RetrogeneDB ID: retro_cfam_2079

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:50922882..50923235(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SPCS1
• Ensembl ID: ENSCAFG00000008927
• Aliases: None
• Description: signal peptidase complex subunit 1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:23401]

Sequence

>retro_cfam_2079
GAGTCTTCATTGTCCTCAGGCCACTGGTAGCCTTATCAGCCAGTTATGCTGGAGAATCTGAGCTCATTGCCTACACGAAT
GTACTACAAGTACTAGAAGCTAGCTGAACAGATGTTTCAGGGAATTATTCTTTTTTTCTGCAATATTTGTATTTATCTAT
GGGTATTTGGCTGAACAATATGGGTGGACTGTCTATATAATTATGGTCAGATTTTCTTTTTCATATTTATTGACACTTCC
TCTATGGCCCATTTACTGCCAGCACCCCCACATGTGATTATGTGTTCAAGAATCAGGCTCAGAAGACAAGAAACCAGCAG
AAAGAAAACAATAAGAGACATGCTAAAAATAAC

Alignment

ORF - retro_cfam_2079 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.75 %
• Parental protein coverage: 92.13 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ETHSPAGACRPSQPAMLEHLSSLPTQMDYKGQKLAEQMFQGIILF-SAIVGFIYGYVAEQFGWTVYIVMA
          E.....G...P.QP.MLE.LSSLPT.M.YK..KLAEQMFQGIILF.SAI..FIYGY.AEQ.GWTVYI.M.
Retrocopy ESSLSSGHW*PYQPVMLENLSSLPTRMYYKY*KLAEQMFQGIILF>SAIFVFIYGYLAEQYGWTVYIIMV

Parental  GFAFSCLLTLPPWPIYRRHPLKWLPVQDSGSEDKKPGERK-IKRHAKNN
          .F.FS.LLTLP.WPIY..HP...L.VQ.SGSEDKKP.ERK..KRHAKNN
Retrocopy RFSFSYLLTLPLWPIYCQHPHM*LCVQESGSEDKKPAERK>NKRHAKNN

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	35.95 RPM
SRP017611_brain	0.00 RPM	34.54 RPM
SRP017611_kidney	0.00 RPM	104.01 RPM
SRP017611_liver	0.00 RPM	29.15 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2079 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2079 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2079 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008426	1 retrocopy	retro_amel_1899,
Canis familiaris	ENSCAFG00000008927	1 retrocopy	retro_cfam_2079 ,
Equus caballus	ENSECAG00000023559	1 retrocopy	retro_ecab_86,
Erinaceus europaeus	ENSEEUG00000007914	1 retrocopy	retro_eeur_25,
Homo sapiens	ENSG00000114902	1 retrocopy	retro_hsap_294,
Gorilla gorilla	ENSGGOG00000028027	1 retrocopy	retro_ggor_332,
Microcebus murinus	ENSMICG00000014061	1 retrocopy	retro_mmur_292,
Myotis lucifugus	ENSMLUG00000000744	1 retrocopy	retro_mluc_2104,
Macaca mulatta	ENSMMUG00000017370	1 retrocopy	retro_mmul_549,
Otolemur garnettii	ENSOGAG00000004106	3 retrocopies	retro_ogar_2119, retro_ogar_2315, retro_ogar_2788,
Pongo abelii	ENSPPYG00000013798	1 retrocopy	retro_pabe_380,
Pan troglodytes	ENSPTRG00000015011	1 retrocopy	retro_ptro_241,
Tarsius syrichta	ENSTSYG00000006854	2 retrocopies	retro_tsyr_1359, retro_tsyr_599,
Tursiops truncatus	ENSTTRG00000008576	1 retrocopy	retro_ttru_806,
Vicugna pacos	ENSVPAG00000007380	1 retrocopy	retro_vpac_269,