RetrogeneDB ID: retro_amel_405

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192428.1:684120..684995(+)
• Located in intron of: ENSAMEG00000008517

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMC1
• Ensembl ID: ENSAMEG00000001839
• Aliases: None
• Description: None

Sequence

>retro_amel_405
TCGGTCATACTCAACCACTAGGAACATGCCATCATTGGGGTGCTCACAGTTTGACAGGGATCCTTTGATCACAGTGATGA
AGGTAGAAAGGCCCCTCAGGAAACCTATGCTGATATTGGAGGATTGGTCAACCAAATCCAGGAAATTCAGGAAACTGTGG
AGCTTCCTCTCAGTCATCCTGAATATTATGAAGAGATGGGTATAAATCCCCCAAAGGGAGTCATTTTCTATGATCCACCT
GGCACAGGTAAAACCTTATTAGCCAAAGCAGTAGCAAACCAAACCTCAGCCACTTTCTTGAAAGTGGTTGGCTCTGAACT
TACTCAGGAGTACCTAGGTGATACCTAGGTACCCATTCGGGAATTGTTTCCAGTTGCTGAAGAACATGCACCATCCATCA
TGTTTATTGATGAAAGGAGATGCCACTGGAAAAAAAGGTATGACTCAAATTCCAATGATGAGAGAGGAATTCAACTAACA
GTGTTGGAACTGTTGAACCAGTTGTATGGATGTGATTCAAGGGGTGACATGAAAGTTATCATGGCCACAAACCAAATAGA
AATTTGGATCCAGCACTTATCACACCAGGCTGCATTGACAGAAAGATCAAGTTCCTCCTGCCCAATGAAAAGACTGTGAA
GTGTATCTTTCAGATCCACACAAGTAGGATGACACCGGCTGATGATGTAACCCTGGATGACTTGATCATGGCTAAAGGTG
ACCTGTCTGGTGTTAACATCAAGGCAATCTGTATAGAAACTGGTCTGATGGCCTTGAGAGAACATAGAATGAAAGTAATA
AATGAAGACTTTAAAAAATCTAAAGAAAATGTTCTTTTTAAAAAACAAGGAGTCACCCCTAAGAGGCTCTATCTC

Alignment

ORF - retro_amel_405 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.31 %
• Parental protein coverage: 66.36 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SVLLNHKVHAVIGVL-MDDTDPLVTVMKVE-KAPQETYADIGGLDNQIQEIKESVELPLTHPEYYEEMGI
          SV.LNH..HA.IGVL...D.DPL.TVMKVE.KAPQETYADIGGL.NQIQEI.E.VELPL.HPEYYEEMGI
Retrocopy SVILNH*EHAIIGVL>QFDRDPLITVMKVE<KAPQETYADIGGLVNQIQEIQETVELPLSHPEYYEEMGI

Parental  KPPKGVILYGPPGTGKTLLAKAVANQTSATFLRVVGSELIQKYLGDGPKLVRELFRVAEEHAPSIVFIDE
          .PPKGVI.Y.PPGTGKTLLAKAVANQTSATFL.VVGSEL.Q.YLGD.....RELF.VAEEHAPSI.FIDE
Retrocopy NPPKGVIFYDPPGTGKTLLAKAVANQTSATFLKVVGSELTQEYLGDT*VPIRELFPVAEEHAPSIMFIDE

Parental  IDAIGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIE-TLDPALIRPGRIDRKIEFPL
          ......KRYDSNS..ER.IQ.T.LELLNQL.G.DSRGD.KVIMATN.IE..LDPALI.PG.IDRKI.F.L
Retrocopy RRCHWKKRYDSNSNDERGIQLTVLELLNQLYGCDSRGDMKVIMATNQIE<NLDPALITPGCIDRKIKFLL

Parental  PDEKTKKRIFQIHTSRMTLADDVTLDDLIMAKDDLSGADIKAICTEAGLMALRERRMKVTNEDFKKSKEN
          P.EKT.K.IFQIHTSRMT.ADDVTLDDLIMAK.DLSG..IKAIC.E.GLMALRE.RMKV.NEDFKKSKEN
Retrocopy PNEKTVKCIFQIHTSRMTPADDVTLDDLIMAKGDLSGVNIKAICIETGLMALREHRMKVINEDFKKSKEN

Parental  VLYKKQEGTPEGLYL
          VL.KKQ..TP..LYL
Retrocopy VLFKKQGVTPKRLYL

Legend:

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

Expression

RNA-Seq

Ailuropoda melanoleuca was not studied using RNA-Seq expression data.

ChIP-Seq

Ailuropoda melanoleuca was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_amel_405 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_405 was not experimentally validated.

Homology

Retrocopy orthology:

Ailuropoda melanoleuca 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,