RetrogeneDB ID: retro_sscr_822

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 5:59188004..59188319(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000000596
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CETN2
• Ensembl ID: ENSSSCG00000012757
• Aliases: None
• Description: centrin, EF-hand protein, 2 [Source:HGNC Symbol;Acc:1867]

Sequence

>retro_sscr_822
AAGGCAAATATGGCACCAACTGTCCAGTGAAAAAGGATGAGTCCTAAACCAGAACCTACTGAGGAGCAGAAACAGGAAAT
CTAGGAAGCTTTTGATCTCTTTGATATTGATTGAGCTGGGACAATAGATGCTAAGAAACTTAAGGTGACAATGAGAGTGC
TAGGCTCTGAGCCCAAGAAAGAAGAGATCAAGAAAATAAGTGAATTTTACAAGGAAGGGACAGGAAAAATGAACTTCATT
GAATTTTTGACTGTTAGGGCTCAGAAAATGTCTGAGAAATATATCAAAGAAGAAATCCAAAAAGCTGGGAAGATA

Alignment

ORF - retro_sscr_822 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.58 %
• Parental protein coverage: 61.63 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KTNVASAAQRKRMSPKPELTEEQKQEIREAFDLFDADGTGTIDVKELKVAMRALGFEPKKEEIKKMISEI
          K.N.A...Q.KRMSPKPE.TEEQKQEI.EAFDLFD.D..GTID.K.LKV.MR.LG.EPKKEEIKK.ISE.
Retrocopy KANMAPTVQ*KRMSPKPEPTEEQKQEI*EAFDLFDID*AGTIDAKKLKVTMRVLGSEPKKEEIKK-ISEF

Parental  DKEGTGKMNFSDFLTVMTQKMSEKDTKEEILKAFKL
          .KEGTGKMNF..FLTV..QKMSEK..KEEI.KA.K.
Retrocopy YKEGTGKMNFIEFLTVRAQKMSEKYIKEEIQKAGKI

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	7.96 RPM
SRP014902_testis	0.00 RPM	29.99 RPM
SRP018288_heart	0.00 RPM	33.71 RPM
SRP018288_kidney	0.00 RPM	44.33 RPM
SRP018288_liver	0.00 RPM	35.50 RPM
SRP018288_lung	0.00 RPM	54.99 RPM
SRP018856_adipose	0.00 RPM	50.47 RPM
SRP035408_brain	0.00 RPM	72.73 RPM
SRP035408_liver	0.00 RPM	77.94 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_822 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_822 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_822 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 28 parental genes, and 44 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000364	1 retrocopy	retro_amel_56,
Bos taurus	ENSBTAG00000007844	1 retrocopy	retro_btau_170,
Canis familiaris	ENSCAFG00000019170	1 retrocopy	retro_cfam_199,
Choloepus hoffmanni	ENSCHOG00000010244	1 retrocopy	retro_chof_39,
Callithrix jacchus	ENSCJAG00000016338	3 retrocopies	retro_cjac_106, retro_cjac_185, retro_cjac_316,
Cavia porcellus	ENSCPOG00000012081	2 retrocopies	retro_cpor_1250, retro_cpor_21,
Equus caballus	ENSECAG00000000796	1 retrocopy	retro_ecab_49,
Felis catus	ENSFCAG00000004901	1 retrocopy	retro_fcat_47,
Homo sapiens	ENSG00000147400	1 retrocopy	retro_hsap_71,
Gorilla gorilla	ENSGGOG00000011378	1 retrocopy	retro_ggor_74,
Loxodonta africana	ENSLAFG00000014424	1 retrocopy	retro_lafr_121,
Microcebus murinus	ENSMICG00000005862	2 retrocopies	retro_mmur_122, retro_mmur_21,
Myotis lucifugus	ENSMLUG00000014520	2 retrocopies	retro_mluc_320, retro_mluc_370,
Macaca mulatta	ENSMMUG00000020743	2 retrocopies	retro_mmul_1127, retro_mmul_176,
Mustela putorius furo	ENSMPUG00000011858	1 retrocopy	retro_mputfur_386,
Mus musculus	ENSMUSG00000031347	2 retrocopies	retro_mmus_107, retro_mmus_838,
Nomascus leucogenys	ENSNLEG00000013860	1 retrocopy	retro_nleu_1221,
Oryctolagus cuniculus	ENSOCUG00000007897	1 retrocopy	retro_ocun_180,
Otolemur garnettii	ENSOGAG00000005301	1 retrocopy	retro_ogar_236,
Procavia capensis	ENSPCAG00000003203	1 retrocopy	retro_pcap_149,
Procavia capensis	ENSPCAG00000007778	1 retrocopy	retro_pcap_364,
Pongo abelii	ENSPPYG00000020833	1 retrocopy	retro_pabe_58,
Pan troglodytes	ENSPTRG00000022389	1 retrocopy	retro_ptro_108,
Rattus norvegicus	ENSRNOG00000017059	5 retrocopies	retro_rnor_2376, retro_rnor_2394, retro_rnor_2920, retro_rnor_304, retro_rnor_775,
Sus scrofa	ENSSSCG00000012757	3 retrocopies	retro_sscr_1175, retro_sscr_57, retro_sscr_822 ,
Ictidomys tridecemlineatus	ENSSTOG00000023853	2 retrocopies	retro_itri_636, retro_itri_91,
Tarsius syrichta	ENSTSYG00000003831	2 retrocopies	retro_tsyr_1142, retro_tsyr_36,
Tursiops truncatus	ENSTTRG00000001236	2 retrocopies	retro_ttru_32, retro_ttru_335,