RetrogeneDB ID: retro_cfam_1549

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 34:39909161..39909581(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDZD11
• Ensembl ID: ENSCAFG00000028800
• Aliases: None
• Description: PDZ domain containing 11 [Source:HGNC Symbol;Acc:28034]

Sequence

>retro_cfam_1549
ATGGACCACTGGATTCCTTATGTTGACTAACTGGAGGTTTTCCTGCCCTACCTATGAGAATCCCCCACCATAGATTTCTC
CTCGTGACCAGGTGAATTACCCAGACTACAAAAATGAGTTGACTCAGTTTTTGCCCTAAATTCTCACACTGAAGAAGCCC
CCTGAAGCTCAGTTGAGATTTAATATCTGAGGAGGAAAGGCCTCCCAATGGGGCATCTATATCTCCAACGTGATTCCTGA
ATCAGATGCACATCAAGAAAACTTCAGGAAGGGGACTAAGTCCTAGCTATGAATTATGTGGATTTCCAAGATATTGAGCA
GAGCAAGGCTGATGAGATCCTGAAGACAGCCTGTGAAAGTGGCATGAGTGGCTGTTTCTCTCCCTACAGTTACCATTGCC
CAAGAGAGAAGACTGTGCAC

Alignment

ORF - retro_cfam_1549 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.9 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MDSRIPYDDYPVVFLP-AYENPPAWIPPHERVYHPDYNNELTQFLPRIVTLKKPPGAQLGFNIRGGKASQ
          MD..IPY.D...VFLP..YENPP..I.P...V..PDY.NELTQFLP.I.TLKKPP.AQL.FNI.GGKASQ
Retrocopy MDHWIPYVD*LEVFLP>TYENPPP*ISPRDQVNYPDYKNELTQFLP*ILTLKKPPEAQLRFNI*GGKASQ

Parental  LGIFISKVIPDSDAHRAG-LQEGDQVLAVNDVDFQDIEHSKAVEILKTAREISMRVRFFPYNYHRQKERT
          .GI.IS.VIP.SDAH....LQEGD.VLA.N.VDFQDIE.SKA.EILKTA.E..M...F.PY.YH...E.T
Retrocopy WGIYISNVIPESDAHQEN<LQEGD*VLAMNYVDFQDIEQSKADEILKTACESGMSGCFSPYSYHCPREKT

Parental  VH
          VH
Retrocopy VH

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	24.40 RPM
SRP017611_brain	0.00 RPM	18.82 RPM
SRP017611_kidney	0.00 RPM	21.00 RPM
SRP017611_liver	0.00 RPM	5.44 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1549 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1549 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1549 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009203	1 retrocopy	retro_amel_158,
Canis familiaris	ENSCAFG00000028800	1 retrocopy	retro_cfam_1549 ,
Callithrix jacchus	ENSCJAG00000012432	1 retrocopy	retro_cjac_138,
Equus caballus	ENSECAG00000010771	1 retrocopy	retro_ecab_940,
Echinops telfairi	ENSETEG00000008626	3 retrocopies	retro_etel_1026, retro_etel_1863, retro_etel_921,
Homo sapiens	ENSG00000120509	1 retrocopy	retro_hsap_1439,
Gorilla gorilla	ENSGGOG00000006626	1 retrocopy	retro_ggor_1108,
Macropus eugenii	ENSMEUG00000012040	1 retrocopy	retro_meug_1858,
Macaca mulatta	ENSMMUG00000013938	1 retrocopy	retro_mmul_2265,
Mustela putorius furo	ENSMPUG00000004220	1 retrocopy	retro_mputfur_823,
Nomascus leucogenys	ENSNLEG00000000863	1 retrocopy	retro_nleu_1414,
Otolemur garnettii	ENSOGAG00000016423	1 retrocopy	retro_ogar_2975,
Pongo abelii	ENSPPYG00000020929	1 retrocopy	retro_pabe_1193,
Pan troglodytes	ENSPTRG00000021995	1 retrocopy	retro_ptro_981,
Sarcophilus harrisii	ENSSHAG00000005380	1 retrocopy	retro_shar_149,
Tupaia belangeri	ENSTBEG00000002767	2 retrocopies	retro_tbel_3155, retro_tbel_3203,
Tursiops truncatus	ENSTTRG00000007864	1 retrocopy	retro_ttru_953,