RetrogeneDB ID: retro_sscr_938

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 7:62178158..62178398(-)
• Located in intron of: ENSSSCG00000001869

Retrocopy information

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

Parental gene information

• Parental gene symbol: COX7B
• Ensembl ID: ENSSSCG00000030970
• Aliases: None
• Description: cytochrome c oxidase subunit VIIb [Source:HGNC Symbol;Acc:2291]

Sequence

>retro_sscr_938
ATGTTTCCCTCAGCCAAAAATGCACTAAGTCGTCTTGGAGTTCGAAACATTCAGCAAACAATGGCAAGGCAGAACCACCA
GAAGTGGGCACTTGATTTCCATGACAAATATGGTAATGCTGTATTAGCTAGTGGAGCCACTTTCTGTGTTGCTGTATGGG
CATATACAGCAACACAAATTGGAATAGAATGGAACCTGTCCCCTATTGGCAGAGTCACCCCAAAGGAATGGAGAGAAGAA

Alignment

ORF - retro_sscr_938 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.5 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MFPLAKNALSRLRVRNIQQTMARQNHQKRAPDFHDKYGNAILASGATFCVAVWAYTATQIGIEWNLSPVG
          MFP.AKNALSRL.VRNIQQTMARQNHQK.A.DFHDKYGNA.LASGATFCVAVWAYTATQIGIEWNLSP.G
Retrocopy MFPSAKNALSRLGVRNIQQTMARQNHQKWALDFHDKYGNAVLASGATFCVAVWAYTATQIGIEWNLSPIG

Parental  RVTPKEWREE
          RVTPKEWREE
Retrocopy RVTPKEWREE

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	41.28 RPM
SRP014902_testis	0.14 RPM	40.88 RPM
SRP018288_heart	0.21 RPM	306.91 RPM
SRP018288_kidney	1.58 RPM	338.76 RPM
SRP018288_liver	1.28 RPM	162.47 RPM
SRP018288_lung	0.00 RPM	35.74 RPM
SRP018856_adipose	0.00 RPM	70.34 RPM
SRP035408_brain	0.16 RPM	177.26 RPM
SRP035408_liver	0.00 RPM	207.78 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_938 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_938 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_938 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 101 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006153	6 retrocopies	retro_amel_25, retro_amel_313, retro_amel_459, retro_amel_484, retro_amel_669, retro_amel_807,
Bos taurus	ENSBTAG00000047768	3 retrocopies	retro_btau_214, retro_btau_22, retro_btau_59,
Callithrix jacchus	ENSCJAG00000004045	5 retrocopies	retro_cjac_2496, retro_cjac_2716, retro_cjac_345, retro_cjac_844, retro_cjac_973,
Cavia porcellus	ENSCPOG00000014781	2 retrocopies	retro_cpor_117, retro_cpor_252,
Echinops telfairi	ENSETEG00000016695	9 retrocopies	retro_etel_1049, retro_etel_1180, retro_etel_1651, retro_etel_1736, retro_etel_1805, retro_etel_2057, retro_etel_59, retro_etel_860, retro_etel_910,
Felis catus	ENSFCAG00000023091	2 retrocopies	retro_fcat_534, retro_fcat_590,
Homo sapiens	ENSG00000131174	4 retrocopies	retro_hsap_157, retro_hsap_16, retro_hsap_2305, retro_hsap_920,
Gorilla gorilla	ENSGGOG00000023347	9 retrocopies	retro_ggor_1539, retro_ggor_1617, retro_ggor_1634, retro_ggor_1707, retro_ggor_1779, retro_ggor_245, retro_ggor_443, retro_ggor_52, retro_ggor_579,
Loxodonta africana	ENSLAFG00000022996	4 retrocopies	retro_lafr_27, retro_lafr_555, retro_lafr_716, retro_lafr_927,
Microcebus murinus	ENSMICG00000014521	3 retrocopies	retro_mmur_256, retro_mmur_379, retro_mmur_56,
Myotis lucifugus	ENSMLUG00000022443	3 retrocopies	retro_mluc_1491, retro_mluc_2521, retro_mluc_277,
Macaca mulatta	ENSMMUG00000015861	5 retrocopies	retro_mmul_1120, retro_mmul_1941, retro_mmul_2400, retro_mmul_571, retro_mmul_800,
Mus musculus	ENSMUSG00000031231	5 retrocopies	retro_mmus_195, retro_mmus_2062, retro_mmus_2157, retro_mmus_2731, retro_mmus_502,
Pongo abelii	ENSPPYG00000020494	18 retrocopies	retro_pabe_1824, retro_pabe_1904, retro_pabe_2016, retro_pabe_2017, retro_pabe_2025, retro_pabe_2026, retro_pabe_2028, retro_pabe_2029, retro_pabe_2030, retro_pabe_2034, retro_pabe_2038, retro_pabe_2121, retro_pabe_22, retro_pabe_270, retro_pabe_465, retro_pabe_587, retro_pabe_793, retro_pabe_836,
Pan troglodytes	ENSPTRG00000022049	9 retrocopies	retro_ptro_12, retro_ptro_1431, retro_ptro_1510, retro_ptro_153, retro_ptro_1629, retro_ptro_1714, retro_ptro_3014, retro_ptro_349, retro_ptro_760,
Pteropus vampyrus	ENSPVAG00000003237	2 retrocopies	retro_pvam_1, retro_pvam_1234,
Rattus norvegicus	ENSRNOG00000028451	5 retrocopies	retro_rnor_2351, retro_rnor_2387, retro_rnor_2959, retro_rnor_763, retro_rnor_999,
Sus scrofa	ENSSSCG00000030970	2 retrocopies	retro_sscr_938 , retro_sscr_991,
Tursiops truncatus	ENSTTRG00000004387	3 retrocopies	retro_ttru_1097, retro_ttru_556, retro_ttru_7,
Vicugna pacos	ENSVPAG00000001324	2 retrocopies	retro_vpac_7, retro_vpac_87,