RetrogeneDB ID: retro_cfam_332

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 1:105059844..105060255(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM216
• Ensembl ID: ENSCAFG00000016171
• Aliases: None
• Description: transmembrane protein 216 [Source:HGNC Symbol;Acc:25018]

Sequence

>retro_cfam_332
AGAGGTAAAGGGCTATTTCCATCCCTTTGGAAATCCTGTTCTTTCTGAATGGTTGGTATTATGCTTACTATTCCTGCTGG
AACTCCTCATATTTCTGTAGAAAGCTCTCCTGCTGCCATCACCAACAGCCCATCTAGTAGTGGATGTGGTGATGCCTTTC
TTTACTTTGGAAATGAAGGAATTCGATTATTTTTTGGTATAAAGGGAAACCTCTGCCATTGAAAGATGCCACTTGGTATT
AGTGTGGACATGACCTTCTAAGATCTGCCCTGTGTCCTCCTATTGCCTGCTGCTGCAGACCTCCATGCTCTTCTTGGAAG
CCATCCTGAACAGCATATTGCTTTTCTTCTGTGGTCAGAGGTTCTGTTTGAGGTGCTCACCCTGGCTGTTTTCTCCAGAA
TGAACAGGATT

Alignment

ORF - retro_cfam_332 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.63 %
• Parental protein coverage: 97.87 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  RGK-RLSSTPLEILFFLNGWYYATY-FLLELFIFLYKALLLPYPTANLVLDVVM-LLLYLGIEVIRLFFG
          RGK.R..S.PLEILFFLNGWYYA.Y.FLLEL.IFL.KALLLP.PTA.LV.DVVM...LY.G.E.IRLFFG
Retrocopy RGK<RAISIPLEILFFLNGWYYAYY<FLLELLIFL*KALLLPSPTAHLVVDVVM<AFLYFGNEGIRLFFG

Parental  TKGNLCQRKMPLGFSVALTF-PSAMMASYYLLLQTYVLRLEAIMNSILLFFCG-SELLLEVLTLTAFSSM
          .KGNLC..KMPLG.SV..TF.......SY.LLLQT..L.LEAI.NSILLFFCG.SE.L.EVLTL..FS.M
Retrocopy IKGNLCH*KMPLGISVDMTF>KICPVSSYCLLLQTSMLFLEAILNSILLFFCG<SEVLFEVLTLAVFSRM

Parental  DRI
          .RI
Retrocopy NRI

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	2.69 RPM
SRP017611_brain	0.00 RPM	2.62 RPM
SRP017611_kidney	0.00 RPM	7.79 RPM
SRP017611_liver	0.00 RPM	2.18 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_332 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_332 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_332 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016592	1 retrocopy	retro_amel_1255,
Bos taurus	ENSBTAG00000021517	1 retrocopy	retro_btau_1184,
Canis familiaris	ENSCAFG00000016171	4 retrocopies	retro_cfam_1342, retro_cfam_331, retro_cfam_332 , retro_cfam_333,
Monodelphis domestica	ENSMODG00000020362	1 retrocopy	retro_mdom_232,
Mustela putorius furo	ENSMPUG00000014169	4 retrocopies	retro_mputfur_1341, retro_mputfur_1536, retro_mputfur_1537, retro_mputfur_1538,
Oryctolagus cuniculus	ENSOCUG00000001682	1 retrocopy	retro_ocun_799,