RetrogeneDB ID: retro_sscr_659

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 2:10609954..10610636(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ADH5
• Ensembl ID: ENSSSCG00000009185
• Aliases: None
• Description: alcohol dehydrogenase 5 (class III), chi polypeptide [Source:HGNC Symbol;Acc:253]

Sequence

>retro_sscr_659
ATGGTGTATCAGGTCATCAAGTGCAGGGCTATGGGTGTCTGGGAGGCTGGAAAGCCTCTCTCCATAGAGGAGATAGAGGT
GGCATCCCCAAAGGCTCATGAAGTTCGAATTAAGATTATTGCTACTGCAGTTTGCCACACTGATGCCCACACCCTGAGTG
GGGCTGATCCTGAAGGGAGTTTTCCAGTGATCTTGGGACATGAAGGTGATAGAATTGTGGAAAGTGTTGGTGAAGGAGTT
ACTAAGCTAAAGGCAGGTGATTCTGTCATCCCACTTTACATCTCACAGTGTGGAGAATGCAAATTTTGTCTAAATCATAA
AACAAACCTTTGCCAGAAAATAAGAGTCACTCAAGGGAAAGGTTTAATGCCAGATGGCACTAGCAGATTTACTTGTAAAG
GAAAGACAATTTTACATTACATGGGAACCAGCACCTTTTCTGAATGCACAGTGTGGCTGATAAATCTGTGACTAAAATTG
ATCCTTTGGCCCCTGTGGATAAAGTGTGCCTCTGGGTTGTGGCATTTCAACTGGTTATGGTGCTGCTGTGAACACTGCCA
AGGTGGAGCCTGGCTCTACTTGTGCTGTCTGTGGCCTGGGAGGAGTTGGATTGGCAGTTATCATGGGCCGTAAGGTAGTT
GGTGTATCCTGGATCATTGGTGTGGACATCAATAAAGATAAA

Alignment

ORF - retro_sscr_659 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.13 %
• Parental protein coverage: 60.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MANQVIKCKAAVAWEAGKPLSIEEIEVAPPKAHEVRIKIIATAVCHTDAYTLSGADPEGSFPVILGHEGA
          M..QVIKC.A...WEAGKPLSIEEIEVA.PKAHEVRIKIIATAVCHTDA.TLSGADPEGSFPVILGHEG.
Retrocopy MVYQVIKCRAMGVWEAGKPLSIEEIEVASPKAHEVRIKIIATAVCHTDAHTLSGADPEGSFPVILGHEGD

Parental  GIVESVGEGVTKLKAGDTVIPLYIPQCGECKFCLNPKTNLCQKIRVTQGKGLMPDGTSRFTCKGKTILHY
          .IVESVGEGVTKLKAGD.VIPLYI.QCGECKFCLN.KTNLCQKIRVTQGKGLMPDGTSRFTCKGKTILHY
Retrocopy RIVESVGEGVTKLKAGDSVIPLYISQCGECKFCLNHKTNLCQKIRVTQGKGLMPDGTSRFTCKGKTILHY

Parental  MGTSTFSEYTV-VADISVAKIDPLAPLDKVCL-LGCGVSTGYGAAVNTAKVEPGSTCAVFGLGGVGLAVI
          MGTSTFSE.TV.VAD.SV.KIDPLAP.DKVCL.LGCG.STGYGAAVNTAKVEPGSTCAV.GLGGVGLAVI
Retrocopy MGTSTFSECTV<VADKSVTKIDPLAPVDKVCL<LGCGISTGYGAAVNTAKVEPGSTCAVCGLGGVGLAVI

Parental  MGCKVAGASRIIGVDINKDK
          MG.KV.G.S.IIGVDINKDK
Retrocopy MGRKVVGVSWIIGVDINKDK

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	30.26 RPM
SRP014902_testis	0.00 RPM	98.87 RPM
SRP018288_heart	0.00 RPM	53.17 RPM
SRP018288_kidney	0.49 RPM	263.60 RPM
SRP018288_liver	0.48 RPM	157.83 RPM
SRP018288_lung	0.00 RPM	34.32 RPM
SRP018856_adipose	0.00 RPM	127.16 RPM
SRP035408_brain	0.00 RPM	62.38 RPM
SRP035408_liver	0.03 RPM	204.87 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_659 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_659 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_659 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013007	1 retrocopy	retro_cfam_14,
Callithrix jacchus	ENSCJAG00000007198	2 retrocopies	retro_cjac_1029, retro_cjac_2933,
Homo sapiens	ENSG00000197894	3 retrocopies	retro_hsap_175, retro_hsap_330, retro_hsap_3607,
Gorilla gorilla	ENSGGOG00000028244	2 retrocopies	retro_ggor_2434, retro_ggor_354,
Myotis lucifugus	ENSMLUG00000002722	1 retrocopy	retro_mluc_1702,
Macaca mulatta	ENSMMUG00000003552	1 retrocopy	retro_mmul_299,
Mustela putorius furo	ENSMPUG00000009642	1 retrocopy	retro_mputfur_1625,
Nomascus leucogenys	ENSNLEG00000013946	3 retrocopies	retro_nleu_1772, retro_nleu_2636, retro_nleu_983,
Pongo abelii	ENSPPYG00000014946	3 retrocopies	retro_pabe_176, retro_pabe_359, retro_pabe_453,
Pan troglodytes	ENSPTRG00000016303	3 retrocopies	retro_ptro_166, retro_ptro_2438, retro_ptro_266,
Sus scrofa	ENSSSCG00000009185	1 retrocopy	retro_sscr_659 ,
Xenopus tropicalis	ENSXETG00000009304	1 retrocopy	retro_xtro_57,