RetrogeneDB ID: retro_sscr_802

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 5:68138251..68138499(+)
• Located in intron of: ENSSSCG00000000723

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFA12
• Ensembl ID: ENSSSCG00000000905
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 12 [Source:HGNC Symbol;Acc:23987]

Sequence

>retro_sscr_802
TTGGCACTGGTCCTGAAGCGCGGGCTGCAGCAGGTCAGCGGCCCCGGCGGGCTCCGCGGCTCGCTATAGGTTCTCTTCAG
GGCAGATGAGGTGAGAGTTGGTACGCGAGTAGGGGAAGACAAATATGGAAACAAATACCATGAAGACAGCAAGCAGTTTT
TTGGCCATCACCATGGGTTATACATACTACTGAGATGAATGGCAAAAACACGTTCTGGGATGTAGATGGAAGCATGGTGC
CCCCTGAA

Alignment

ORF - retro_sscr_802 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.76 %
• Parental protein coverage: 56.46 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LVQVLRRGLQQVSGHGGLRGYLRVLFRANDVRVGTLVGEDKYGNKYYEDNKQFFGRHR-WVIYTTEMNGR
          L..VL.RGLQQVSG.GGLRG.L.VLFRA..VRVGT.VGEDKYGNKY.ED.KQFFG.H..WVI.TTEMNG.
Retrocopy LALVLKRGLQQVSGPGGLRGSL*VLFRADEVRVGTRVGEDKYGNKYHEDSKQFFGHHH<WVIHTTEMNGK

Parental  DTFWDVDGSMVPPE
          .TFWDVDGSMVPPE
Retrocopy NTFWDVDGSMVPPE

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	32.78 RPM
SRP014902_testis	0.57 RPM	42.29 RPM
SRP018288_heart	0.08 RPM	169.79 RPM
SRP018288_kidney	0.10 RPM	111.41 RPM
SRP018288_liver	0.16 RPM	29.58 RPM
SRP018288_lung	0.20 RPM	16.80 RPM
SRP018856_adipose	0.40 RPM	90.11 RPM
SRP035408_brain	0.00 RPM	96.52 RPM
SRP035408_liver	0.00 RPM	59.36 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_802 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_802 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_802 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 28 parental genes, and 61 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002294	2 retrocopies	retro_amel_1069, retro_amel_1414,
Bos taurus	ENSBTAG00000014669	4 retrocopies	retro_btau_1294, retro_btau_1377, retro_btau_1449, retro_btau_869,
Choloepus hoffmanni	ENSCHOG00000007134	2 retrocopies	retro_chof_2234, retro_chof_2322,
Callithrix jacchus	ENSCJAG00000002846	2 retrocopies	retro_cjac_1796, retro_cjac_1862,
Cavia porcellus	ENSCPOG00000010154	2 retrocopies	retro_cpor_1326, retro_cpor_650,
Dasypus novemcinctus	ENSDNOG00000009192	1 retrocopy	retro_dnov_1859,
Equus caballus	ENSECAG00000015836	1 retrocopy	retro_ecab_910,
Echinops telfairi	ENSETEG00000010118	2 retrocopies	retro_etel_1401, retro_etel_787,
Felis catus	ENSFCAG00000023050	3 retrocopies	retro_fcat_1283, retro_fcat_1483, retro_fcat_362,
Homo sapiens	ENSG00000184752	3 retrocopies	retro_hsap_1293, retro_hsap_3199, retro_hsap_3312,
Gorilla gorilla	ENSGGOG00000012880	1 retrocopy	retro_ggor_1015,
Loxodonta africana	ENSLAFG00000030887	1 retrocopy	retro_lafr_671,
Microcebus murinus	ENSMICG00000008634	3 retrocopies	retro_mmur_1630, retro_mmur_224, retro_mmur_544,
Myotis lucifugus	ENSMLUG00000027131	1 retrocopy	retro_mluc_908,
Macaca mulatta	ENSMMUG00000018897	1 retrocopy	retro_mmul_1321,
Mustela putorius furo	ENSMPUG00000007354	1 retrocopy	retro_mputfur_1257,
Mus musculus	ENSMUSG00000020022	1 retrocopy	retro_mmus_2605,
Nomascus leucogenys	ENSNLEG00000005766	2 retrocopies	retro_nleu_2105, retro_nleu_2756,
Otolemur garnettii	ENSOGAG00000010853	5 retrocopies	retro_ogar_1158, retro_ogar_1310, retro_ogar_2943, retro_ogar_455, retro_ogar_896,
Pongo abelii	ENSPPYG00000004839	2 retrocopies	retro_pabe_1071, retro_pabe_2652,
Pan troglodytes	ENSPTRG00000005306	2 retrocopies	retro_ptro_2159, retro_ptro_885,
Pteropus vampyrus	ENSPVAG00000007564	5 retrocopies	retro_pvam_1141, retro_pvam_1457, retro_pvam_33, retro_pvam_375, retro_pvam_661,
Rattus norvegicus	ENSRNOG00000007407	1 retrocopy	retro_rnor_874,
Sorex araneus	ENSSARG00000013220	1 retrocopy	retro_sara_442,
Sus scrofa	ENSSSCG00000000905	1 retrocopy	retro_sscr_802 ,
Tupaia belangeri	ENSTBEG00000013724	8 retrocopies	retro_tbel_1707, retro_tbel_2577, retro_tbel_2822, retro_tbel_2888, retro_tbel_3320, retro_tbel_3566, retro_tbel_4553, retro_tbel_4577,
Tursiops truncatus	ENSTTRG00000015720	2 retrocopies	retro_ttru_1607, retro_ttru_1880,
Vicugna pacos	ENSVPAG00000008508	1 retrocopy	retro_vpac_332,