RetrogeneDB ID: retro_cfam_1335

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 3:22580402..22580857(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PAFAH1B2
• Ensembl ID: ENSCAFG00000013226
• Aliases: None
• Description: platelet-activating factor acetylhydrolase 1b, catalytic subunit 2 (30kDa) [Source:HGNC Symbol;Acc:8575]

Sequence

>retro_cfam_1335
ATGAGCCAAGGGGACTCAAACCTACCAGCTACTTTACATGCAGCAGACAACATTTAAAGAGATGACAAATGTATGTCTCA
GCACAACAGATTTGTCCTGGATGTAAAGACAATAAGCCTGATGTACTATTTGTGGGGGACTCCACGGTACAGTTAATGCA
GCAATATGGGATATGGCGAGAGCTTTTTTTCCCCACTTTGTACATGGAATTTTGGAATTGGAGCAGATGCGACAAGACTT
GTTTCATGCAGACTAAAGGATGGAGAACTGGAGAATATTAAACTTGAGGTCATTTTTGTCTGGGAAGAAAGAAACAACCA
TAAAAACACAGCAGAAGTGGCAAATGGAATTAGGCCATCATACAATTTATCAACGCAAGGTAGCCACAGGCCAAAATCAT
TGTACTGGGTTTGTTTCCTCGAGGTAAGAAGCCCAACCCTCTGAGGCAAACCAAC

Alignment

ORF - retro_cfam_1335 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.44 %
• Parental protein coverage: 66.81 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSQGDSNPAAIPHAAEDIQGDDRWMSQHNRFVLD-CKDKEPDVLFVGDSMVQLMQQYEIWREL-FSPLHA
          MSQGDSN..A..HAA..I..DD..MSQHNRFVLD.CKD..PDVLFVGDS.VQLMQQY.IWREL.FSPL..
Retrocopy MSQGDSNLPATLHAADNI*RDDKCMSQHNRFVLD<CKDNKPDVLFVGDSTVQLMQQYGIWREL>FSPLCT

Parental  LNFGIGGDTTRHVLWRLKNGELENIKPKVIVVWVGTNNHENTAEEVAGGIE-AIVQLINTRQPQAKIIVL
          .NFGIG.D.TR.V..RLK.GELENIK..VI.VW...NNH.NTA.EVA.GI..AI.Q.IN.R.PQAKIIVL
Retrocopy WNFGIGADATRLVSCRLKDGELENIKLEVIFVWEERNNHKNTA-EVANGIR<AIIQFINAR*PQAKIIVL

Parental  GLLPRGEKPNPLRQKN
          GL.PRG.KPNPLRQ.N
Retrocopy GLFPRGKKPNPLRQTN

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	102.39 RPM
SRP017611_brain	0.00 RPM	85.19 RPM
SRP017611_kidney	0.00 RPM	24.76 RPM
SRP017611_liver	0.00 RPM	7.76 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1335 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1335 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1335 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008628	2 retrocopies	retro_amel_1145, retro_amel_818,
Canis familiaris	ENSCAFG00000004847	1 retrocopy	retro_cfam_610,
Canis familiaris	ENSCAFG00000013226	1 retrocopy	retro_cfam_1335 ,
Callithrix jacchus	ENSCJAG00000012698	1 retrocopy	retro_cjac_3325,
Dipodomys ordii	ENSDORG00000011274	1 retrocopy	retro_dord_560,
Felis catus	ENSFCAG00000029945	1 retrocopy	retro_fcat_270,
Homo sapiens	ENSG00000168092	2 retrocopies	retro_hsap_1148, retro_hsap_4661,
Gorilla gorilla	ENSGGOG00000028197	2 retrocopies	retro_ggor_2893, retro_ggor_893,
Macaca mulatta	ENSMMUG00000002050	2 retrocopies	retro_mmul_2481, retro_mmul_892,
Mustela putorius furo	ENSMPUG00000004246	1 retrocopy	retro_mputfur_898,
Nomascus leucogenys	ENSNLEG00000007337	2 retrocopies	retro_nleu_1096, retro_nleu_946,
Pongo abelii	ENSPPYG00000003907	2 retrocopies	retro_pabe_3621, retro_pabe_953,
Pan troglodytes	ENSPTRG00000004318	2 retrocopies	retro_ptro_3097, retro_ptro_782,
Rattus norvegicus	ENSRNOG00000018032	1 retrocopy	retro_rnor_2585,
Sarcophilus harrisii	ENSSHAG00000011403	1 retrocopy	retro_shar_617,