RetrogeneDB ID: retro_sscr_812

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 5:38534290..38534664(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C1D
• Ensembl ID: ENSSSCG00000008354
• Aliases: None
• Description: C1D nuclear receptor corepressor [Source:HGNC Symbol;Acc:29911]

Sequence

>retro_sscr_812
TTATCAACATCTGAGAATTCCACTGGGGTTGTGGATAAGATGCTGAAGACCATAATGTCTGTTTCTAGAAATGAGTTGTT
GAAGAAGTGGGGCCCTCTTGAATAAGGGAAAGTGTAATTAGTTTCTGCTTATACATTATTAAATTCAATGTTTTGGGTTT
ATGTGGCAATTCAGGGAGTTAATCATAAGGAACATCCAGTAAACAGGAATTGGAAGGATGAGAGTATACATGAACAGAGT
CGAGAAAATAACAGAAAAGAAAAAGGCTGGCAAACTGCACAGAAGTGTGGCTTCAAGATTTGTAAAAAAATGCCCTCTGG
GAGCCAAAACCTAAAAATGCATACAAAGTTGCCAACACAGGATAAAGTAAAAAT

Alignment

ORF - retro_sscr_812 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.19 %
• Parental protein coverage: 87.94 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LSTFENSIGAVDEMLKTMMSVSRNELLQKLDPLEQAKVDLVSAYT-LNSMFWVYLATQGVNPKEHPV-KQ
          LST.ENS.G.VD.MLKT.MSVSRNELL.K..PLE..KV.LVSAYT.LNSMFWVY.A.QGVN.KEHPV.KQ
Retrocopy LSTSENSTGVVDKMLKTIMSVSRNELLKKWGPLE*GKV*LVSAYTLLNSMFWVYVAIQGVNHKEHPV<KQ

Parental  EL-GKINLVLNIIRESFLESLVGMLQRGAASRFV-KNALWEPKPKNASKVANKGKSKN
          EL.G......N...........G.L.R..ASRFV.KNALWEPKPKNA.KVAN.G.SKN
Retrocopy EL<GRMRVYMNRVEKITEKKKAGKLHRSVASRFV>KNALWEPKPKNAYKVANTG*SKN

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	2.92 RPM
SRP014902_testis	0.00 RPM	6.22 RPM
SRP018288_heart	0.00 RPM	9.12 RPM
SRP018288_kidney	0.10 RPM	9.46 RPM
SRP018288_liver	0.00 RPM	4.48 RPM
SRP018288_lung	0.10 RPM	14.87 RPM
SRP018856_adipose	0.00 RPM	7.34 RPM
SRP035408_brain	0.00 RPM	5.21 RPM
SRP035408_liver	0.00 RPM	7.81 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_812 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_812 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_812 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 25 parental genes, and 57 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004859	1 retrocopy	retro_amel_561,
Bos taurus	ENSBTAG00000004567	1 retrocopy	retro_btau_1532,
Canis familiaris	ENSCAFG00000030099	1 retrocopy	retro_cfam_1469,
Choloepus hoffmanni	ENSCHOG00000006719	3 retrocopies	retro_chof_1368, retro_chof_2011, retro_chof_710,
Callithrix jacchus	ENSCJAG00000006589	2 retrocopies	retro_cjac_2930, retro_cjac_856,
Cavia porcellus	ENSCPOG00000006739	1 retrocopy	retro_cpor_1251,
Echinops telfairi	ENSETEG00000014857	5 retrocopies	retro_etel_152, retro_etel_1820, retro_etel_2119, retro_etel_2163, retro_etel_524,
Felis catus	ENSFCAG00000028933	1 retrocopy	retro_fcat_1091,
Homo sapiens	ENSG00000197223	5 retrocopies	retro_hsap_659, retro_hsap_699, retro_hsap_700, retro_hsap_701, retro_hsap_904,
Gorilla gorilla	ENSGGOG00000025982	3 retrocopies	retro_ggor_573, retro_ggor_596, retro_ggor_731,
Loxodonta africana	ENSLAFG00000002083	1 retrocopy	retro_lafr_1016,
Myotis lucifugus	ENSMLUG00000010791	4 retrocopies	retro_mluc_1048, retro_mluc_2082, retro_mluc_235, retro_mluc_391,
Macaca mulatta	ENSMMUG00000017209	3 retrocopies	retro_mmul_1109, retro_mmul_334, retro_mmul_336,
Monodelphis domestica	ENSMODG00000003561	3 retrocopies	retro_mdom_1237, retro_mdom_1677, retro_mdom_941,
Nomascus leucogenys	ENSNLEG00000009973	4 retrocopies	retro_nleu_2506, retro_nleu_2507, retro_nleu_2948, retro_nleu_379,
Oryctolagus cuniculus	ENSOCUG00000009771	1 retrocopy	retro_ocun_142,
Ochotona princeps	ENSOPRG00000009586	3 retrocopies	retro_opri_1141, retro_opri_193, retro_opri_718,
Pongo abelii	ENSPPYG00000012354	1 retrocopy	retro_pabe_202,
Pan troglodytes	ENSPTRG00000023558	3 retrocopies	retro_ptro_443, retro_ptro_479, retro_ptro_624,
Rattus norvegicus	ENSRNOG00000005982	1 retrocopy	retro_rnor_2402,
Sorex araneus	ENSSARG00000003913	1 retrocopy	retro_sara_566,
Sarcophilus harrisii	ENSSHAG00000008352	1 retrocopy	retro_shar_603,
Sus scrofa	ENSSSCG00000008354	2 retrocopies	retro_sscr_660, retro_sscr_812 ,
Tupaia belangeri	ENSTBEG00000009797	4 retrocopies	retro_tbel_1112, retro_tbel_2362, retro_tbel_864, retro_tbel_898,
Tursiops truncatus	ENSTTRG00000013982	2 retrocopies	retro_ttru_1192, retro_ttru_423,