RetrogeneDB ID: retro_cfam_1213

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 26:31690342..31690726(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TM2D1
• Ensembl ID: ENSCAFG00000018838
• Aliases: None
• Description: TM2 domain containing 1 [Source:HGNC Symbol;Acc:24142]

Sequence

>retro_cfam_1213
TCCATGACCACAGGACCTTGGGGAGCTGATGCGACCATTACCATGATGGCAAAGAGAGGCTTAAATGCAAGAGCCTCAAA
GTGAGGGAGTATAATTGTAAGGATTGGAAAGGAAATGATGCTACACAAGAACCATTTAACTGTACAATCTGTACAACTCA
TGGTCCTTGTTTTCCAACACCCAACATAACTTGTAGGGATGTTGGTGGCACTGAAACACATTTTACTGGAAATGGAGTTG
GCTTCCCCAGGCCCATATCTTGCTGAAATGCCAATGGCTATTTGTCATCAAGTGGAAGCTGCACTGTCTCATTCCCTTGG
AAAGATTGATTTTTGCCTTGGATACCCTGCCTTGTGTTTATTAACGTTTTGCACCGTCGAGTTT

Alignment

ORF - retro_cfam_1213 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.9 %
• Parental protein coverage: 62.09 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SVTTGPWGAAAIAAA-GGEETLKCEDLKLGQYICKDPKINDATQEPVNCTNYTAHVPCFPAPNVTCKDFS
          S.TTGPWGA.A......G.E.LKC..LK...Y.CKD.K.NDATQEP.NCT..T.H.PCFP.PN.TC.D..
Retrocopy SMTTGPWGADATITM<DGKERLKCKSLKVREYNCKDWKGNDATQEPFNCTICTTHGPCFPTPNITCRDVG

Parental  GNETHFTGNEVGFLKPISCRNVNGY-SYKVAVALSLFLGWLGADRFYLGYPALGLLKFCTVGF
          G.ETHFTGN.VGF..PISC.N.NGY....V..ALS..LG......F.LGYPAL.LL.FCTV.F
Retrocopy GTETHFTGNGVGFPRPISC*NANGY>CHQVEAALSHSLGKID---FCLGYPALCLLTFCTVEF

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	15.67 RPM
SRP017611_brain	0.00 RPM	18.58 RPM
SRP017611_kidney	0.00 RPM	22.78 RPM
SRP017611_liver	0.00 RPM	4.71 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1213 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1213 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1213 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011705	1 retrocopy	retro_amel_1290,
Canis familiaris	ENSCAFG00000018838	1 retrocopy	retro_cfam_1213 ,
Choloepus hoffmanni	ENSCHOG00000013535	1 retrocopy	retro_chof_1494,
Cavia porcellus	ENSCPOG00000012287	1 retrocopy	retro_cpor_471,
Equus caballus	ENSECAG00000015035	1 retrocopy	retro_ecab_556,
Erinaceus europaeus	ENSEEUG00000001567	1 retrocopy	retro_eeur_708,
Loxodonta africana	ENSLAFG00000013979	1 retrocopy	retro_lafr_662,
Mus musculus	ENSMUSG00000028563	2 retrocopies	retro_mmus_1412, retro_mmus_1981,
Rattus norvegicus	ENSRNOG00000007527	1 retrocopy	retro_rnor_1104,
Tupaia belangeri	ENSTBEG00000002089	3 retrocopies	retro_tbel_1156, retro_tbel_1730, retro_tbel_201,