RetrogeneDB ID: retro_sscr_444

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 14:97480203..97480736(-)
• Located in intron of: ENSSSCG00000010385

Retrocopy information

• Ensembl ID: ENSSSCG00000010386
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000006166
• Aliases: None
• Description: Sus scrofa NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 8, 19kDa (NDUFB8), nuclear gene encoding mitochondrial protein, mRNA. [Source:RefSeq mRNA;Acc:NM_001144842]

Sequence

>retro_sscr_444
AGGGCGGGGGTCCTGGGAGTCCAATGGCTGCAAAGGGCAGCCCGGAACACGGTGCCATTGGATGCACATACAGCCTCCCA
TATTACCAGGGACATGCTCCCAGGACCCAATTCCAAGACCCCAGAAGAATGGGTTGCTGCTGCTAAGAAGCATAATATGC
AGGTAGAAGACTATGGGCCCTACCCAGATGATGGCCTGGGGTATGGTGACTACCTGAAGATCCTTGACTGCTCACAGCAG
GAGAGGCATCCTGGTATGACTGGGACCACCCAGACCTGTGGTTGAACTGGGGTGAACCAATGCTCTGGGACCTAGACATG
TATATCAGGAACCGTGTGTATACATCCCCGGCTCCTGTTTCTTGGAATTTCATGTGTAAGCACTTCTTTGGCTTCGTGCC
GTTCATGCTGTTCATGTTTTGAGTAGGGGAGACTTACCCCATGGAGCCAAAGCAGTATCCTTACGATGATCTGTACCTAG
AACAAGGCTTCCATCCCACCAAAGAACCTGGGCTAGTGGTTCACTATGAGATC

Alignment

ORF - retro_sscr_444 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.41 %
• Parental protein coverage: 97.85 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KAGVLGVRWLQRAARKVVPLGARTASHVTKDMFPGPYPKTPEERAAAAKKYNMRVEDYEPYPDDGMGYGD
          .AGVLGV.WLQRAAR..VPL.A.TASH.T.DM.PGP..KTPEE..AAAKK.NM.VEDY.PYPDDG.GYGD
Retrocopy RAGVLGVQWLQRAARNTVPLDAHTASHITRDMLPGPNSKTPEEWVAAAKKHNMQVEDYGPYPDDGLGYGD

Parental  YPKLPDRSQQERDP-WYDWDHPDLRLNWGEPIHWDLDMYIRNRVDTSPTPVSWNTMCKHLFGFVAFMLFM
          Y.K..D.SQQER.P.WYDWDHPDL.LNWGEP..WDLDMYIRNRV.TSP.PVSWN.MCKH.FGFV.FMLFM
Retrocopy YLKILDCSQQERHP<WYDWDHPDLWLNWGEPMLWDLDMYIRNRVYTSPAPVSWNFMCKHFFGFVPFMLFM

Parental  FWVGEIYPSYQPVGPKQYPYNDLYLERGGDPTKEPEPVVHYEI
          F.VGE.YP......PKQYPY.DLYLE.G..PTKEP..VVHYEI
Retrocopy F*VGETYP----MEPKQYPYDDLYLEQGFHPTKEPGLVVHYEI

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	32.25 RPM
SRP014902_testis	0.00 RPM	36.63 RPM
SRP018288_heart	0.00 RPM	142.15 RPM
SRP018288_kidney	0.00 RPM	121.26 RPM
SRP018288_liver	0.00 RPM	57.25 RPM
SRP018288_lung	0.00 RPM	30.96 RPM
SRP018856_adipose	0.00 RPM	92.84 RPM
SRP035408_brain	0.00 RPM	36.68 RPM
SRP035408_liver	0.00 RPM	27.01 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_444 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_444 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_444 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006651	3 retrocopies	retro_amel_1460, retro_amel_1467, retro_amel_931,
Bos taurus	ENSBTAG00000000091	1 retrocopy	retro_btau_1844,
Canis familiaris	ENSCAFG00000009698	2 retrocopies	retro_cfam_1405, retro_cfam_1947,
Callithrix jacchus	ENSCJAG00000037906	1 retrocopy	retro_cjac_870,
Dasypus novemcinctus	ENSDNOG00000003661	1 retrocopy	retro_dnov_65,
Felis catus	ENSFCAG00000006453	2 retrocopies	retro_fcat_501, retro_fcat_856,
Homo sapiens	ENSG00000166136	3 retrocopies	retro_hsap_1363, retro_hsap_1772, retro_hsap_770,
Gorilla gorilla	ENSGGOG00000027239	3 retrocopies	retro_ggor_1062, retro_ggor_2240, retro_ggor_639,
Microcebus murinus	ENSMICG00000001341	1 retrocopy	retro_mmur_859,
Myotis lucifugus	ENSMLUG00000015094	1 retrocopy	retro_mluc_1830,
Macaca mulatta	ENSMMUG00000006636	5 retrocopies	retro_mmul_1098, retro_mmul_1232, retro_mmul_1620, retro_mmul_415, retro_mmul_753,
Monodelphis domestica	ENSMODG00000019356	1 retrocopy	retro_mdom_1543,
Mustela putorius furo	ENSMPUG00000016959	1 retrocopy	retro_mputfur_1259,
Mus musculus	ENSMUSG00000025204	2 retrocopies	retro_mmus_1995, retro_mmus_2909,
Nomascus leucogenys	ENSNLEG00000014774	3 retrocopies	retro_nleu_1068, retro_nleu_2810, retro_nleu_398,
Otolemur garnettii	ENSOGAG00000030711	3 retrocopies	retro_ogar_1237, retro_ogar_152, retro_ogar_2593,
Pongo abelii	ENSPPYG00000002570	3 retrocopies	retro_pabe_1131, retro_pabe_1541, retro_pabe_756,
Pan troglodytes	ENSPTRG00000002851	3 retrocopies	retro_ptro_1186, retro_ptro_539, retro_ptro_936,
Sus scrofa	ENSSSCG00000006166	2 retrocopies	retro_sscr_1092, retro_sscr_444 ,
Tupaia belangeri	ENSTBEG00000000209	8 retrocopies	retro_tbel_1872, retro_tbel_2950, retro_tbel_3122, retro_tbel_322, retro_tbel_3696, retro_tbel_4042, retro_tbel_4718, retro_tbel_540,