RetrogeneDB ID: retro_cfam_1748

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 5:81050506..81050902(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM168B
• Ensembl ID: ENSCAFG00000004222
• Aliases: None
• Description: family with sequence similarity 168, member B [Source:HGNC Symbol;Acc:27016]

Sequence

>retro_cfam_1748
GTATCCTGTTCCCCCACCAGCAGGGCAGTGCCACCATATTCCTCTTCCCCCAACCCTTCGCAGACTGCTATGTACCCTAT
GCGAAGTGCCTACCCCCAGCAGAGCCCCTATGCACAAGGCAAGTAGGACACACACCATATGCCCCGCCTAGTCACACCAT
CCACCATATCACAGTGTTGCAGCCCAACCGCATGCTGGCGATGGTATACCCTGCTCTCATCCCTCCACTTAGAGGCAATG
GCATCACCATGAGCATGGTATCTGGGACCACTATGGCCATGTCAACAGGTATCCTGTTGACCATCCACTCCCCAACTCCT
GTTGTCCCCCACCCAGTCACTGTGCGCACATATTGGAGCCCTGGGAATGCCCATCTACAGCTATGTCCCCTCTCAG

Alignment

ORF - retro_cfam_1748 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.38 %
• Parental protein coverage: 68.72 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VSCSPTSGAVPPYSSSPNPYQTAVYPVRSAY-PQQSPYAQQGTYYTQPLYAAPPHVIHHTTVVQPNGMPA
          VSCSPTS.AVPPYSSSPNP.QTA.YP.RSAY.P...P........T...YA.P.H.IHH.TV.QPN.M.A
Retrocopy VSCSPTSRAVPPYSSSPNPSQTAMYPMRSAY<PPAEPLCTRQVGHTP--YAPPSHTIHHITVLQPNRMLA

Parental  TVYPAPIPPPRGNGVTMGMVAGTTMAMSAGTLLTAHSPTPVAPHPVTVPTYRAPGT-PTYSYVPPQ
          .VYPA.IPP.RGNG.TM.MV.GTTMAMS.G.LLT.HSPTPV.PHPVTV.TY..PG..P.YSYVP.Q
Retrocopy MVYPALIPPLRGNGITMSMVSGTTMAMSTGILLTIHSPTPVVPHPVTVRTYWSPGN>PIYSYVPSQ

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	37.13 RPM
SRP017611_brain	0.00 RPM	31.04 RPM
SRP017611_kidney	0.00 RPM	18.03 RPM
SRP017611_liver	0.00 RPM	8.70 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1748 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1748 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1748 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000004222	2 retrocopies	retro_cfam_1748 , retro_cfam_344,
Choloepus hoffmanni	ENSCHOG00000009590	1 retrocopy	retro_chof_551,
Equus caballus	ENSECAG00000017018	1 retrocopy	retro_ecab_27,
Felis catus	ENSFCAG00000000303	1 retrocopy	retro_fcat_1218,
Monodelphis domestica	ENSMODG00000018633	1 retrocopy	retro_mdom_1625,
Mustela putorius furo	ENSMPUG00000011824	1 retrocopy	retro_mputfur_454,
Ictidomys tridecemlineatus	ENSSTOG00000000206	2 retrocopies	retro_itri_191, retro_itri_262,
Tupaia belangeri	ENSTBEG00000017162	1 retrocopy	retro_tbel_83,