RetrogeneDB ID: retro_cfam_62

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:108285207..108285423(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000030333
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000023527
• Aliases: None
• Description: None

Sequence

>retro_cfam_62
ATGGTGCTGCTGGTGCAAGTCTCTCCACTCATCAAGCTCAACCATGACCCTGTCCTATTCCTCAGTGTGGCCTATGGAGT
CAAGCGCTACAGTTACCTGAGACCTCAGGCAAAAGATGAAAGGAGGAGAGCAGCTGAGGAGAAAAAGAAGCAGGATGAGC
AGAAATGGATTGAGAGAGAATTGTCAGAAGCCCAGGATGACAGCTTACTAAAGTGA

Alignment

ORF - retro_cfam_62 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.38 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVPPVQVSPLIKVNRALRPSAGARYGAKRYSYLKPRAEEERRVAAEEKKQQEERKRIERELAEARDDSIL
          MV..VQVSPLIK.N..........YG.KRYSYL.P.A..ERR.AAEEKK.Q.E.K.IEREL.EA.DDS.L
Retrocopy MVLLVQVSPLIKLNHDPVLFLSVAYGVKRYSYLRPQAKDERRRAAEEKKKQDEQKWIERELSEAQDDSLL

Parental  K
          K
Retrocopy K

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	74.80 RPM
SRP017611_brain	0.00 RPM	15.88 RPM
SRP017611_kidney	0.00 RPM	81.16 RPM
SRP017611_liver	0.00 RPM	17.33 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_62 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_62 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_62 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016722	2 retrocopies	retro_amel_1171, retro_amel_1761,
Bos taurus	ENSBTAG00000017496	2 retrocopies	retro_btau_1222, retro_btau_219,
Canis familiaris	ENSCAFG00000023527	1 retrocopy	retro_cfam_62 ,
Callithrix jacchus	ENSCJAG00000001989	1 retrocopy	retro_cjac_352,
Cavia porcellus	ENSCPOG00000008678	1 retrocopy	retro_cpor_98,
Felis catus	ENSFCAG00000029708	1 retrocopy	retro_fcat_268,
Mustela putorius furo	ENSMPUG00000011414	1 retrocopy	retro_mputfur_494,
Mus musculus	ENSMUSG00000050856	1 retrocopy	retro_mmus_3152,
Otolemur garnettii	ENSOGAG00000012271	1 retrocopy	retro_ogar_1292,
Rattus norvegicus	ENSRNOG00000000064	1 retrocopy	retro_rnor_697,
Tursiops truncatus	ENSTTRG00000002962	1 retrocopy	retro_ttru_1938,