RetrogeneDB ID: retro_cfam_355

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 10:37112222..37113094(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000002082
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_355
ATGGAGGAGACACTGCCCCAGGGCTGCAACAAGCAGCACCTGGAGAAGCTGACCCTGGGGATCACCTGCATCCTCAAATC
TCCCCTAGGTGTGGCAGAGATGACTAGCATAGAAAAACTACCTGCTGAACGTTATATGATTTCTTTATGGGAACAACAAC
AACAACAAAATAACTACATGCTACATGAGGATTTGAAGAATTTTTACCTGGTGACCAATGGCTTCCACATGACATGGAGT
GTGAAGCTGGAAGAGCACACCATTCCACCGGGAAGCATGGCGATTAACAGCATCTCAAAACTGACTCCACTCAACCAGTC
CTCCATGTATTCATTCCCTAATGCACCAACTCTGGCAGACCTGGAGGATGATACACTTGAAGCCAGTGAGAACCCGCCAG
AGAAGCCTCACTTTGAGTCTTGCAGTGTGATATTTGAGCTGGATCCTTGCAATGGGAACAGAAAGGTTTGCCTTGTCTAT
GAAACAGGGAAACCCGTGTTAGCACAAGATACTGAGATCTGGTCCCTGGACAGAGCGTTCTCCTGAATTTTCTCACAGAT
ACCTTTACCACTTACTACCGCCTGCTCATCACGCACCTGGGCCTGCTGCAGTGGCAGTATGCCCTCCCCAGCTATGGCAT
TAGCCCCCAGGCCAAGCAATGGTTCAGCATGTGTAAACCCATCACCTACAACACAGACCTGCTAGCAGAAGAGACCAGCT
TCTTGGTGAATAAGCCTGGATCCCAGCAGAGTATTCAAGAGCAAGAATAATACCTTAATCCCAAAAAGAAAGGGCCTGTT
CAGCCTGCAGGTGGCCAGAAAGGCCCCGAAGTTTCTCTCTCCACCTCTAACTCCTCTTCTGGTCCTGGAAAC

Alignment

ORF - retro_cfam_355 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.59 %
• Parental protein coverage: 98.63 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MEETPPPGCSKPHLEKLTLGITRILESSPGVTEVTIIEKPPAERHMISSWE---QKNNCMLPEDVKNFYL
          MEET.P.GC.K.HLEKLTLGIT.IL.S..GV.E.T.IEK.PAER.MIS.WE...Q.NN.ML.ED.KNFYL
Retrocopy MEETLPQGCNKQHLEKLTLGITCILKSPLGVAEMTSIEKLPAERYMISLWEQQQQQNNYMLHEDLKNFYL

Parental  MTNGFHMTWSVKLDEHTIPLGSMAINSISKLTQLNQSSVYSLPNAPTLADLEDDTLEASENQPEKPHFDS
          .TNGFHMTWSVKL.EHTIP.GSMAINSISKLT.LNQSS.YS.PNAPTLADLEDDTLEASEN.PEKPHF.S
Retrocopy VTNGFHMTWSVKLEEHTIPPGSMAINSISKLTPLNQSSMYSFPNAPTLADLEDDTLEASENPPEKPHFES

Parental  RSVIFELDSCNGNGKVCLVYKTGKPALAQDTEIWFLDRA-LYWHFLTDTFTAYYRLLITHLGLPQWQYAF
          .SVIFELD.CNGN.KVCLVY.TGKP.LAQDTEIW.LDRA.....FLTDTFT.YYRLLITHLGL.QWQYA.
Retrocopy CSVIFELDPCNGNRKVCLVYETGKPVLAQDTEIWSLDRA<VLLNFLTDTFTTYYRLLITHLGLLQWQYAL

Parental  TSYGISPQAKQWFNMYKPITYNTNLLAEETNSFVNK-LDPSRVFKSKNKTLI-PKKKGPVQPPGGQKGPS
          .SYGISPQAKQWF.M.KPITYNT.LLAEET...VNK.LDPSRVFKSKN.TLI.PKKKGPVQP.GGQKGP.
Retrocopy PSYGISPQAKQWFSMCKPITYNTDLLAEETSFLVNK>LDPSRVFKSKNNTLI<PKKKGPVQPAGGQKGPE

Parental  GPPSTSKSSSSPGN
          ...STS.SSS.PGN
Retrocopy VSLSTSNSSSGPGN

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	0.00 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_355 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_355 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_355 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,