RetrogeneDB ID: retro_sscr_662

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 2:41395239..41395832(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IDH3G
• Ensembl ID: ENSSSCG00000012783
• Aliases: None
• Description: isocitrate dehydrogenase 3 (NAD+) gamma [Source:HGNC Symbol;Acc:5386]

Sequence

>retro_sscr_662
ATAGCATTGAAGATACTGCCAGCTGCCAGATGCTCTGTGAAAGGCCATGTTCCCACCAGCTATTCAAGGCCATTTTGGAA
AGATTTTCTTGGCTGGGAGATCTAACGGAAGGACCTCTCTTTTAAACACAGCATTCCTCCAGCAGCCAAGCATGGTGGGT
GGCATACTGTGATCACGATTCCTGAGGATGGCATTGGGCCAGAACTTATGTTGCATATTAAGAATGTGTTCAGACATGCA
TGCGTGCCTGTGGACTCTGAGGAGGTGTGGGTTAACGCCACTTCTTGTGAAGAGGAAGTTCACAACGCCATTATGGTGGT
CTGCGGAAACCACATGGACTTGAAGGGCAACTTTGAGACTGCCTACAACCTGCCACCATCTCACAAATCCCAAAACAGTG
GGTTTCACAATACTTTAGATCTCTATGCCAGCGTCATCCATTTTAAGAGTCTTCTAGGTGTGGAGTCTCGCACAAGAACA
TAGATATCTTAGTTGTTTGGAAAAACACAGAGGGTTAATACAGCAACCTGGAACATGAAAGGATGAAAGGAGTGATAGAA
AGCCTTAAGCTCCATTCCTATGCCACTGCCATT

Alignment

ORF - retro_sscr_662 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.0 %
• Parental protein coverage: 50.26 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MALKVATAAGGAAKAVLRPALLCRP-WEVLGAHEAPRRSFS-QQTIPPSAKYGGRHTVTMIPGDGIGPEL
          .ALK...AA....K....P....RP.W......E..R...S....IPP.AK.GG.HTV..IP.DGIGPEL
Retrocopy IALKILPAARCSVKGHV-PTSYSRPFWKDFLGWEI*RKDLSFKHSIPPAAKHGGWHTVITIPEDGIGPEL

Parental  MLHVKSVFRHACVPVDFEEVHVSSNADEEDIRNAIMAIRRNRVALKGNIETNHNLPPSHKSRNNILRTSL
          MLH.K.VFRHACVPVD.EEV.V.....EE...NAIM....N...LKGN.ET..NLPPSHKS.N......L
Retrocopy MLHIKNVFRHACVPVDSEEVWVNATSCEEEVHNAIMVVCGNHMDLKGNFETAYNLPPSHKSQNSGFHNTL

Parental  DLYANVIHCKSLPGVVTR-HRDVDILIVRENTEGEYSSLEHESVAGVVESLKIITKAKSL
          DLYA.VIH.KSL.GV..R.H...DIL.V..NTEG.YS.LEHE...GV.ESLK....A...
Retrocopy DLYASVIHFKSLLGVESR<HKNIDILVVWKNTEG*YSNLEHERMKGVIESLKLHSYATAI

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	95.96 RPM
SRP014902_testis	0.00 RPM	85.15 RPM
SRP018288_heart	0.00 RPM	63.94 RPM
SRP018288_kidney	0.00 RPM	77.72 RPM
SRP018288_liver	0.00 RPM	52.29 RPM
SRP018288_lung	0.00 RPM	57.53 RPM
SRP018856_adipose	0.00 RPM	130.65 RPM
SRP035408_brain	0.00 RPM	74.83 RPM
SRP035408_liver	0.00 RPM	64.29 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_662 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_662 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_662 has 7 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_759
Pan troglodytes	retro_ptro_534
Mus musculus	retro_mmus_134
Oryctolagus cuniculus	retro_ocun_80
Bos taurus	retro_btau_1194
Canis familiaris	retro_cfam_1023
Equus caballus	retro_ecab_941

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018466	1 retrocopy	retro_amel_1892,
Bos taurus	ENSBTAG00000001059	1 retrocopy	retro_btau_1194,
Canis familiaris	ENSCAFG00000019286	1 retrocopy	retro_cfam_1023,
Callithrix jacchus	ENSCJAG00000011185	1 retrocopy	retro_cjac_1597,
Equus caballus	ENSECAG00000018509	1 retrocopy	retro_ecab_941,
Homo sapiens	ENSG00000067829	1 retrocopy	retro_hsap_759,
Latimeria chalumnae	ENSLACG00000007365	1 retrocopy	retro_lcha_17,
Loxodonta africana	ENSLAFG00000006904	1 retrocopy	retro_lafr_560,
Macropus eugenii	ENSMEUG00000013934	1 retrocopy	retro_meug_203,
Myotis lucifugus	ENSMLUG00000004457	1 retrocopy	retro_mluc_396,
Mustela putorius furo	ENSMPUG00000008781	1 retrocopy	retro_mputfur_644,
Mus musculus	ENSMUSG00000002010	1 retrocopy	retro_mmus_134,
Nomascus leucogenys	ENSNLEG00000013540	1 retrocopy	retro_nleu_394,
Otolemur garnettii	ENSOGAG00000006735	1 retrocopy	retro_ogar_25,
Pteropus vampyrus	ENSPVAG00000013163	1 retrocopy	retro_pvam_373,
Rattus norvegicus	ENSRNOG00000037284	1 retrocopy	retro_rnor_209,
Sus scrofa	ENSSSCG00000012783	1 retrocopy	retro_sscr_662 ,
Tursiops truncatus	ENSTTRG00000011728	1 retrocopy	retro_ttru_848,