RetrogeneDB ID: retro_cfam_2206

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:105772722..105773477(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000018893
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PSMD8
• Ensembl ID: ENSCAFG00000005931
• Aliases: None
• Description: proteasome (prosome, macropain) 26S subunit, non-ATPase, 8 [Source:HGNC Symbol;Acc:9566]

Sequence

>retro_cfam_2206
CTTAAGGGCAAGTGGAACCGTAAAAGCTCCAGTCTTACAAGCACAGTGAACAACTAAGGCCATCTCAAGCTGGTTCTGCT
GGAGCTCAACTTCTTGTCAACCACAGGGACCCAACTGACCAAACAGCAGTTCATTCTGGCTGGTAACATTTTGGAGATTG
GGGCTCAGTGGAGCATCCTGTGCAAGGACGTCCCCTCCTTTCAGCACTACATGACCCAGCTCAAATGCTACTATTTCAAC
TGTGAGGAGCAACTCTCCGAGTCAGCCGACATGCACCAACTCTCAGGCCTCAACTTCCTCTTCCTGCTGTCCCAGAACCG
GGTGGCTGAGTTCCACACAAGAGTTGGAGCAGCTGCCTGCCAAGGACATGCAGACCAAGGTATATACATCAAGCGTCCTG
TGTCCCTGCAGCAATACGTGATGGAGAGAAGCTATCACAGGGTTTTCTTGGCCAAAGGCAACATTCCTGCTGAGAGCTAT
ACCTTCTTCACTGACATCCTGCTTGACACTCTGATGAGATTGCTGGGTGCATCGAGGAGGCCTATGAGCAAATGCTTTTC
ACTGAGGCCACCCAGATCCTCTTCTTTAACACACCCAAAAAGAAGGCAGACTGCACGAAGAAGCGAGGGTGGGTTCTGGG
CCTTAGCAACTACTACAGCTTTGTCAGCCAGCAGCAGAAGCCAGAAGGTACCACCATCCCCTCCACAGAACTGGCTACAC
AGGTCATTGAGTATGCCTGGCAGCTAGAGATGGTC

Alignment

ORF - retro_cfam_2206 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.08 %
• Parental protein coverage: 71.79 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LKGEWNRKSPNLSKCGEELGRLKLVLLELNFLPTTGTKLTKQQLILARDILEIGAQWSILRKDIPSFERY
          LKG.WNRKS..L.......G.LKLVLLELNFL.TTGT.LTKQQ.ILA..ILEIGAQWSIL.KD.PSF..Y
Retrocopy LKGKWNRKSSSLTSTVNN*GHLKLVLLELNFLSTTGTQLTKQQFILAGNILEIGAQWSILCKDVPSFQHY

Parental  MAQLKCYYFDYKEQLPESAYMHQLLGLNLLFLLSQNRVAEFHTELERLPAKD-IQTNVYIKHPVSLEQYL
          M.QLKCYYF...EQL.ESA.MHQL.GLN.LFLLSQNRVAEFHT...............YIK.PVSL.QY.
Retrocopy MTQLKCYYFNCEEQLSESADMHQLSGLNFLFLLSQNRVAEFHTRVGAAACQGHADQGIYIKRPVSLQQYV

Parental  MEGSYNKVFLAKGNIPAESYTFFIDILLDTIRDEIAGCIEKAYEK-ILFTEATRILFFNTPKKMTDYAKK
          ME.SY..VFLAKGNIPAESYTFF.DILLDT......G.......K..LFTEAT.ILFFNTPKK..D..KK
Retrocopy MERSYHRVFLAKGNIPAESYTFFTDILLDTLM-RLLGASRRPMSK<MLFTEATQILFFNTPKKKADCTKK

Parental  RGWVLGLNNYYSFASQQQKPEDTTIPSTELAKQVIEYARQLEMI
          RGWVLGL.NYYSF.SQQQKPE.TTIPSTELA.QVIEYA.QLEM.
Retrocopy RGWVLGLSNYYSFVSQQQKPEGTTIPSTELATQVIEYAWQLEMV

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	82.28 RPM
SRP017611_brain	0.00 RPM	73.12 RPM
SRP017611_kidney	0.00 RPM	122.37 RPM
SRP017611_liver	0.00 RPM	36.98 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2206 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2206 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2206 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005931	1 retrocopy	retro_cfam_2206 ,
Myotis lucifugus	ENSMLUG00000009902	2 retrocopies	retro_mluc_2137, retro_mluc_2480,
Monodelphis domestica	ENSMODG00000013151	1 retrocopy	retro_mdom_58,
Sus scrofa	ENSSSCG00000002956	1 retrocopy	retro_sscr_195,
Ictidomys tridecemlineatus	ENSSTOG00000014464	1 retrocopy	retro_itri_10,