RetrogeneDB ID: retro_cfam_451

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 11:26747300..26748036(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJC7
• Ensembl ID: ENSCAFG00000015749
• Aliases: None
• Description: DnaJ (Hsp40) homolog, subfamily C, member 7 [Source:HGNC Symbol;Acc:12392]

Sequence

>retro_cfam_451
GAAGGGGCTTGCATTGCTTACAGAAATGCTAAAGCACTTAAAGATGGGAATAAAGCATTTAAAGAAGGAAATTACAAGCT
AGCCTATGAACTGTACACAGAAGCCCTGGGGATAGACCCTAACAATATAAAAACAAATGCTAAACTCTACTGTAATCAGG
GCACAGTTAACTCCAAGCTTAGGAAACTAGATGATGCAATAGAAGACTGCACGAGTGCAGTGAAGCTCGATGCCACTTAT
ATAAAAGCCTACTTGAGAAGAGCTCAGTGTTACATGGACACAGAACAGTATGAAGAAGCAGTGCGGGACTATGAAAAAGT
ATATCAGACGGAGAAAACAAAAGAACACAAACAGCTCCTAAAAAATGCACAGCTGGAACGAAGAAGATTAAGAGGAAAGA
TTACTACAAAATTCTGGGAGTGGACAAGAATGCCTCTGAGGATGAAATCAAGAAAGCTTACCGACAACGGGCCTTGATGC
ACCATCCAGATCGGCACAGTGGAGCCAGTGCCGAAGTTCAGGAGAGGAGAAATAGTTCAAGGAAGTTGGAGAAGCTTTTA
CCATCCTGTCTGATCCCAAGAAAAAGACTCGCTATGACAGTGGACAGGACCTAGATGAGGAAGGCATGAATATGGGCGAT
TTTGACGCAAACAATATCTTCAAGGCATTCTTTGGCGGTCCTGGGGGCTTCAGCTTTGAAGCATCTGGTCCAGGGAATTT
CTTTTTTCAATTTGGC

Alignment

ORF - retro_cfam_451 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.07 %
• Parental protein coverage: 50.81 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EKACIACRNAKALKAKKEDGNKAFKEGNYKLAYELYTEALGIDPNNIKTNAKLYCNRGTVNSKLRKLDDA
          E.ACIA.RNAKALK....DGNKAFKEGNYKLAYELYTEALGIDPNNIKTNAKLYCN.GTVNSKLRKLDDA
Retrocopy EGACIAYRNAKALK----DGNKAFKEGNYKLAYELYTEALGIDPNNIKTNAKLYCNQGTVNSKLRKLDDA

Parental  IEDCTSAVKLDATYIKAYLRRAQCYMDTEQYEEAVRDYEKVYQTEKTKEHKQLLKNAQLE-LKKSKRKDY
          IEDCTSAVKLDATYIKAYLRRAQCYMDTEQYEEAVRDYEKVYQTEKTKEHKQLLKNAQLE..KK.KRKDY
Retrocopy IEDCTSAVKLDATYIKAYLRRAQCYMDTEQYEEAVRDYEKVYQTEKTKEHKQLLKNAQLE<TKKIKRKDY

Parental  YKILGVDKNASEDEIKKAYRKRALMHHPDRHSGASAEVQK-EEEKKFKEVGEAFTILSDPKKKTRYDSGQ
          YKILGVDKNASEDEIKKAYR.RALMHHPDRHSGASAEVQ..EE.K.FKEVGEAFTILSDPKKKTRYDSGQ
Retrocopy YKILGVDKNASEDEIKKAYRQRALMHHPDRHSGASAEVQE<EE-K*FKEVGEAFTILSDPKKKTRYDSGQ

Parental  DLDEEGMNMGDFDANNIFKAFFGGPGGFSFEASGPGNFFFQFG
          DLDEEGMNMGDFDANNIFKAFFGGPGGFSFEASGPGNFFFQFG
Retrocopy DLDEEGMNMGDFDANNIFKAFFGGPGGFSFEASGPGNFFFQFG

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	1.51 RPM	62.91 RPM
SRP017611_brain	0.40 RPM	60.10 RPM
SRP017611_kidney	0.20 RPM	72.91 RPM
SRP017611_liver	0.00 RPM	19.58 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_451 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_451 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_451 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015749	1 retrocopy	retro_cfam_451 ,
Callithrix jacchus	ENSCJAG00000035699	2 retrocopies	retro_cjac_2381, retro_cjac_2475,
Homo sapiens	ENSG00000168259	1 retrocopy	retro_hsap_3524,
Gorilla gorilla	ENSGGOG00000010230	2 retrocopies	retro_ggor_2382, retro_ggor_396,
Myotis lucifugus	ENSMLUG00000011968	2 retrocopies	retro_mluc_1232, retro_mluc_1527,
Macaca mulatta	ENSMMUG00000016118	3 retrocopies	retro_mmul_1084, retro_mmul_1854, retro_mmul_501,
Nomascus leucogenys	ENSNLEG00000011230	2 retrocopies	retro_nleu_1569, retro_nleu_490,
Pongo abelii	ENSPPYG00000008402	2 retrocopies	retro_pabe_2911, retro_pabe_317,
Pan troglodytes	ENSPTRG00000009188	2 retrocopies	retro_ptro_2393, retro_ptro_304,