RetrogeneDB ID: retro_cfam_1981

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 9:35211728..35212116(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000017742
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PFDN6
• Ensembl ID: ENSCAFG00000000956
• Aliases: None
• Description: Canis lupus familiaris prefoldin subunit 6 (PFDN6), mRNA. [Source:RefSeq mRNA;Acc:NM_001048089]

Sequence

>retro_cfam_1981
ATGGCTGAGCTAATCCAGAAGAAGCTACAGGGAGAAGTGGAGAAATATCAGCAGCTACAGAAGGACTTGAGTAAAATCCA
TGTCGGGGAGACAGAAGCTTGAGGCGCAGCTAACAGAAAATAATATCGTGAAGGAGGAGCTGGCCCTGCTAGATGGATCC
AACGTGGTCTTTAAACTTCTGGGTCCTGTGCTGGTCAAACAGGAGCTGGGAGAGGCTCGTGCCACAGTGGGGAAGAGGCT
GGACTATATCACAGCTGAAATTAAGCGATACGAATCCCAGCTCCGGGACCTTGAGCGGCAGTCAGAGCAACAGAGGGAGA
CCCTGGCTCAGCTGCAGCAGGAGTTCCAGAGGGCCCAGGCAGCCAAGGCAGGGGCTTCTGGGAAGGCC

Alignment

ORF - retro_cfam_1981 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.23 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAELIQKKLQGEVEKYQQLQKDLS-KSMSGRQKLEAQLTENNIVKEELALLDGSNVVFKLLGPVLVKQEL
          MAELIQKKLQGEVEKYQQLQKDLS.KSMSGRQKLEAQLTENNIVKEELALLDGSNVVFKLLGPVLVKQEL
Retrocopy MAELIQKKLQGEVEKYQQLQKDLS>KSMSGRQKLEAQLTENNIVKEELALLDGSNVVFKLLGPVLVKQEL

Parental  GEARATVGKRLDYITAEIKRYESQLRDLERQSEQQRETLAQLQQEFQRAQAAKAGASGKA
          GEARATVGKRLDYITAEIKRYESQLRDLERQSEQQRETLAQLQQEFQRAQAAKAGASGKA
Retrocopy GEARATVGKRLDYITAEIKRYESQLRDLERQSEQQRETLAQLQQEFQRAQAAKAGASGKA

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	0.08 RPM	26.92 RPM
SRP017611_brain	0.00 RPM	13.42 RPM
SRP017611_kidney	0.00 RPM	27.87 RPM
SRP017611_liver	0.00 RPM	12.04 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1981 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1981 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1981 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001576	2 retrocopies	retro_amel_221, retro_amel_824,
Bos taurus	ENSBTAG00000010723	1 retrocopy	retro_btau_619,
Canis familiaris	ENSCAFG00000000956	2 retrocopies	retro_cfam_1749, retro_cfam_1981 ,
Dipodomys ordii	ENSDORG00000013828	1 retrocopy	retro_dord_453,
Felis catus	ENSFCAG00000028199	1 retrocopy	retro_fcat_1784,
Macropus eugenii	ENSMEUG00000016778	1 retrocopy	retro_meug_1930,
Microcebus murinus	ENSMICG00000000922	1 retrocopy	retro_mmur_1520,
Mustela putorius furo	ENSMPUG00000002364	1 retrocopy	retro_mputfur_608,
Oryctolagus cuniculus	ENSOCUG00000010559	1 retrocopy	retro_ocun_711,
Otolemur garnettii	ENSOGAG00000028341	4 retrocopies	retro_ogar_1185, retro_ogar_2023, retro_ogar_3508, retro_ogar_85,
Ochotona princeps	ENSOPRG00000000983	1 retrocopy	retro_opri_12,
Pteropus vampyrus	ENSPVAG00000001910	1 retrocopy	retro_pvam_391,