RetrogeneDB ID: retro_cfam_626

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 14:19389918..19390589(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TPGS2
• Ensembl ID: ENSCAFG00000017766
• Aliases: None
• Description: tubulin polyglutamylase complex subunit 2 [Source:HGNC Symbol;Acc:24561]

Sequence

>retro_cfam_626
CTACAGAATTTTTACCCGATGACCAATGGCTTCCACACGACATGGAGTATGAAGCTGAATGAGCACAGTACTCCAACTGG
GCAGCATGGCAATTAGCAGCATCTCAAAGCTGACTCAACTCAACCAGTCTTCTGTGTATTTGCTCCCTAATACACCAACT
CTGGCAGACCTGGAAGTTGATACACTTGAAGCCCAGTGAAAACAACCAGAGAAGCCTCACTTTGATTCTCACAGTGTGAT
ATTTGAACTGGATCCTTGCAATGGGAATAGGAAGGTTGGCTTTATCCATAATAGGGGAAACCCAGCATTCACAAGACACT
GAGATCTGGTTCCTAAACAGAATGTTACACCAGCATTTTCTCACAGATACCTTTACCACTTACTATCACTTGCTTATCAT
GTACTTGGGCCTGCTATAGTATGCCTTCACCAGCTATGGGTTTAGCTCATAGGTCAAGCAATGGTTCAACATGTATAAAC
TTATCACCTACAACCCAAACCTGCTTTCAGAATAGACCAAATCCTTTGTGAACAAGCTGGACCCCAGCAAAGAGTTTAAG
AGCAAGAACAAGATTTTACTCCCCAAAAAGAGAGGGCCTATCCAACCTGCAGGTGGCCAGAAAGGGCCCTCAGGCCCTCC
CTCCACCTCTAAGTCCTCTTCTAGTCCTGGA

Alignment

ORF - retro_cfam_626 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.24 %
• Parental protein coverage: 77.4 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VKNFYLMTNGFHMTWSVKLDEHTIP-LGSMAINSISKLTQLNQSSVYSLPNAPTLADLEDDTLEASENQP
          ..NFY.MTNGFH.TWS.KL.EH..P.LGSMAI.SISKLTQLNQSSVY.LPN.PTLADLE.DTLEA...QP
Retrocopy LQNFYPMTNGFHTTWSMKLNEHSTP>LGSMAISSISKLTQLNQSSVYLLPNTPTLADLEVDTLEAQ*KQP

Parental  EKPHFDSRSVIFELDSCNGNGKVCLVYKTG-KPAL-AQDTEIWFLDRALYWHFLTDTFTAYYRLLITHLG
          EKPHFDS.SVIFELD.CNGN.KV......G.KP....QDTEIWFL.R.L..HFLTDTFT.YY.LLI..LG
Retrocopy EKPHFDSHSVIFELDPCNGNRKVGFIHNRG<KPSI<SQDTEIWFLNRMLHQHFLTDTFTTYYHLLIMYLG

Parental  LPQWQYAFTSYGISPQAKQWFNMYKPITYNTNLLAEETNSFVNKLDPSRVFKSKNKTLIPKKKGPVQPPG
          L.....AFTSYG.S...KQWFNMYK.ITYN.NLL.E.T.SFVNKLDPS..FKSKNK.L.PKK.GP.QP.G
Retrocopy LL*Y--AFTSYGFSS*VKQWFNMYKLITYNPNLLSE*TKSFVNKLDPSKEFKSKNKILLPKKRGPIQPAG

Parental  GQKGPSGPPSTSKSSSSPG
          GQKGPSGPPSTSKSSSSPG
Retrocopy GQKGPSGPPSTSKSSSSPG

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
SRP012049_cerebellum	0.00 RPM	26.21 RPM
SRP017611_brain	0.00 RPM	18.97 RPM
SRP017611_kidney	0.07 RPM	23.97 RPM
SRP017611_liver	0.00 RPM	10.80 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_626 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_626 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_626 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017766	3 retrocopies	retro_cfam_355, retro_cfam_457, retro_cfam_626 ,
Choloepus hoffmanni	ENSCHOG00000007960	1 retrocopy	retro_chof_1642,
Erinaceus europaeus	ENSEEUG00000005257	3 retrocopies	retro_eeur_208, retro_eeur_324, retro_eeur_516,
Myotis lucifugus	ENSMLUG00000001739	1 retrocopy	retro_mluc_1194,
Mustela putorius furo	ENSMPUG00000001097	2 retrocopies	retro_mputfur_1622, retro_mputfur_507,
Mus musculus	ENSMUSG00000024269	1 retrocopy	retro_mmus_2648,
Otolemur garnettii	ENSOGAG00000008218	1 retrocopy	retro_ogar_686,
Rattus norvegicus	ENSRNOG00000014957	1 retrocopy	retro_rnor_2961,
Sus scrofa	ENSSSCG00000026953	1 retrocopy	retro_sscr_590,
Tarsius syrichta	ENSTSYG00000005299	2 retrocopies	retro_tsyr_1161, retro_tsyr_512,
Tursiops truncatus	ENSTTRG00000007153	1 retrocopy	retro_ttru_1112,