RetrogeneDB ID: retro_cfam_1777

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 6:6672035..6672358(+)
• Located in intron of: ENSCAFG00000013010

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATPIF1
• Ensembl ID: ENSCAFG00000032458
• Aliases: None
• Description: ATPase inhibitory factor 1 [Source:HGNC Symbol;Acc:871]

Sequence

>retro_cfam_1777
ATGGCTGTCATGGACGTGTCCACACAGATGTGGCTGGGCATGTGGGGCTTAGGGCACTGTAACCTGAGGCTTCGCCTCTG
AACGATCAGAAGACTCAGAGGATGCCAGCACCGCCAGCTTGATCCAGGAGGCAGGTGGGGCCTTTGGAAAGAAAGAGCAA
GCTGAAGAGGAATGATACTTCCGAGTACATACTAGAGAACAACTGGCAGCCTTGAAGAAACACCATGAAGATGAGATCAC
TCATCATGTAAAGGAGATTGAGCATCTGCAGAAAGAAATTGAATGGCACAAGAAGAAAATTTAAAAATCTAAAACATGAT
GAT

Alignment

ORF - retro_cfam_1777 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.97 %
• Parental protein coverage: 99.06 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAVSAVSSRVWLGMWGV-RAL-QTRGFGSER---SEDPGSAGSIREAGGAFGKREQAEEERYFRARTREQ
          MAV..VS...WLGMWG..RAL..T.GF.SER...SED...A..I.EAGGAFGK.EQAEEE.YFR..TREQ
Retrocopy MAVMDVSTQMWLGMWGL<RAL<VT*GFASERSEDSEDASTASLIQEAGGAFGKKEQAEEE*YFRVHTREQ

Parental  LAALKKHHEDEISHHIKEIERLQKEIERHKKKI-KNLKSDD
          LAALKKHHEDEI.HH.KEIE.LQKEIE.HKKKI.KNLK.DD
Retrocopy LAALKKHHEDEITHHVKEIEHLQKEIEWHKKKI>KNLKHDD

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	0.34 RPM	90.76 RPM
SRP017611_brain	0.16 RPM	37.24 RPM
SRP017611_kidney	0.07 RPM	172.22 RPM
SRP017611_liver	0.15 RPM	30.53 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1777 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1777 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1777 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000032458	2 retrocopies	retro_cfam_1777 , retro_cfam_651,
Callithrix jacchus	ENSCJAG00000009581	1 retrocopy	retro_cjac_1406,
Dasypus novemcinctus	ENSDNOG00000015460	1 retrocopy	retro_dnov_2592,
Myotis lucifugus	ENSMLUG00000000170	1 retrocopy	retro_mluc_363,
Mustela putorius furo	ENSMPUG00000015536	1 retrocopy	retro_mputfur_1570,
Mus musculus	ENSMUSG00000054428	2 retrocopies	retro_mmus_2516, retro_mmus_908,
Otolemur garnettii	ENSOGAG00000010337	2 retrocopies	retro_ogar_116, retro_ogar_268,
Pteropus vampyrus	ENSPVAG00000017615	1 retrocopy	retro_pvam_817,
Rattus norvegicus	ENSRNOG00000013300	1 retrocopy	retro_rnor_2655,
Sorex araneus	ENSSARG00000010860	1 retrocopy	retro_sara_458,
Ictidomys tridecemlineatus	ENSSTOG00000020766	1 retrocopy	retro_itri_1240,