RetrogeneDB ID: retro_sscr_1061

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 9:73756204..73756630(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SDHC
• Ensembl ID: ENSSSCG00000030318
• Aliases: SDHC, CYBL
• Description: Succinate dehydrogenase cytochrome b560 subunit, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:D0VWV4]

Sequence

>retro_sscr_1061
GCTATTTCTTTGGGAACCCCAGCCTAAGAAGAGAAGGTAGAGCTTCTGGAATAAGAACACCAGTTCAAACGATCCTTTGT
CTCCCCATTTCACTATCTACAGCTGGTCTCTTCCCATGGCGATGTCCATTTGCCACCACGGCACTGGTATTTCCTTGAGT
GCAGGGGTGTCTCTCTTTGGTTTGTCAGCCCTCTTGTTTCCTGGAAACTTTGGATCTCTTTTGAACTTGTGAGTCCCTGT
GTTTGGGGCCAGCATTATTTCCACAGCCAAATTTGCACTTGTCTTCCCTTTCATGTATCACACCCAGGATGGGATCTGAC
ACTTGATGTGGGACCTATGAAAAGGCCTGATGATTTCCCAGCTACCCCAGGCTGGAGTGGTTGCACTGGTTCTTACTGTG
TTGTCCTCTGAGGAGTGGCAGCCATG

Alignment

ORF - retro_sscr_1061 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.28 %
• Parental protein coverage: 84.62 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AVPLGTTAKEEMER-FWNKNLGSNRPLSPHITIYRWSLPMAMSICHRGTGIALSAGVSLFGLSALLLPGN
          A..LGT.A.EE....FWNKN..SN.PLSPH.TIY.WSLPMAMSICH.GTGI.LSAGVSLFGLSALL.PGN
Retrocopy AISLGTPA*EEKVE>FWNKNTSSNDPLSPHFTIYSWSLPMAMSICHHGTGISLSAGVSLFGLSALLFPGN

Parental  FESHLELVKSLCLGPTLIYTAKFGIVFPLMYHTWNGIRHLIWDLGKGLTIPQLTQSGVVVLILTVLSSV-
          F.S.L.L......G...I.TAKF..VFP.MYHT..GI.HL.WDL.KGL.I.QL.Q.GVV.L.LTVLSS..
Retrocopy FGSLLNL*VPV-FGASIISTAKFALVFPFMYHTQDGI*HLMWDL*KGLMISQLPQAGVVALVLTVLSSE<

Parental  GLAAM
          G.AAM
Retrocopy GVAAM

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	21.24 RPM
SRP014902_testis	0.00 RPM	47.81 RPM
SRP018288_heart	0.00 RPM	158.26 RPM
SRP018288_kidney	0.00 RPM	436.97 RPM
SRP018288_liver	0.00 RPM	181.50 RPM
SRP018288_lung	0.00 RPM	28.21 RPM
SRP018856_adipose	0.00 RPM	142.44 RPM
SRP035408_brain	0.00 RPM	95.98 RPM
SRP035408_liver	0.00 RPM	273.27 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1061 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1061 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1061 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015351	2 retrocopies	retro_amel_468, retro_amel_803,
Bos taurus	ENSBTAG00000015853	1 retrocopy	retro_btau_835,
Canis familiaris	ENSCAFG00000012992	2 retrocopies	retro_cfam_1529, retro_cfam_275,
Callithrix jacchus	ENSCJAG00000004757	3 retrocopies	retro_cjac_1119, retro_cjac_2455, retro_cjac_988,
Echinops telfairi	ENSETEG00000015767	1 retrocopy	retro_etel_675,
Felis catus	ENSFCAG00000000499	1 retrocopy	retro_fcat_1609,
Homo sapiens	ENSG00000143252	4 retrocopies	retro_hsap_1794, retro_hsap_1896, retro_hsap_609, retro_hsap_854,
Gorilla gorilla	ENSGGOG00000008017	3 retrocopies	retro_ggor_1390, retro_ggor_536, retro_ggor_697,
Macaca mulatta	ENSMMUG00000012411	11 retrocopies	retro_mmul_1063, retro_mmul_1323, retro_mmul_1338, retro_mmul_1686, retro_mmul_1845, retro_mmul_2002, retro_mmul_2087, retro_mmul_239, retro_mmul_2416, retro_mmul_369, retro_mmul_672,
Mustela putorius furo	ENSMPUG00000014439	1 retrocopy	retro_mputfur_1201,
Nomascus leucogenys	ENSNLEG00000014367	3 retrocopies	retro_nleu_1476, retro_nleu_420, retro_nleu_439,
Pan troglodytes	ENSPTRG00000001585	4 retrocopies	retro_ptro_1274, retro_ptro_2458, retro_ptro_449, retro_ptro_593,
Pteropus vampyrus	ENSPVAG00000005544	2 retrocopies	retro_pvam_879, retro_pvam_974,
Rattus norvegicus	ENSRNOG00000003163	2 retrocopies	retro_rnor_1486, retro_rnor_1487,
Sarcophilus harrisii	ENSSHAG00000016835	1 retrocopy	retro_shar_205,
Sus scrofa	ENSSSCG00000030318	2 retrocopies	retro_sscr_1050, retro_sscr_1061 ,
Takifugu rubripes	ENSTRUG00000001873	1 retrocopy	retro_trub_41,
Tursiops truncatus	ENSTTRG00000009234	1 retrocopy	retro_ttru_196,