RetrogeneDB ID: retro_cfam_75

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 8:3355287..3356136(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000011311
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: PSMB8
• Ensembl ID: ENSCAFG00000000829
• Aliases: PSMB8, ATP6V0D2
• Description: Canis lupus familiaris proteasome (prosome, macropain) subunit, beta type, 8 (large multifunctional peptidase 7) (PSMB8), mRNA. [Source:RefSeq mRNA;Acc:NM_001048085]

Sequence

>retro_cfam_75
ATGGCTCTGCAGGACGTATGCAAGTGGCAGGCCCCCGACACCCAGGGGCTATCGCCTCACCTGCCTCCAGCCGGTGGCTG
GTCCGTGCCCCTGGGCTGTGACCCTCAAACCTTCCTGCGGCTGCACGGCCCCAGGCTGGCCCACGGCACTACCACGTTGG
CCTTCCGCTTCCGGCACGGAGTCATCGCCGCCGCTGACACGCGTTCCTCCTGCGGCAACTACGTGGCGTGTCCGGCCTCA
CGAAAGATCATCCCCGTGCACCAGCACCTCCTGGGCACCACCTCCGGCACCTCGGCCGACTGCGCCGCCTGGTACCGCGT
GCTGCGGCGGGAGCTGCGGCTGCGGGCGCTGAGGGAGGGCCGGCTGCCCAGCGTGGCCGGCGCCGCCAGGCTCCTGTCCG
CCATGATGTCTTGCTACCGGGGCCTGGATCTGTGCGTGGCCACGGCCCTGTGCGGCTGGGACCGCTCTGGGCCTGCGCTC
TTCTACGTGTGCAGCGACGGCACCCGCCTGCCGGGGAACGTCTTCTCGGTGGGCTCTGGGTCTCCGTACGCCTACGGCGT
GCTGGACCGCGGCTACCGCTACGACCTGAGCCCCCAGGAGGCCTACGCCCTGGCCCGGCGCGCCGTGGCCCACGCCACCC
ACCGCGACGCCTACTCCGGGGGTTCCGTAGACCTTTTCCACGTGCGGGAGGACGGATGGGAGTATGTGTCACGCGACGAC
GCCTGCGTGCTCTACTCGGAACTGCAGAAGCTTCCGGAGCCGGAGGGGGCGGCGGCGGAGGAGGGCCACGCTGAGCCTGC
CACCCTGCGCGGAGACTCCAGGATGCCCGCGGGGACTGAGATGCTGTGA

Alignment

ORF - retro_cfam_75 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.68 %
• Parental protein coverage: 74.28 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVHGTTTLAFKFQHGVIVAVDSRATAGNYISSSRVNKVIEINPSLLGTMSGCAADCQYWERLLAKECRLY
          ..HGTTTLAF.F.HGVI.A.D.R...GNY.......K.I.....LLGT.SG..ADC..W.R.L..E.RL.
Retrocopy LAHGTTTLAFRFRHGVIAAADTRSSCGNYVACPASRKIIPVHQHLLGTTSGTSADCAAWYRVLRRELRLR

Parental  YLRNGERISVSAASKLLSNMVYQYRGMDLSMGSMICGWDKKGPGLYYVDQNGTRLSGNMFSTGSGSTYAY
          .LR.G...SV..A..LLS.M...YRG.DL......CGWD..GP.L.YV...GTRL.GN.FS.GSGS.YAY
Retrocopy ALREGRLPSVAGAARLLSAMMSCYRGLDLCVATALCGWDRSGPALFYVCSDGTRLPGNVFSVGSGSPYAY

Parental  GVMDSGYQPSLSPEEAYELGRRAITYATHRDSYSGGIINMYHMKEDGWVKVESTDVNELLHQYQE
          GV.D.GY...LSP.EAY.L.RRA...ATHRD.YSGG.....H..EDGW..V...D...L....Q.
Retrocopy GVLDRGYRYDLSPQEAYALARRAVAHATHRDAYSGGSVDLFHVREDGWEYVSRDDACVLYSELQK

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	0.04 RPM	5.59 RPM
SRP017611_brain	0.00 RPM	3.81 RPM
SRP017611_kidney	0.00 RPM	7.26 RPM
SRP017611_liver	0.00 RPM	9.86 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_75 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_75 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_75 has 9 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_95
Pan troglodytes	retro_ptro_97
Gorilla gorilla	retro_ggor_156
Pongo abelii	retro_pabe_171
Callithrix jacchus	retro_cjac_35
Oryctolagus cuniculus	retro_ocun_176
Bos taurus	retro_btau_11
Sus scrofa	retro_sscr_90
Equus caballus	retro_ecab_18

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002026	1 retrocopy	retro_amel_27,
Bos taurus	ENSBTAG00000003039	1 retrocopy	retro_btau_11,
Canis familiaris	ENSCAFG00000000829	1 retrocopy	retro_cfam_75 ,
Equus caballus	ENSECAG00000018887	1 retrocopy	retro_ecab_18,
Felis catus	ENSFCAG00000023131	1 retrocopy	retro_fcat_30,
Loxodonta africana	ENSLAFG00000003213	1 retrocopy	retro_lafr_65,
Microcebus murinus	ENSMICG00000015254	1 retrocopy	retro_mmur_33,
Myotis lucifugus	ENSMLUG00000013876	1 retrocopy	retro_mluc_285,
Monodelphis domestica	ENSMODG00000014366	1 retrocopy	retro_mdom_179,
Otolemur garnettii	ENSOGAG00000013830	1 retrocopy	retro_ogar_256,
Procavia capensis	ENSPCAG00000016741	1 retrocopy	retro_pcap_21,
Pan troglodytes	ENSPTRG00000018022	2 retrocopies	retro_ptro_1102, retro_ptro_97,
Pteropus vampyrus	ENSPVAG00000002800	1 retrocopy	retro_pvam_20,
Sus scrofa	ENSSSCG00000026951	1 retrocopy	retro_sscr_90,
Tupaia belangeri	ENSTBEG00000007794	1 retrocopy	retro_tbel_2055,
Tarsius syrichta	ENSTSYG00000007730	1 retrocopy	retro_tsyr_1639,