG00000007471	2 retrocopies	retro_mluc_2490, retro_mluc_508,
Macaca mulatta	ENSMMUG00000022990	1 retrocopy	retro_mmul_255,
Mustela putorius furo	ENSMPUG00000008150	4 retrocopies	retro_mputfur_1602, retro_mputfur_409, retro_mputfur_654, retro_mputfur_815,
Mus musculus	ENSMUSG00000021178	3 retrocopies	retro_mmus_1517, retro_mmus_1826, retro_mmus_812,
Nomascus leucogenys	ENSNLEG00000017013	10 retrocopies	retro_nleu_1123, retro_nleu_1163, retro_nleu_1589, retro_nleu_1625, retro_nleu_1669, retro_nleu_2318, retro_nleu_2625, retro_nleu_429, retro_nleu_616, retro_nleu_706,
Oryctolagus cuniculus	ENSOCUG00000006231	4 retrocopies	retro_ocun_1135, retro_ocun_1212, retro_ocun_1654, retro_ocun_411,
Otolemur garnettii	ENSOGAG00000032343	2 retrocopies	retro_ogar_3014, retro_ogar_367,
Pongo abelii	ENSPPYG00000025948	9 retrocopies	retro_pabe_1059, retro_pabe_153, retro_pabe_2379, retro_pabe_2408, retro_pabe_2737, retro_pabe_2832, retro_pabe_3099, retro_pabe_825, retro_pabe_907,
Pan troglodytes	ENSPTRG00000006623	9 retrocopies	retro_ptro_1530, retro_ptro_1904, retro_ptro_1944, retro_ptro_2153, retro_ptro_2321, retro_ptro_2573, retro_ptro_672, retro_ptro_742, retro_ptro_874,
Pteropus vampyrus	ENSPVAG00000010020	3 retrocopies	retro_pvam_1190, retro_pvam_350, retro_pvam_500,
Ictidomys tridecemlineatus	ENSSTOG00000001655	1 retrocopy	retro_itri_780,
Tursiops truncatus	ENSTTRG00000013582	1 retrocopy	retro_ttru_239,