RetrogeneDB ID: retro_amel_73

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL194391.1:161442..162723(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSAMEG00000018790
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: DCAF12
• Ensembl ID: ENSAMEG00000000309
• Aliases: None
• Description: DDB1 and CUL4 associated factor 12 [Source:HGNC Symbol;Acc:19911]

Sequence

>retro_amel_73
CTGCCCAAGAAGCTGAAGCGGCCGGCGACGCGGCGTTCGCTGGTGCACTACCTGAAGGGCCGTGAGGTGGGCGCGAGGGG
CGGCGCCGGGCTCTCGGGCTCCGAGGGCGAGCTGCGCGGCTATGCGGTGCAGAAGCTGCCCGAGCTGTTGAGGGAGCGCG
AGCTGGCCCTGGGCACCCTCAACAAGGTGTTCGCGTCGCAGTGGCTGAACGCCAGGCAGGTGGTGTGTGGCACCAAGTGT
AACACCCTCTTCGTGGTGGATGTGCATTCGGGCCAGATCACGCGCATCCCCCTGCTGCGGGACCGGGGGCCCTGGTTGGC
CCGGGCCCAGCCCACCTGCGGCATCCACGCCATTGAGCTGAATCCCTCCAAGACGCTTCTGGCCACTGGGGGCGAGAACC
CCAACAGCCTGGCGGTCTACCAGCTGCCCACCCTGGACCCCGTGTGCCTGGGGGACCGCCATGGCCACAAGGACTGGATC
TTCACCATCGCCTGGATGAGTGACACAGTGGCTGTGAGCGGCTCCCGCGACGGCACAGTGGCGCTGTGGCGGATGGATCC
CGACATGTTCAGTGGCAGCATCGCCTGGCACAACGACGCGGGGCTCCCTGTGTACGCCCACATCCGTCCGAAGGACACGG
AGACCATCCCCAGGTCCAGCACCAGCCCCAGTAACCGCAAGGTGCGGGCTCTGGCCTTCAGCGGCAAGAACCAAGAGCTG
GGAGCGGTGTCCCTGGACGGCTACTTCCACCTGTGGAAAGCCCGGAGCACTCTGTCCAGGCTGCTGTCCATCAGGCTGCC
CTACTGCCGAGAGAACGTGTGCCTGACCTACTGTGATGAGTTGTCCCTGTACGCGGTGGGCTCCCAGTCCCATGTCTCCT
TCTTAGATCCGCGCCAACGTCAGCAGAATATCCGGCCCCTGTGCTCCCGAGAGGGCGGCACGGGTGTGCGCTCGCTGAGT
TTCTACCAGCACATCATCACAGTGGGCACGGGCCATGGCTCCCTGCTCTTCTATGATATCCGCGCCCAGAAGTTCCTGGA
GGAGAGGGCCTCAGCCAGCCCGGACTCCTCTCCTGGGCCCTCGGGAAGGAAGCTCAAGCTCACCTGTGGCAGAGGCTGGC
TTAACCATGATGACCTGTGGGTGAACTACTTCGGTGGGATTGGCGAGTTCCCCAATGCGCTCTACACGCACTGCTACAAC
TGGCCTGAGATGAAGCTCTTCGTGGCTGGGGGACCTCTCCCTTCAGGCCTCCATGGGAACTACGCAGGCCTCTGGAGCTA
A

Alignment

ORF - retro_amel_73 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.69 %
• Parental protein coverage: 85.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LHGYAAQQLPSLLKEREFHLGTLNKVFASQWLNHRQVVCGTKCNTLFVVDVQTSQITKIPILKDREPG-G
          L.GYA.Q.LP.LL.ERE..LGTLNKVFASQWLN.RQVVCGTKCNTLFVVDV...QIT.IP.L.DR.P...
Retrocopy LRGYAVQKLPELLRERELALGTLNKVFASQWLNARQVVCGTKCNTLFVVDVHSGQITRIPLLRDRGPWLA

Parental  VTQQGCGIHAIELNPSRTLLATGGDNPNSLAIYRLPTLDPVCVGD-DGHKDWIFSIAWISDTMAVSGSRD
          ..Q..CGIHAIELNPS.TLLATGG.NPNSLA.Y.LPTLDPVC.GD..GHKDWIF.IAW.SDT.AVSGSRD
Retrocopy RAQPTCGIHAIELNPSKTLLATGGENPNSLAVYQLPTLDPVCLGDRHGHKDWIFTIAWMSDTVAVSGSRD

Parental  GSMGLWEVTDDVLTKSDARHNVSRVPVYAHITHKALKDIPKEDTNPDNCKVRALAFNNKNKELGAVSLDG
          G...LW....D....S.A.HN....PVYAHI..K....IP...T.P.N.KVRALAF..KN.ELGAVSLDG
Retrocopy GTVALWRMDPDMFSGSIAWHNDAGLPVYAHIRPKDTETIPRSSTSPSNRKVRALAFSGKNQELGAVSLDG

Parental  YFHLWKAENTLSKLLSTKLPYCRENVCLAYGSEWSVYAVGSQAHVSFLDPRQPSYNVKSVCSRERGSGIR
          YFHLWKA..TLS.LLS..LPYCRENVCL.Y..E.S.YAVGSQ.HVSFLDPRQ...N....CSRE.G.G.R
Retrocopy YFHLWKARSTLSRLLSIRLPYCRENVCLTYCDELSLYAVGSQSHVSFLDPRQRQQNIRPLCSREGGTGVR

Parental  SVSFYEHIITVGTGQGSLLFYDIRAQRFLEERLSACYGSKPRLAGENLKLTTGKGWLNHDETWRNYFSDI
          S.SFY.HIITVGTG.GSLLFYDIRAQ.FLEER.SA...S.P...G..LKLT.G.GWLNHD..W.NYF..I
Retrocopy SLSFYQHIITVGTGHGSLLFYDIRAQKFLEERASASPDSSPGPSGRKLKLTCGRGWLNHDDLWVNYFGGI

Parental  DFFPNAVYTHCYDSSGTKLFVAGGPLPSGLHGNYAGLWS
          ..FPNA.YTHCY.....KLFVAGGPLPSGLHGNYAGLWS
Retrocopy GEFPNALYTHCYNWPEMKLFVAGGPLPSGLHGNYAGLWS

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_73 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_73 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 15 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000309	1 retrocopy	retro_amel_73 ,
Bos taurus	ENSBTAG00000021573	3 retrocopies	retro_btau_1794, retro_btau_1795, retro_btau_1796,
Equus caballus	ENSECAG00000023064	2 retrocopies	retro_ecab_1128, retro_ecab_1129,
Erinaceus europaeus	ENSEEUG00000013279	1 retrocopy	retro_eeur_403,
Microcebus murinus	ENSMICG00000005881	1 retrocopy	retro_mmur_14,
Macaca mulatta	ENSMMUG00000017458	1 retrocopy	retro_mmul_202,
Nomascus leucogenys	ENSNLEG00000004996	1 retrocopy	retro_nleu_6,
Otolemur garnettii	ENSOGAG00000015799	1 retrocopy	retro_ogar_237,
Ochotona princeps	ENSOPRG00000001281	2 retrocopies	retro_opri_1178, retro_opri_470,
Pongo abelii	ENSPPYG00000019127	1 retrocopy	retro_pabe_64,
Pteropus vampyrus	ENSPVAG00000008654	1 retrocopy	retro_pvam_16,
Sus scrofa	ENSSSCG00000010986	1 retrocopy	retro_sscr_17,
Ictidomys tridecemlineatus	ENSSTOG00000006904	1 retrocopy	retro_itri_168,
Tarsius syrichta	ENSTSYG00000014394	1 retrocopy	retro_tsyr_1965,
Tursiops truncatus	ENSTTRG00000010591	1 retrocopy	retro_ttru_8,