RetrogeneDB ID: retro_cfam_1082

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 22:41916045..41916435(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HEBP1
• Ensembl ID: ENSCAFG00000013209
• Aliases: None
• Description: heme binding protein 1 [Source:HGNC Symbol;Acc:17176]

Sequence

>retro_cfam_1082
AGCATAGAGATGTGGCCTTGGCAGGTCCTGAGCAAAGAAGGCAAGGAAGAAGTCTCCTCTGAGGTAAGGTTCTATGAAGG
CAGAAGGTTTGCCACAGGGGATATGACAGATAAGACTGTGAGTGAGGATCTATGGGAAGCAATGCCCAAAGTCATGAAGT
ATGTGGGAGGAACCAATGACAAGGGAATCAGGATGGGGATGACAGTTCCTATTTCTTTGCTGTATTTCCCAGTGAAGATG
GCTCCCCTCAAAAGAAATTAAAAGTCTGGTTCCAGATTCCAAACTAGTTTTAGAGCAACTCCACTAGTTCCTACCAATAA
CAGCATCAAGACTGTGGACAGGGAAAGCATCACCATCTACTCCTTGCAATTTGGTGGTTATGCCAAGGAA

Alignment

ORF - retro_cfam_1082 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.73 %
• Parental protein coverage: 68.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SVETWPWQVVSQGGKEEVSYEERTCEGGRFATVEVTDKPVDEGLREAMPKVMKYVGGTNDKGIGMGMTVP
          S.E.WPWQV.S..GKEEVS.E.R..EG.RFAT...TDK.V.E.L.EAMPKVMKYVGGTNDKGI.MGMTVP
Retrocopy SIEMWPWQVLSKEGKEEVSSEVRFYEGRRFATGDMTDKTVSEDLWEAMPKVMKYVGGTNDKGIRMGMTVP

Parental  VS-FAVFPGDDGSLQKKLKVWFRIPN-QFQSNPPVPTDDSIKIEERESITVYSLQFGGYAKE
          .S.FAVFP..DGS.QKKLKVWF.IPN..F...P.VPT..SIK...RESIT.YSLQFGGYAKE
Retrocopy IS<FAVFPSEDGSPQKKLKVWFQIPN>SFRATPLVPTNNSIKTVDRESITIYSLQFGGYAKE

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	12.22 RPM
SRP017611_brain	0.00 RPM	25.64 RPM
SRP017611_kidney	0.00 RPM	31.90 RPM
SRP017611_liver	0.00 RPM	100.36 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1082 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1082 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1082 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010728	1 retrocopy	retro_amel_1466,
Canis familiaris	ENSCAFG00000013209	1 retrocopy	retro_cfam_1082 ,
Callithrix jacchus	ENSCJAG00000021628	1 retrocopy	retro_cjac_2023,
Mustela putorius furo	ENSMPUG00000011702	1 retrocopy	retro_mputfur_498,
Otolemur garnettii	ENSOGAG00000033976	1 retrocopy	retro_ogar_756,
Tarsius syrichta	ENSTSYG00000014555	1 retrocopy	retro_tsyr_2076,