RetrogeneDB ID: retro_cfam_1947

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 8:28441091..28441503(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000009698
• Aliases: None
• Description: None

Sequence

>retro_cfam_1947
ATGGGTGTGCAGACAGTCTTCTGCATTACTAAGGCCATGCTTCTGGGGGCCCTATCCCAAAACTCCAGAAGAACTAGCTA
TACTGCTAAAAAAGTATAATAATGTGAATGGAAAACTAGAAGAAGTACCTGGTTGATGGCATGGGATATGGTGGTTACCA
GGACCTCCCTGACCACTCACAGCAGGAATGTGGTCTGTAGTATGACTGGGACTAGGACTACCCAGACCTGAGGTTGAATT
GGGGTGAACTCAGGCACTGGGACCTAGGTGCACAATCAGGAACCAAGTGGCCACACCCCCCACACCCGTTTCTTGGAATC
TAAGATATAAGCAGCTCATCAGCTTACTAGCCTTCTTGCTGTTCATGTTTTAGGTGTAGAATTACCCCACCCACCAGCCC
GTGGAGCCCCAA

Alignment

ORF - retro_cfam_1947 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.45 %
• Parental protein coverage: 73.12 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LGARTASHITKDMLPG-PYPKTPEERAAAAKKYN-MRVEDYEPYPDDGMGYGDYPKLPDRSQQERDPWYN
          .G..T...ITK.ML.G.PYPKTPEE.A...KKYN.M..E....Y..DGMGYG.Y..LPD.SQQE....Y.
Retrocopy MGVQTVFCITKAMLLG>PYPKTPEELAILLKKYN>M*MEN*KKYLVDGMGYGGYQDLPDHSQQECGL*YD

Parental  W--DHSDLRLNWGEPMHWDLDMY-IRNRVDTSPTPVSWSLMCKHLFGFVAFMLFMFWVGENYRTYQPVGP
          W..D..DLRLNWGE..HWDL....IRN.V.T.PTPVSW.L..K.L....AF.LFMF.V..NY.T.QPV.P
Retrocopy WD*DYPDLRLNWGELRHWDLGAQ<IRNQVATPPTPVSWNLRYKQLISLLAFLLFMF*V-*NYPTHQPVEP

Parental  K
          .
Retrocopy Q

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	72.28 RPM
SRP017611_brain	0.00 RPM	34.54 RPM
SRP017611_kidney	0.00 RPM	129.76 RPM
SRP017611_liver	0.00 RPM	27.77 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1947 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1947 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1947 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006651	3 retrocopies	retro_amel_1460, retro_amel_1467, retro_amel_931,
Bos taurus	ENSBTAG00000000091	1 retrocopy	retro_btau_1844,
Canis familiaris	ENSCAFG00000009698	2 retrocopies	retro_cfam_1405, retro_cfam_1947 ,
Callithrix jacchus	ENSCJAG00000037906	1 retrocopy	retro_cjac_870,
Dasypus novemcinctus	ENSDNOG00000003661	1 retrocopy	retro_dnov_65,
Felis catus	ENSFCAG00000006453	2 retrocopies	retro_fcat_501, retro_fcat_856,
Homo sapiens	ENSG00000166136	3 retrocopies	retro_hsap_1363, retro_hsap_1772, retro_hsap_770,
Gorilla gorilla	ENSGGOG00000027239	3 retrocopies	retro_ggor_1062, retro_ggor_2240, retro_ggor_639,
Microcebus murinus	ENSMICG00000001341	1 retrocopy	retro_mmur_859,
Myotis lucifugus	ENSMLUG00000015094	1 retrocopy	retro_mluc_1830,
Macaca mulatta	ENSMMUG00000006636	5 retrocopies	retro_mmul_1098, retro_mmul_1232, retro_mmul_1620, retro_mmul_415, retro_mmul_753,
Monodelphis domestica	ENSMODG00000019356	1 retrocopy	retro_mdom_1543,
Mustela putorius furo	ENSMPUG00000016959	1 retrocopy	retro_mputfur_1259,
Mus musculus	ENSMUSG00000025204	2 retrocopies	retro_mmus_1995, retro_mmus_2909,
Nomascus leucogenys	ENSNLEG00000014774	3 retrocopies	retro_nleu_1068, retro_nleu_2810, retro_nleu_398,
Otolemur garnettii	ENSOGAG00000030711	3 retrocopies	retro_ogar_1237, retro_ogar_152, retro_ogar_2593,
Pongo abelii	ENSPPYG00000002570	3 retrocopies	retro_pabe_1131, retro_pabe_1541, retro_pabe_756,
Pan troglodytes	ENSPTRG00000002851	3 retrocopies	retro_ptro_1186, retro_ptro_539, retro_ptro_936,
Sus scrofa	ENSSSCG00000006166	2 retrocopies	retro_sscr_1092, retro_sscr_444,
Tupaia belangeri	ENSTBEG00000000209	8 retrocopies	retro_tbel_1872, retro_tbel_2950, retro_tbel_3122, retro_tbel_322, retro_tbel_3696, retro_tbel_4042, retro_tbel_4718, retro_tbel_540,