RetrogeneDB ID: retro_sscr_642

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 2:124473177..124473423(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFA4
• Ensembl ID: ENSSSCG00000024313
• Aliases: None
• Description: Sus scrofa NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 4, 9kDa (NDUFA4), nuclear gene encoding mitochondrial protein, mRNA. [Source:RefSeq mRNA;Acc:NM_001097468]

Sequence

>retro_sscr_642
ATACTCCACCAGATCATCAGTCAGGCTAAGAAGCATCCTAGCTTGATCCCCCTCTTCATATTTATTGGTGCAGGAGGTAC
TGCAGCAGCACTGTATGTCATGGGCCTAGCACTGTTCAATCCAGATATCAGTTGGGACAGGAAGAATAACCCAGAACCCT
AGAATAAACTGGGTGCCAGTGATCAATACAAGTTCTTAGCAGTGCATGGAGATTACAGCAAACTGAAGAAAGAAGATCTG
GACTTC

Alignment

ORF - retro_sscr_642 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.27 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLRQIITQAKKHPSLIPLFVFIGAGGTGAALYVTRLALFNPDVCWDRKNNPEPWNKLGPNDQYKFFAVNV
          .L.QII.QAKKHPSLIPLF.FIGAGGT.AALYV..LALFNPD..WDRKNNPEP.NKLG..DQYKF.AV..
Retrocopy ILHQIISQAKKHPSLIPLFIFIGAGGTAAALYVMGLALFNPDISWDRKNNPEP*NKLGASDQYKFLAVHG

Parental  DYSKLKKEGPDF
          DYSKLKKE..DF
Retrocopy DYSKLKKEDLDF

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	58.14 RPM
SRP014902_testis	0.00 RPM	36.92 RPM
SRP018288_heart	0.00 RPM	841.08 RPM
SRP018288_kidney	0.00 RPM	371.66 RPM
SRP018288_liver	0.00 RPM	173.98 RPM
SRP018288_lung	0.00 RPM	54.17 RPM
SRP018856_adipose	0.00 RPM	76.74 RPM
SRP035408_brain	0.00 RPM	162.36 RPM
SRP035408_liver	0.00 RPM	105.92 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_642 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_642 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_642 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 123 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002493	10 retrocopies	retro_amel_1356, retro_amel_1633, retro_amel_18, retro_amel_1800, retro_amel_1866, retro_amel_533, retro_amel_608, retro_amel_638, retro_amel_845, retro_amel_955,
Bos taurus	ENSBTAG00000011145	7 retrocopies	retro_btau_1075, retro_btau_1155, retro_btau_1375, retro_btau_1454, retro_btau_1710, retro_btau_645, retro_btau_800,
Callithrix jacchus	ENSCJAG00000000748	3 retrocopies	retro_cjac_3291, retro_cjac_36, retro_cjac_90,
Equus caballus	ENSECAG00000026987	1 retrocopy	retro_ecab_370,
Felis catus	ENSFCAG00000024790	4 retrocopies	retro_fcat_261, retro_fcat_449, retro_fcat_459, retro_fcat_905,
Gorilla gorilla	ENSGGOG00000001437	3 retrocopies	retro_ggor_249, retro_ggor_30, retro_ggor_567,
Myotis lucifugus	ENSMLUG00000006470	6 retrocopies	retro_mluc_1778, retro_mluc_1821, retro_mluc_329, retro_mluc_450, retro_mluc_517, retro_mluc_849,
Macaca mulatta	ENSMMUG00000020894	2 retrocopies	retro_mmul_272, retro_mmul_274,
Monodelphis domestica	ENSMODG00000014107	2 retrocopies	retro_mdom_1095, retro_mdom_1593,
Mustela putorius furo	ENSMPUG00000014152	8 retrocopies	retro_mputfur_1127, retro_mputfur_1600, retro_mputfur_416, retro_mputfur_696, retro_mputfur_711, retro_mputfur_790, retro_mputfur_827, retro_mputfur_880,
Mus musculus	ENSMUSG00000029632	4 retrocopies	retro_mmus_2172, retro_mmus_3219, retro_mmus_3412, retro_mmus_3620,
Oryctolagus cuniculus	ENSOCUG00000029372	1 retrocopy	retro_ocun_41,
Otolemur garnettii	ENSOGAG00000000358	17 retrocopies	retro_ogar_1023, retro_ogar_1026, retro_ogar_1319, retro_ogar_1403, retro_ogar_1566, retro_ogar_1960, retro_ogar_1976, retro_ogar_2050, retro_ogar_2350, retro_ogar_2528, retro_ogar_3023, retro_ogar_3413, retro_ogar_3434, retro_ogar_3457, retro_ogar_694, retro_ogar_731, retro_ogar_997,
Ochotona princeps	ENSOPRG00000014186	3 retrocopies	retro_opri_1138, retro_opri_275, retro_opri_633,
Pongo abelii	ENSPPYG00000017780	5 retrocopies	retro_pabe_2296, retro_pabe_24, retro_pabe_301, retro_pabe_3339, retro_pabe_678,
Pteropus vampyrus	ENSPVAG00000006660	5 retrocopies	retro_pvam_1092, retro_pvam_1436, retro_pvam_1441, retro_pvam_545, retro_pvam_798,
Rattus norvegicus	ENSRNOG00000005512	3 retrocopies	retro_rnor_1880, retro_rnor_2327, retro_rnor_2985,
Sorex araneus	ENSSARG00000011125	8 retrocopies	retro_sara_160, retro_sara_203, retro_sara_316, retro_sara_339, retro_sara_49, retro_sara_536, retro_sara_659, retro_sara_747,
Sus scrofa	ENSSSCG00000024313	6 retrocopies	retro_sscr_1155, retro_sscr_367, retro_sscr_552, retro_sscr_642 , retro_sscr_682, retro_sscr_733,
Tupaia belangeri	ENSTBEG00000016629	16 retrocopies	retro_tbel_1049, retro_tbel_1848, retro_tbel_2008, retro_tbel_2058, retro_tbel_2194, retro_tbel_2274, retro_tbel_2423, retro_tbel_2761, retro_tbel_3262, retro_tbel_4255, retro_tbel_4309, retro_tbel_436, retro_tbel_4380, retro_tbel_4426, retro_tbel_4719, retro_tbel_815,
Tursiops truncatus	ENSTTRG00000013045	8 retrocopies	retro_ttru_1057, retro_ttru_132, retro_ttru_1709, retro_ttru_1745, retro_ttru_1841, retro_ttru_218, retro_ttru_257, retro_ttru_308,
Vicugna pacos	ENSVPAG00000010003	1 retrocopy	retro_vpac_262,