RetrogeneDB ID: retro_cfam_999

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 21:1505876..1506340(+)
• Located in intron of: ENSCAFG00000004018

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP6V1D
• Ensembl ID: ENSCAFG00000016369
• Aliases: None
• Description: None

Sequence

>retro_cfam_999
TCCCTCGTGCATGAAACCATCATGAAAGCCTATTAAAAGGAGTACAGACAGGTTGAAGCCTCCTCAAGAAAAAATCTGAT
TCCGTAGCTCTTCAATTTCAACAGATCCTAAAGAAGATAATCAAGACTAGAATGCTGATGGGTGAAATGATGAGAAAAGC
TGCCTTTTCACTTACTGAGGTCAAGTTCACAGCAGGAAACTTCAACACCACAGTTACCCAAAATGTAAATAAAGCTCCAG
TGAGGATTCTAGCTAAGAAAGATAATATAGCAGGTGTTACTTTCCCAGTGTTTGAACATTACCATGAAAGAACTGATAGT
TATGAACTGACTGGGTTAGCCAGAAGTGGGGAACAATTGGATAAATTAAACAGGAATTATGTTAAAGCAGTGGAATTCCT
GGTGGAACTAGCTTCCCTTCAGACTTCCTTTGTTACTTTGGATGAACCTATTAAGATAACCAAT

Alignment

ORF - retro_cfam_999 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.56 %
• Parental protein coverage: 62.25 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SRMAQTIMKAR-LKGAQTGRNLLKKKSDALTLRFRQILKKIIETKMLMGEVMREAAFSLAEAKFTAGDFS
          S....TIMKA..LKG.QTG..LLKKKSD...L.F.QILKKII.T.MLMGE.MR.AAFSL.E.KFTAG.F.
Retrocopy SLVHETIMKAY<LKGVQTG*SLLKKKSDSVALQFQQILKKIIKTRMLMGEMMRKAAFSLTEVKFTAGNFN

Parental  TTVIQNVNKAQVKIRAKKDNVAGVTLPVFEHYHEGTDSYELTGLARGGEQLAKLKRNYAKAVELLVELAS
          TTV.QNVNKA.V.I.AKKDN.AGVT.PVFEHYHE.TDSYELTGLAR.GEQL.KL.RNY.KAVE.LVELAS
Retrocopy TTVTQNVNKAPVRILAKKDNIAGVTFPVFEHYHERTDSYELTGLARSGEQLDKLNRNYVKAVEFLVELAS

Parental  LQTSFVTLDEAIKITN
          LQTSFVTLDE.IKITN
Retrocopy LQTSFVTLDEPIKITN

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	42.75 RPM
SRP017611_brain	0.00 RPM	54.22 RPM
SRP017611_kidney	0.00 RPM	85.06 RPM
SRP017611_liver	0.00 RPM	9.14 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_999 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_999 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_999 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008240	1 retrocopy	retro_amel_332,
Bos taurus	ENSBTAG00000016309	2 retrocopies	retro_btau_1757, retro_btau_408,
Canis familiaris	ENSCAFG00000016369	2 retrocopies	retro_cfam_1186, retro_cfam_999 ,
Choloepus hoffmanni	ENSCHOG00000003733	5 retrocopies	retro_chof_1229, retro_chof_2711, retro_chof_54, retro_chof_926, retro_chof_938,
Cavia porcellus	ENSCPOG00000009085	1 retrocopy	retro_cpor_36,
Felis catus	ENSFCAG00000011078	1 retrocopy	retro_fcat_632,
Myotis lucifugus	ENSMLUG00000006244	5 retrocopies	retro_mluc_2345, retro_mluc_442, retro_mluc_540, retro_mluc_666, retro_mluc_94,
Macaca mulatta	ENSMMUG00000021418	1 retrocopy	retro_mmul_1159,
Monodelphis domestica	ENSMODG00000009896	5 retrocopies	retro_mdom_1196, retro_mdom_1522, retro_mdom_1730, retro_mdom_390, retro_mdom_594,
Mustela putorius furo	ENSMPUG00000007002	2 retrocopies	retro_mputfur_1381, retro_mputfur_748,
Otolemur garnettii	ENSOGAG00000015052	1 retrocopy	retro_ogar_966,
Sus scrofa	ENSSSCG00000002288	1 retrocopy	retro_sscr_357,
Ictidomys tridecemlineatus	ENSSTOG00000027710	1 retrocopy	retro_itri_383,
Vicugna pacos	ENSVPAG00000005696	1 retrocopy	retro_vpac_232,
Drosophila melanogaster	FBgn0040377	1 retrocopy	retro_dmel_70,