RetrogeneDB ID: retro_pvam_16

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_13693:13924..15217(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPVAG00000007260
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: DCAF12
• Ensembl ID: ENSPVAG00000008654
• Aliases: None
• Description: DDB1 and CUL4 associated factor 12 [Source:HGNC Symbol;Acc:19911]

Sequence

>retro_pvam_16
GAGGGCCCACTGGTGCCCAAGAAGCAGAAACGGCCGGCAGCGCAGCGCTCGCTGGTGCACTACCTGAAAGGCCGCGAGGT
GGGCGCGCAGAGCCACGCGGGGCTCTCGAGATTCGAGGGCGAGCTGCGCGGCTACGCCGTGCGGAAGCTGCCCGAGCTGC
TGTGCGAGAGCGAGCTGGCCCTGGGCACCCTCAACAAGGTGTTTGCTTCCCAGTGGCTGAATGCCAGGCAGGTGGTGTGC
GGCACCAAGTGCAACACGCTCTTCGTAGTGGACGTGCAGTCGGTTCAGATCACGCGCATCCCGCTCATGCGGGACAGGGG
AGCTGGGCTGGCCCGGGCCCAGCCGAGCTGCGGCATCCACGCCATTGAGCTGAATCCCTCCAGGACGCTTCTGGCCACTG
GAGGCGAAAACCCCAACAGCCTGGCGGTCTACCAGCTGCCCACCCTGGACCCTGTGTGCCTGGGTGACCGTCACGGCCAC
AAAGATTGGATCTTCGCCATCGCCTGGATGAGTGACACAGTGGCTGTGAGCGGTTCCCGCGACGGCACTGTGGCACTGTG
GAGGATGGATCCCGACATGTTCAATGGCAGCATAGCCTGGCACAATGACGCAGGGCTGCCGGTGTACGCCCATATCCGTC
CGAGGGACATGGAGACCATCCCTAGGGCCAGCACCAACCCCAGTAACCGCAAGGTACGAGCCCTGGCCTTCAGTGGCAAG
AATCAGGAGCTGGGAGCGGTGTCCCTAGATGGCTACTTCCACCTGTGGAAAGTCAGGAGCACCCTGTCCAGGCTGCTGTC
CATCAGGCTGCCCTACTGCCGAGAGAACGTGTGCTTGACCTACTGCGACGAGTTGTCTCTGTACGCGGTGGGCTCCCAGT
CCCACGTCTCCTTCCTGGATCCGCGCCAGCGCCAGCAGAATATTCGACCCCTTTGCTCCCGAGAGGGCGGTACAGGCGTG
CGCTCGCTGAGTTTCTATCAGTACATCATCACCGTGGGCACGGGCCACGGCTCCCTGCTCTTCTATGACATCCGCGCCCA
GAAGTTCCTGGAGGAGAGGGCCTCGGCCAGCCCCGACTCCTCCCTGGGGCCCACAGGGAGTAAGCTCAAGCTCACCTGTG
GCAGAGGCTGGCTCAACCATGATGACCTGTGGGTGAACTACTTTGGCGGCATGGATGAGTTCCCCAACGCGCTCTACACT
CACTGCTACAACTGGCCGGAGATGAAGCTCTTCGTGGCTGGGGGGCCTCTCCCTTCAGGTCTCCATGGGAACTACGCAGG
CCTCTGGAGCTAA

Alignment

ORF - retro_pvam_16 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.22 %
• Parental protein coverage: 92.49 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KRKRLPPVKRSLVYYLKNREVRLQNETSYSRV---LHGYAAQQLPSLLKEREFHLGTLNKVFASQWLNHR
          K....P...RSLV.YLK.REV..Q.....SR....L.GYA...LP.LL.E.E..LGTLNKVFASQWLN.R
Retrocopy KKQKRPAAQRSLVHYLKGREVGAQSHAGLSRFEGELRGYAVRKLPELLCESELALGTLNKVFASQWLNAR

Parental  QVVCGTKCNTLFVVDVQTSQITKIPILKDREPG-GVTQQGCGIHAIELNPSRTLLATGGDNPNSLAIYRL
          QVVCGTKCNTLFVVDVQ..QIT.IP...DR..G....Q..CGIHAIELNPSRTLLATGG.NPNSLA.Y.L
Retrocopy QVVCGTKCNTLFVVDVQSVQITRIPLMRDRGAGLARAQPSCGIHAIELNPSRTLLATGGENPNSLAVYQL

Parental  PTLDPVCVGD-DGHKDWIFSIAWINDTMAVSGSRDGSMGLWEVTDDVLTRSDARHNVSQVPVYAHITHKA
          PTLDPVC.GD..GHKDWIF.IAW..DT.AVSGSRDG...LW....D....S.A.HN....PVYAHI....
Retrocopy PTLDPVCLGDRHGHKDWIFAIAWMSDTVAVSGSRDGTVALWRMDPDMFNGSIAWHNDAGLPVYAHIRPRD

Parental  LKDIPKEDTNPDNCKVRALAFNNKNKELGAVSLDGYFHLWKAENTLSKLLSTKLPYCRENVCLAYGSEWS
          ...IP...TNP.N.KVRALAF..KN.ELGAVSLDGYFHLWK...TLS.LLS..LPYCRENVCL.Y..E.S
Retrocopy METIPRASTNPSNRKVRALAFSGKNQELGAVSLDGYFHLWKVRSTLSRLLSIRLPYCRENVCLTYCDELS

Parental  VYAVGSQAHVSFLDPRQPSYNIKSVCSRERGSGIRSVSFYEHIITVGTGQGSLLFYDIRAQRFLEERLAA
          .YAVGSQ.HVSFLDPRQ...NI...CSRE.G.G.RS.SFY..IITVGTG.GSLLFYDIRAQ.FLEER..A
Retrocopy LYAVGSQSHVSFLDPRQRQQNIRPLCSREGGTGVRSLSFYQYIITVGTGHGSLLFYDIRAQKFLEERASA

Parental  CYGSKPRLAGENLKLTTGKGWLNHDETWRNYFSDIDFFPNAVYTHCYDSSGTKLFVAGGPLPSGLHGNYA
          ...S.....G..LKLT.G.GWLNHD..W.NYF...D.FPNA.YTHCY.....KLFVAGGPLPSGLHGNYA
Retrocopy SPDSSLGPTGSKLKLTCGRGWLNHDDLWVNYFGGMDEFPNALYTHCYNWPEMKLFVAGGPLPSGLHGNYA

Parental  GLWS
          GLWS
Retrocopy GLWS

Legend:

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

Expression

RNA-Seq

Pteropus vampyrus was not studied using RNA-Seq expression data.

ChIP-Seq

Pteropus vampyrus was not studied using ChIP-Seq data.

EST

Pteropus vampyrus was not studied using EST data.

TSS

Pteropus vampyrus was not studied using FANTOM5 data.

Lab

retro_pvam_16 was not experimentally validated.

Homology

Retrocopy orthology:

Pteropus vampyrus 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,