RetrogeneDB ID: retro_sscr_17

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: X:118321678..118323073(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000012645
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: DCAF12
• Ensembl ID: ENSSSCG00000010986
• Aliases: None
• Description: DDB1 and CUL4 associated factor 12 [Source:HGNC Symbol;Acc:19911]

Sequence

>retro_sscr_17
ATGGCCCCGCAGCAAACAGGTAGCAGGAAGCGGAAAGCGCCCGCGCTCGAGGCGGCCGCCGCGGGCTCGTCGTCGCAGGG
CTCGGCGGCGGCGGCGGACGGAGACGGGCCGCTGCTGCCCAAGAAGCCGAAGCGGCCGGCGGCAAGACGCTCGCTGCTGC
ACTACCTGAAGGGCCGCGAGGTGGGCGCGCGGGGCCGCGCCGGGCTCCCAGGCTTCGAGGGCGAGCTGCGCGGCTACGCG
GTGCAGAAGCTGCCTGAGCTGCTGAGGGAGCGCGAGCTGGCGCTGGGCACCCTCAACAAGGTGTTCGCGTCGCAGTGGCT
GAACGCCAGGCAGGTGGTGTGCGGCACCAAGTGTAACACGCTCTTCGTGGTGGACGTGCAGTCGGGTCAGATCACGCGCA
TACCTCTGATGCGGGATCGGGCGCCCGGGCCGGCCCGGGCCCAGCCGAGCTGCGGCATCCATGCCATCCAGCTAAACCCC
TCCAAGACGCTTCTGGCCACCGGGGGGGAGAACCCCAACAGCCTGGCCGTCTACCAGTTGCCCACGCTGGATCCCGTGTG
CCTAGGAGACCGCCATGGCCACAAGGACTGGATCTTCGCCATTGCCTGGATGAGCGACACGGTGGCCGTGAGCGGCTCCC
GCGACGGCACCGTGGCGCTGTGGAGGATGGACCCCGACGTGTTCCAGGGCAGCATCGCCTGGCACAACAACGCTGGGCTC
CCCGTCTACGCCCACATCCGTCCGCGGGACGTGGAGACCATCCCCAGGGCCAGCACCAACCCCAGTAACCGCAAGGTGCG
GGCCCTGGCCTTCAGCGGCAAGAACCAGGAGCTGGGAGCCGTGTCCCTGGACGGCTACTTCCACCTGTGGAAAGCGCGGA
GCACCCTGACCAGGCTGCTGTCCATCAGGCTGCCCTACTGCAGAGAGAACGTGTGCCTGACCTACTGCGACGAGTTGTCC
TTGTACGCGGTGGGCTCCCAGTCCCACGTGTCCTTCCTGGATCCGAGGCAACGCCAGCAGAACATCCGGCCCCTGTGCTC
CCGAGAGGGCGGCACGGGTGTGCGCTCCCTGAGCTTCTACCAGCACATCGTCACGGTGGGCACGGGCCACGGCTCTCTGC
TCTTCTATGACATCCGCGCGCAGAAGTTCCTGGAGGAGAAGGCCTGGGCCACCCCGCACTCCTCCCCGGGGCCCGCAGGG
AGGAAGCTCAAGCTCACCTGCGGCAGAGGCTGGCTCAACCACGACGACCTGTGGGTGAACTACTTCGGTGGCATTGGCGA
ATTCCCCAACGCGCTCTACACCCACTGCTACAACTGGCCTGAGATGAAGCTCTTCGTCGCTGGGGGGCCTCTCCCTTCAG
GCCTCCATGGGAACTACGCTGGCCTCTGGAGCTAA

Alignment

ORF - retro_sscr_17 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.98 %
• Parental protein coverage: 98.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LTKKRKRLPPVKRSLVYYLKNREVRLQNETN---YSRVLHGYAAQQLPSLLKEREFHLGTLNKVFASQWL
          L.KK.KR.P...RSL..YLK.REV..............L.GYA.Q.LP.LL.ERE..LGTLNKVFASQWL
Retrocopy LPKKPKR-PAARRSLLHYLKGREVGARGRAGLPGFEGELRGYAVQKLPELLRERELALGTLNKVFASQWL

Parental  NHRQVVCGTKCNTLFVVDVQTSQITKIPILKDREPGGV-TQQGCGIHAIELNPSRTLLATGGDNPNSLAI
          N.RQVVCGTKCNTLFVVDVQ..QIT.IP...DR.PG....Q..CGIHAI.LNPS.TLLATGG.NPNSLA.
Retrocopy NARQVVCGTKCNTLFVVDVQSGQITRIPLMRDRAPGPARAQPSCGIHAIQLNPSKTLLATGGENPNSLAV

Parental  YRLPTLDPVCVGDFCDGHKDWIFSIAWISDTMAVSGSRDGSMGLWEVTDDVLTKSDARHNVSRVPVYAHI
          Y.LPTLDPVC.GD...GHKDWIF.IAW.SDT.AVSGSRDG...LW....DV...S.A.HN....PVYAHI
Retrocopy YQLPTLDPVCLGDR-HGHKDWIFAIAWMSDTVAVSGSRDGTVALWRMDPDVFQGSIAWHNNAGLPVYAHI

Parental  THKALKDIPKEDTNPDNCKVRALAFNNKNKELGAVSLDGYFHLWKAENTLSTGFLLSTKLPYCRENVCLA
          .......IP...TNP.N.KVRALAF..KN.ELGAVSLDGYFHLWKA..TL....LLS..LPYCRENVCL.
Retrocopy RPRDVETIPRASTNPSNRKVRALAFSGKNQELGAVSLDGYFHLWKARSTLTR--LLSIRLPYCRENVCLT

Parental  YGSEWSVYAVGSQAHVSFLDPRQPSYNVKSVCSRERGSGIRSVSFYEHIITVGTGQGSLLFYDIRAQRFL
          Y..E.S.YAVGSQ.HVSFLDPRQ...N....CSRE.G.G.RS.SFY.HI.TVGTG.GSLLFYDIRAQ.FL
Retrocopy YCDELSLYAVGSQSHVSFLDPRQRQQNIRPLCSREGGTGVRSLSFYQHIVTVGTGHGSLLFYDIRAQKFL

Parental  EERLSACYGSKPRLAGENLKLTTGKGWLNHDETWRNYFSDIDFFPNAVYTHCYDSSGTKLFVAGGPLPSG
          EE...A...S.P..AG..LKLT.G.GWLNHD..W.NYF..I..FPNA.YTHCY.....KLFVAGGPLPSG
Retrocopy EEKAWATPHSSPGPAGRKLKLTCGRGWLNHDDLWVNYFGGIGEFPNALYTHCYNWPEMKLFVAGGPLPSG

Parental  LHGNYAGLWS
          LHGNYAGLWS
Retrocopy LHGNYAGLWS

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
SRP014902_placenta	0.00 RPM	5.31 RPM
SRP014902_testis	3.54 RPM	21.50 RPM
SRP018288_heart	0.00 RPM	8.51 RPM
SRP018288_kidney	0.00 RPM	15.27 RPM
SRP018288_liver	0.00 RPM	5.76 RPM
SRP018288_lung	0.51 RPM	17.51 RPM
SRP018856_adipose	0.37 RPM	29.47 RPM
SRP035408_brain	0.32 RPM	2.38 RPM
SRP035408_liver	0.00 RPM	2.64 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_17 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_17 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_17 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Bos taurus	retro_btau_1794
Equus caballus	retro_ecab_1128

---

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,