RetrogeneDB ID: retro_pabe_64

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:125779483..125780875(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000020700
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: DCAF12
• Ensembl ID: ENSPPYG00000019127
• Aliases: None
• Description: DDB1 and CUL4 associated factor 12 [Source:HGNC Symbol;Acc:19911]

Sequence

>retro_pabe_64
ATGGCCCAGCAGCAAACAGGTAGCAGGAAACGGAAAGCGCCCGCGGTCGAGGCGGGCGCCGAGAGCTCGCCGTCGCAGGG
CTTGGCGGCAGCGGACGGTGAGGGGCCGCTGCTACTCAAGAGGCAGAGGCGGCCGGCGACGTCTCGCTCGATGGTGCACT
ATCTGAAGGTTCGGGAGGTAGGCGGGTGGGGCCCCGCCAGGCTCCAGAGCTTCGATGGCGAGATGCGAGGCTACGCGGTA
CAGAGGCTGCCCGAGCTGCTGACGGAGCGCCAACTGGACCTGGGCACCCTCAACAAGGTGTTCGCGTCACAGTGGCTGAA
CGCCAGGCAGGTGGTGTGCGGCACCAAGTGTAACACGCTTTTCGTGGTGGACGTGCAGTCAGGCCACATCGCGCGCATTC
CCCTCTTGCGGGACAGGGAGGCCAGGCTGGCCCAAGACCAACAGGGCTGCGGCATCCATGCCATCGAGCTGAATCCCTCC
AAGACGCTTCTGGCCACCGGCGGCGAAAACCCCAACAGCCTGGCCATCTACCAGCTGCCCTCCCTGGATCCCCTGTGCCT
GGGCGACCGCCATGGCCACAAGGACTGGATCTTCGCTGTCGCCTGGCTGAGTGACACCGTAGCCGTGAGCGGCTCCCGCG
ACGGCACTGTGGCGCTGTGGCGGATGGACCCGGACAAGTTCGATGACACTGTTGCCTGGCATAGCGAGGTGGGTCTCCCC
GTATATGCCCATATCCGTCCGAGGGATGTGGAGGCCATCCCCAGGGCCATCATCAACCCCAGTAACCGCAAGGTGCGGGC
CCTGGCCTGCGGCGGCAAGAACCAGGAACTGGGAGCGGTGTCCTTGGACGGCTACTTCCACCTGTGGAAAGTCCGGAGCA
CACTATCCAGGCTGCTGTCCATCAGGCTGCCCTACTTCCGGGATAATGTGTGCCTGACCTACTGTGATGATATGTCTGTG
TACGCCGTGGGCTCCCATTCCCACGTCTCTTTCCTGGATCTGCGCCAGGACCAGCAGAACATCCGGCCCCTGTGTTCTCG
AGAGGGTGGCACGGGAGTGCGGTCGCTGAGCTTCTACCGCCACATCATCACTGTGGGCACCGGTCAGGGCTCCCTGCTCT
TCTATGACGTCCGGGCCCAGAAATTCCTGGAGGAAAGAGCCTCCGCCACCCTGGAGTCCTCTTCAGGACCTGCAAGGAGG
AAGCTCAGGCTTGCCTGTGGCAGAGGCTGGCTCAACCACAATGATTTCTGGGTGAATTACTTTGGTGGCATGGAAGTGTT
TCCCAGTGCGCTCTACACCCACTGCTACAACTGGCCGGAGATGAAGCTCTTTGTGGCTGGGGGGCCTCTCCCTGCAGGCC
TCCATGGGAACTATGCAGGCCTCTGGAGCTAA

Alignment

ORF - retro_pabe_64 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.23 %
• Parental protein coverage: 86.53 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SYSRVLHGYAAQQLPSLLKEREFHLGTLNKVFASQWLNHRQVVCGTKCNTLFVVDVQTSQITKIPILKDR
          S......GYA.Q.LP.LL.ER...LGTLNKVFASQWLN.RQVVCGTKCNTLFVVDVQ...I..IP.L.DR
Retrocopy SFDGEMRGYAVQRLPELLTERQLDLGTLNKVFASQWLNARQVVCGTKCNTLFVVDVQSGHIARIPLLRDR

Parental  EPG-GVTQQGCGIHAIELNPSRTLLATGGDNPNSLAIYRLPTLDPVCVGD-DGHKDWIFSIAWISDTMAV
          E......QQGCGIHAIELNPS.TLLATGG.NPNSLAIY.LP.LDP.C.GD..GHKDWIF..AW.SDT.AV
Retrocopy EARLAQDQQGCGIHAIELNPSKTLLATGGENPNSLAIYQLPSLDPLCLGDRHGHKDWIFAVAWLSDTVAV

Parental  SGSRDGSMGLWEVTDDVLTKSDARHNVSRVPVYAHITHKALKDIPKEDTNPDNCKVRALAFNNKNKELGA
          SGSRDG...LW....D......A.H.....PVYAHI.......IP....NP.N.KVRALA...KN.ELGA
Retrocopy SGSRDGTVALWRMDPDKFDDTVAWHSEVGLPVYAHIRPRDVEAIPRAIINPSNRKVRALACGGKNQELGA

Parental  VSLDGYFHLWKAENTLSKLLSTKLPYCRENVCLAYGSEWSVYAVGSQAHVSFLDPRQPSYNVKSVCSRER
          VSLDGYFHLWK...TLS.LLS..LPY.R.NVCL.Y....SVYAVGS..HVSFLD.RQ...N....CSRE.
Retrocopy VSLDGYFHLWKVRSTLSRLLSIRLPYFRDNVCLTYCDDMSVYAVGSHSHVSFLDLRQDQQNIRPLCSREG

Parental  GSGIRSVSFYEHIITVGTGQGSLLFYDIRAQRFLEERLSACYGSKPRLAGENLKLTTGKGWLNHDETWRN
          G.G.RS.SFY.HIITVGTGQGSLLFYD.RAQ.FLEER.SA...S....A...L.L..G.GWLNH...W.N
Retrocopy GTGVRSLSFYRHIITVGTGQGSLLFYDVRAQKFLEERASATLESSSGPARRKLRLACGRGWLNHNDFWVN

Parental  YFSDIDFFPNAVYTHCYDSSGTKLFVAGGPLPSGLHGNYAGLWS
          YF.....FP.A.YTHCY.....KLFVAGGPLP.GLHGNYAGLWS
Retrocopy YFGGMEVFPSALYTHCYNWPEMKLFVAGGPLPAGLHGNYAGLWS

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
SRP007412_brain_prefrontal_cortex	0.22 RPM	12.72 RPM
SRP007412_cerebellum	0.12 RPM	14.11 RPM
SRP007412_heart	0.00 RPM	7.50 RPM
SRP007412_kidney	0.00 RPM	18.06 RPM
SRP007412_liver	0.00 RPM	15.73 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_64 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_64 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_64 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Equus caballus	retro_ecab_1129

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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,