RetrogeneDB ID: retro_mputfur_1602

Retrocopy location

• Organism: Ferret (Mustela putorius furo)
• Coordinates: GL897327.1:428410..429722(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMPUG00000001607
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PSMC1
• Ensembl ID: ENSMPUG00000008150
• Aliases: None
• Description: proteasome (prosome, macropain) 26S subunit, ATPase, 1 [Source:HGNC Symbol;Acc:9547]

Sequence

>retro_mputfur_1602
ATGGGTCAGAGTCAGAGTGGTGGTCATGCCCCTGTAGGTGGCAAGAAGGATAACAAAGACAAGAAAAAGAAATATGAACC
TTCTGCACCAACCAGAGTAGGGAAAAAGAAGAAGAAAACAAAGGAACCAGATGCTACCAGCAAGCTGCCACTGGTGACAC
ATCACACTCAGTACCATTTAAAATTATTGAAGTTAGAATTGAATACTATCTTCTCACGGAGGAAGAATTCATTAGAAATC
AGGAACAAATGAAGCCTTTAGAAGAAAAGCAAGAGGAGGAAAGATTTAAGAGTGGATGATCTGAGGGGGACCCCAAAGTC
AATAGGAAACTTGGAAGAGATCCCTGTTGACAATCGTGTTATCCTGTCTACATCTGTGGGCTCAGAACACTGCATAAGTA
TTCTTTCCTTTGTAGACAAAGATCTACTGGAACCAGGCTGCTCCATCCTGATCAACCACAAGGTACATGCCATCCATGTG
CTCATGGATGACACAGATCCCTTGGTCACAGTGATGAAGGTAGAAAAGTCACTCCAAGAAACCTATGCTGATACTGGGCG
GCTGGACAACCAAATCCAGGAAATTAAGGAATCTGCAGAGCTTCCTCTCACTCATCCTGAATATTATGAAGAGATGGTAT
AAAGCCCCCAGAAGGCATTATTCTCTATGGTCCATCTGGCACAAGTAAAACTTTATTAGCCAATGCAGTAGCAAACCAAT
CCTCAGCCACCTTCTTGAGAGTGGTTGGCTCTGAACTTATTCAGAAGTTCCCAGGTCACGGGCCCAAACTAGTTCGGAAA
TTGTTTCCAGTTGTGGAAGAACATGCACCAACCACCATGTTTACTGATGGAATTCATGCCATTGGAACAAAAAGATACAA
GTCAAATTCTGGTGGTGAGAGAGAAATTCAGCAAACAATGTTGGAACTGCTGAGCCAATTGGATGGAGTTGATTTGAGGG
ATGATATGAAAGTTATCGCAGCCACAGACCAAACTGAGACTCTGGATATGGCCCTTATCAGACCAGGTTGCATCAACAGG
AAGCCTGAATTCCCTCAGCCTGACAAAAAGACTAAGAAGTACATCTTTCAGATCCACACAAGCAGGGTGACACTAGCTGA
TGATGGGACTCCAGACGACTTGATCATGACTAAAGATACCTCTTGGGTGCTAACATCAAGGCAATTTGTACAGAAACTGG
TGTGATGGCCTTCAGAGAATGTAGAATGAAAGTAACAAATGAAGACTTCAAGAAATCTAAAGAAAATGCTCTTTATAAAA
AGCAAGAAGGCATTCCTGAGGGACTGTTTCTC

Alignment

ORF - retro_mputfur_1602 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.28 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MGQSQSGGHGPGGGKKDDKDKKKKYEPPVPTRVGKKKKKTKGPDAASKLPLVTPHTQCRL-KLLKLERIK
          MGQSQSGGH.P.GGKKD.KDKKKKYEP..PTRVGKKKKKTK.PDA.SKLPLVT.HTQ..L.K.....RI.
Retrocopy MGQSQSGGHAPVGGKKDNKDKKKKYEPSAPTRVGKKKKKTKEPDATSKLPLVTHHTQYHL<KIIEV-RIE

Parental  DYLLMEEEFIRNQEQMKPLEEKQEEERSK-VDDLRGTPMSVGTLEEIIDDNHAIVSTSVGSEHYVSILSF
          .YLL.EEEFIRNQEQMKPLEEKQEEER.K.VDDLRGTP.S.G.LEEI..DN..I.STSVGSEH..SILSF
Retrocopy YYLLTEEEFIRNQEQMKPLEEKQEEERFK>VDDLRGTPKSIGNLEEIPVDNRVILSTSVGSEHCISILSF

Parental  VDKDLLEPGCSVLLNHKVHAVIGVLMDDTDPLVTVMKVEKAPQETYADIGGLDNQIQEIKESVELPLTHP
          VDKDLLEPGCS.L.NHKVHA.I.VLMDDTDPLVTVMKVEK..QETYAD.G.LDNQIQEIKES.ELPLTHP
Retrocopy VDKDLLEPGCSILINHKVHA-IHVLMDDTDPLVTVMKVEKSLQETYADTGRLDNQIQEIKESAELPLTHP

Parental  EYYEEM-GIKPPKGVILYGPPGTGKTLLAKAVANQTSATFLRVVGSELIQKYLGDGPKLVRELFRVAEEH
          EYYEEM.GIKPP.G.ILYGP.GT.KTLLA.AVANQ.SATFLRVVGSELIQK..G.GPKLVR.LF.V.EEH
Retrocopy EYYEEM<GIKPPEGIILYGPSGTSKTLLANAVANQSSATFLRVVGSELIQKFPGHGPKLVRKLFPVVEEH

Parental  APSIVFIDEIDAIGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRI
          AP...F.D.I.AIGTKRY.SNSGGEREIQ.TMLELL.QLDG.D.R.D.KVI.AT...ETLD.ALIRPG.I
Retrocopy APTTMFTDGIHAIGTKRYKSNSGGEREIQQTMLELLSQLDGVDLRDDMKVIAATDQTETLDMALIRPGCI

Parental  DRKIEFPLPDEKTKKRIFQIHTSRMTLADDVTLDDLIMAKDD-LSGADIKAICTEAGLMALRERRMKVTN
          .RK.EFP.PD.KTKK.IFQIHTSR.TLADD.T.DDLIM.KD..L.GA.IKAICTE.G.MA.RE.RMKVTN
Retrocopy NRKPEFPQPDKKTKKYIFQIHTSRVTLADDGTPDDLIMTKDT<LLGANIKAICTETGVMAFRECRMKVTN

Parental  EDFKKSKENVLYKKQEGTPEGLYL
          EDFKKSKEN.LYKKQEG.PEGL.L
Retrocopy EDFKKSKENALYKKQEGIPEGLFL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Mustela putorius furo was not studied using RNA-Seq expression data.

ChIP-Seq

Mustela putorius furo was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mputfur_1602 retrocopy.

TSS

Mustela putorius furo was not studied using FANTOM5 data.

Lab

retro_mputfur_1602 was not experimentally validated.

Homology

Retrocopy orthology:

Mustela putorius furo does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 48 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,
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,
Macropus eugenii	ENSMEUG00000001526	1 retrocopy	retro_meug_623,
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,
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,
Pteropus vampyrus	ENSPVAG00000010020	3 retrocopies	retro_pvam_1190, retro_pvam_350, retro_pvam_500,
Tursiops truncatus	ENSTTRG00000013582	1 retrocopy	retro_ttru_239,