RetrogeneDB ID: retro_cfam_933

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 2:44327750..44328095(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PLP2
• Ensembl ID: ENSCAFG00000015798
• Aliases: None
• Description: proteolipid protein 2 (colonic epithelium-enriched) [Source:HGNC Symbol;Acc:9087]

Sequence

>retro_cfam_933
CTGGTGATTCGGATCTGCTTCAGCACCTCCACACCAGGATACTCCTCCCTGACAGTGGATGAGATGATCCTTGCTGGGGT
TTTTTGCAATCTATATGTGTGACTTGCACACCAAGATGCAGATCATCACTGGCCTTGGAGTGATTTCTTCCACACCCTCA
TCGCGGCCATCCTCTATCCAATGACCTCCTTGTTGTCCTTCTTGAGAGAGGAAACCACTCCTAAATCATTGCAGGGTTAC
TGGGCCTAATCCCTATGTGCCTCTTTGGTATAATGTCTATGCCTCACCTACCCTGTGACAGTAAGGACATACAGCAGCCC
CACTGACTCAGTGGATGGCCCAGTG

Alignment

ORF - retro_cfam_933 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.5 %
• Parental protein coverage: 78.52 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LVILICFSASTPGYSSLSVVEMILAAIFFVIYMCDLHTKIQIINWPWSDFFRTLIAAILYLITS-IVVLV
          LVI.ICFS.STPGYSSL.V.EMILA..F...Y....H.......WPWSDFF.TLIAAILY..TS..VVL.
Retrocopy LVIRICFSTSTPGYSSLTVDEMILAGVFCNLYV*LAHQDAD-HHWPWSDFFHTLIAAILYPMTS<LVVLL

Parental  EGGNHSKIIAGVLGLIATSLFG-YDAYITFPLRQQRHTAA-PTDPADGPV
          E.GNHS.IIAG.LGLI...LFG.Y..Y....L.Q..HTAA.PTD..DGPV
Retrocopy ERGNHS*IIAGLLGLIPMCLFG<YNVYASPTL*Q*GHTAA<PTDSVDGPV

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	1.64 RPM
SRP017611_brain	0.00 RPM	1.98 RPM
SRP017611_kidney	0.00 RPM	11.69 RPM
SRP017611_liver	0.00 RPM	1.02 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_933 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_933 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_933 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012288	1 retrocopy	retro_amel_1129,
Bos taurus	ENSBTAG00000016093	3 retrocopies	retro_btau_1574, retro_btau_73, retro_btau_810,
Canis familiaris	ENSCAFG00000015798	1 retrocopy	retro_cfam_933 ,
Equus caballus	ENSECAG00000000216	1 retrocopy	retro_ecab_971,
Felis catus	ENSFCAG00000003820	2 retrocopies	retro_fcat_1547, retro_fcat_256,
Homo sapiens	ENSG00000102007	1 retrocopy	retro_hsap_3411,
Loxodonta africana	ENSLAFG00000004483	1 retrocopy	retro_lafr_427,
Macaca mulatta	ENSMMUG00000023022	1 retrocopy	retro_mmul_2124,
Mustela putorius furo	ENSMPUG00000013817	3 retrocopies	retro_mputfur_107, retro_mputfur_462, retro_mputfur_969,
Mus musculus	ENSMUSG00000031146	1 retrocopy	retro_mmus_94,
Nomascus leucogenys	ENSNLEG00000001317	1 retrocopy	retro_nleu_2887,
Otolemur garnettii	ENSOGAG00000003865	3 retrocopies	retro_ogar_2568, retro_ogar_2865, retro_ogar_473,
Pan troglodytes	ENSPTRG00000021885	1 retrocopy	retro_ptro_2316,
Pteropus vampyrus	ENSPVAG00000011770	2 retrocopies	retro_pvam_1214, retro_pvam_810,
Rattus norvegicus	ENSRNOG00000039496	1 retrocopy	retro_rnor_2686,
Tursiops truncatus	ENSTTRG00000016968	2 retrocopies	retro_ttru_1586, retro_ttru_767,