RetrogeneDB ID: retro_cfam_1893

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 7:77811491..77811851(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PFDN1
• Ensembl ID: ENSCAFG00000005742
• Aliases: None
• Description: Canis lupus familiaris prefoldin subunit 1 (PFDN1), mRNA. [Source:RefSeq mRNA;Acc:NM_001252417]

Sequence

>retro_cfam_1893
GCTCCCGTGGATCTGGAGTTGAACAAGGCCTTCACAGAACTTTAAGCCAAAGATATTGACATTCAGCAGAAGGTGAAGCT
TGCAGACATACGGATTGAACAGCTAAACAGAACGAAAAAGCACGCACATCTTACAGATACAGAGATTATGACTTTGGTAG
ATGAGACTAACATGTATGAAGGTGTAGGAAGAATGTTTATTCTTCAGTCCAAGGAGGTAATTCACCATCAACTGTTAGAG
AAACAGAAAATAGCAGAAGAAAAAATTAAAGAACTGGAACAGAAAAAATCCTACCTGGAGCGGAGTGTGAAGGAAGCTGA
GGACAACATCCGGGAGATGCTGATGGCACGAAGGGCACAG

Alignment

ORF - retro_cfam_1893 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.17 %
• Parental protein coverage: 98.36 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  APVDLELKKAFTELQAKVIDTQQKVKLADIQIEQLNRTKKHAHLTDTEIMTLVDETNMYEGVGRMFILQS
          APVDLEL.KAFTEL.AK.ID.QQKVKLADI.IEQLNRTKKHAHLTDTEIMTLVDETNMYEGVGRMFILQS
Retrocopy APVDLELNKAFTEL*AKDIDIQQKVKLADIRIEQLNRTKKHAHLTDTEIMTLVDETNMYEGVGRMFILQS

Parental  KEVIHSQLLEKQKIAEEKIKELEQKKSYLERSVKEAEDNIREMLMARRAQ
          KEVIH.QL...................YLERSVKEAEDNIREMLMARRAQ
Retrocopy KEVIHHQLXXXXXXXXXXXXXXXXXXXYLERSVKEAEDNIREMLMARRAQ

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	7.31 RPM
SRP017611_brain	0.00 RPM	4.45 RPM
SRP017611_kidney	0.00 RPM	17.63 RPM
SRP017611_liver	0.00 RPM	4.06 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1893 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1893 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1893 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005742	8 retrocopies	retro_cfam_1742, retro_cfam_1893 , retro_cfam_1943, retro_cfam_251, retro_cfam_276, retro_cfam_417, retro_cfam_788, retro_cfam_997,
Equus caballus	ENSECAG00000011843	1 retrocopy	retro_ecab_53,
Erinaceus europaeus	ENSEEUG00000005357	1 retrocopy	retro_eeur_537,
Echinops telfairi	ENSETEG00000019281	1 retrocopy	retro_etel_1629,
Felis catus	ENSFCAG00000001272	1 retrocopy	retro_fcat_1323,
Homo sapiens	ENSG00000113068	1 retrocopy	retro_hsap_2606,
Macropus eugenii	ENSMEUG00000002726	3 retrocopies	retro_meug_380, retro_meug_686, retro_meug_801,
Microcebus murinus	ENSMICG00000000349	1 retrocopy	retro_mmur_1121,
Oryctolagus cuniculus	ENSOCUG00000009432	4 retrocopies	retro_ocun_1049, retro_ocun_1885, retro_ocun_804, retro_ocun_999,
Otolemur garnettii	ENSOGAG00000003376	6 retrocopies	retro_ogar_1025, retro_ogar_1216, retro_ogar_1412, retro_ogar_2217, retro_ogar_3129, retro_ogar_89,
Pan troglodytes	ENSPTRG00000017310	1 retrocopy	retro_ptro_1757,
Rattus norvegicus	ENSRNOG00000018653	1 retrocopy	retro_rnor_985,