RetrogeneDB ID: retro_sscr_627

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 2:73879504..73879839(+)
• Located in intron of: ENSSSCG00000013522

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000015034
• Aliases: SDHD, CII-4, CybS, QPs3
• Description: Sus scrofa succinate dehydrogenase complex, subunit D, integral membrane protein (SDHD), nuclear gene encoding mitochondrial protein, mRNA. [Source:RefSeq mRNA;Acc:NM_001097516]

Sequence

>retro_sscr_627
ATGGCGACTCTCTGGAGGCTGAGCACCCTCTGTGGGGCCCAAAAAGGAGGAGCTCTGTTCCTCTGAACCCCGGTGGTCAA
ACCTGCTCATGTCTCAGCATTTCTCCGGAGCCGACCTTCCGGGGGATGGTGTGGAATGCAGCACATTCACCTGTCACCCA
GCCACCAGTCTGATTCCAAGGCTGCATCTCTCCACTGGACTGGCAAGAGGGCTGTCAGCGTTTTGCTCCTGGGCCTATTT
CCAGCGGCTTATTTGAATCCTTGCTCGGCAATGGACTACCCTCTGGCCACAGCCCTCACTCTCCATGTCACTGGGACACT
GGACAAGTTGTTACT

Alignment

ORF - retro_sscr_627 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.88 %
• Parental protein coverage: 70.44 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MATLWRLSVLCGPRGGGALVLRTSVVRPAHVSAFLQDRHTPGWCGVQHIHLSPSHQASSKAASLHWTGER
          MATLWRLS.LCG...GGAL.L.T.VV.PAHVSAFL..R...GWCG.QHIHLSPSHQ..SKAASLHWTG.R
Retrocopy MATLWRLSTLCGAQKGGALFL*TPVVKPAHVSAFLRSRPSGGWCGMQHIHLSPSHQSDSKAASLHWTGKR

Parental  VVSVLLLGLLPAAYLNPCSAMDYSLAAALTLH-GHWGIGQVVT
          .VSVLLLGL.PAAYLNPCSAMDY.LA.ALTLH..HW..GQVVT
Retrocopy AVSVLLLGLFPAAYLNPCSAMDYPLATALTLH<CHWDTGQVVT

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	47.92 RPM
SRP014902_testis	0.00 RPM	37.62 RPM
SRP018288_heart	0.00 RPM	234.72 RPM
SRP018288_kidney	0.00 RPM	260.25 RPM
SRP018288_liver	0.00 RPM	149.84 RPM
SRP018288_lung	0.10 RPM	34.42 RPM
SRP018856_adipose	0.00 RPM	112.71 RPM
SRP035408_brain	0.00 RPM	58.88 RPM
SRP035408_liver	0.00 RPM	114.78 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_627 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_627 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_627 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004066	3 retrocopies	retro_amel_1556, retro_amel_1588, retro_amel_998,
Erinaceus europaeus	ENSEEUG00000013091	1 retrocopy	retro_eeur_336,
Echinops telfairi	ENSETEG00000008424	1 retrocopy	retro_etel_252,
Felis catus	ENSFCAG00000022580	3 retrocopies	retro_fcat_1371, retro_fcat_175, retro_fcat_492,
Homo sapiens	ENSG00000204370	8 retrocopies	retro_hsap_124, retro_hsap_1912, retro_hsap_2132, retro_hsap_2182, retro_hsap_2729, retro_hsap_2784, retro_hsap_355, retro_hsap_3791,
Gorilla gorilla	ENSGGOG00000026496	1 retrocopy	retro_ggor_50,
Loxodonta africana	ENSLAFG00000002763	1 retrocopy	retro_lafr_432,
Myotis lucifugus	ENSMLUG00000012228	3 retrocopies	retro_mluc_2418, retro_mluc_457, retro_mluc_756,
Macaca mulatta	ENSMMUG00000015247	1 retrocopy	retro_mmul_224,
Rattus norvegicus	ENSRNOG00000022980	3 retrocopies	retro_rnor_1529, retro_rnor_1686, retro_rnor_744,
Sus scrofa	ENSSSCG00000015034	3 retrocopies	retro_sscr_1060, retro_sscr_626, retro_sscr_627 ,
Tursiops truncatus	ENSTTRG00000010520	5 retrocopies	retro_ttru_1554, retro_ttru_238, retro_ttru_616, retro_ttru_633, retro_ttru_885,