RetrogeneDB ID: retro_pcap_361

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_4960:18678..19605(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IDH3G
• Ensembl ID: ENSPCAG00000008973
• Aliases: None
• Description: isocitrate dehydrogenase 3 (NAD+) gamma [Source:HGNC Symbol;Acc:5386]

Sequence

>retro_pcap_361
CACGTACGTGTGCCTGTGGATTTTGAGGAGGTACAGGTGCACTCAGCTTGTAGTGTAGAGGACATTCACAATGCCATCTT
GTCCATTCGTCGAAATGGTGTAGCACTAAAGGGCAACACTGCAACGAACCTTAACCTACCATCAACTCATTCATCCCTCA
ACACGGTACTTCGCACCTCCCTAGATCTCTTTGCCAGTGTCGTCCACTGTAAGAGTCTACCAAGTGTGGTTACCCACCAC
AGTGATGTAGACATCATTGTCATCCGGGAAAGCACAGAGGGGGAGTACAGCAATCTGGAACACGAGAGTGTGAATGGAGT
GGTAGAGACCCTGAAGATCACTACTGAGAGCAAGTCTTTGCGCATTGCTGAATATGCCTTCCAGTTGGCAGAGGAGTTAG
GGCGCAAGAAAGTGACAGCTGTGCACAAGGCCAACGTCATGAAACTGACAGATGGTCTCTTCCTCCAGTGTTGCACTGAG
GTGGCATCTCGCTATCCTCAGGTCACCTTTGAGAGCATGAATGTGGACTACACCACCAAGCAGCTGGTAACTCAGCCTGA
GCAGTTTGATGTCATGGTGATGCCTAATCTTTATGGCAACGTTATCAGCAATATTTGCACAGGGTTGGTCGGGGGGGCAG
GCCTTGTGCCTGGAGCTAGCTATGGCCAGCTGTATGCAGTGTTTGAGACAGGTACAAGGCAAATAGGCAAGTATATAGCC
AAGAAGAATGTTGCCAACCCTACTGCTATTCTTCTGGCAAGTTGTATTATGCTGGATTACCTTGAGCTCAATTCCTATGC
CACGTCCATTCGCAATGCAGTCTTGGAAGCCTTGAACTACAAAGATATGCATACCCCAGACATTGGAGGATATAGTACTA
CATCGGAAATCATTGAATACATTATGAACCGCATCCAGATCTGAAAT

Alignment

ORF - retro_pcap_361 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.26 %
• Parental protein coverage: 78.57 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  HACVPVDFEEVHVSTA-DEEDIRNAIMAIRRNRVALKGNIETNHNLPPSHKSRNNILRTSLDLYANVIHC
          H..VPVDFEEV.V..A...EDI.NAI..IRRN.VALKGN..TN.NLP..H.S.N..LRTSLDL.A.V.HC
Retrocopy HVRVPVDFEEVQVHSACSVEDIHNAILSIRRNGVALKGNTATNLNLPSTHSSLNTVLRTSLDLFASVVHC

Parental  KSLPGVVTRHKDIDILIVRENTEGEYSSLEHESVAGVVESLKIITKAKSLRIAEYAFKLAQDSGRKKVTA
          KSLP.VVT.H.D.DI...RE.TEGEYS.LEHESV.GVVE.LKI.T..KSLRIAEYAF.LA...GRKKVTA
Retrocopy KSLPSVVTHHSDVDIIVIRESTEGEYSNLEHESVNGVVETLKITTESKSLRIAEYAFQLAEELGRKKVTA

Parental  VHKANIMKLGDGLFLQCCREVAAGYPQITFENMIVDNATMQLVSRPQQFDVMVMPNLYGNIVNNVCAGLV
          VHKAN.MKL.DGLFLQCC.EVA..YPQ.TFE.M.VD..T.QLV..P.QFDVMVMPNLYGN...N.C.GLV
Retrocopy VHKANVMKLTDGLFLQCCTEVASRYPQVTFESMNVDYTTKQLVTQPEQFDVMVMPNLYGNVISNICTGLV

Parental  GGPGLVAGANYGHVYAVFETATRNTGKSIANKNIANPTATLLASCVMLDHLQLHSYATSIRKAVLASMDN
          GG.GLV.GA.YG..YAVFET.TR..GK.IA.KN.ANPTA.LLASC.MLD.L.L.SYATSIR.AVL.....
Retrocopy GGAGLVPGASYGQLYAVFETGTRQIGKYIAKKNVANPTAILLASCIMLDYLELNSYATSIRNAVLEALNY

Parental  ENMHTPDIGGQGTTSEAIQDIIRHIRIIN
          ..MHTPDIGG..TTSE.I..I...I.I.N
Retrocopy KDMHTPDIGGYSTTSEIIEYIMNRIQI*N

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Procavia capensis was not studied using RNA-Seq expression data.

ChIP-Seq

Procavia capensis was not studied using ChIP-Seq data.

EST

Procavia capensis was not studied using EST data.

TSS

Procavia capensis was not studied using FANTOM5 data.

Lab

retro_pcap_361 was not experimentally validated.

Homology

Retrocopy orthology:

Procavia capensis does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000006029	1 retrocopy	retro_dord_38,
Erinaceus europaeus	ENSEEUG00000015625	1 retrocopy	retro_eeur_248,
Latimeria chalumnae	ENSLACG00000007365	1 retrocopy	retro_lcha_17,
Macropus eugenii	ENSMEUG00000013934	1 retrocopy	retro_meug_203,
Myotis lucifugus	ENSMLUG00000004457	1 retrocopy	retro_mluc_396,
Oryctolagus cuniculus	ENSOCUG00000016554	1 retrocopy	retro_ocun_80,
Procavia capensis	ENSPCAG00000008973	1 retrocopy	retro_pcap_361 ,
Pan troglodytes	ENSPTRG00000024398	1 retrocopy	retro_ptro_534,