RetrogeneDB ID: retro_cfam_344

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 10:9697696..9698275(+)
• 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_344
ATGAGTTGGGTTTATAGCCCTAGTTCTTCTGGGGTTCCCTATGCAAATGCCAAAGGAATTGCTTATCCAGCTGATTTCTC
CCTGTGCTATGCAGCCACCACTCCTGCTTGCTCCCCCAACATGTATTTTGGAGCAAATCCTAACTTTCAAACAGGTTAAA
CTCCTGGCACACTCTGCACAGCATCCTGTTCCTCCAACAGCAGGGTAGCGCCACCGTACTCCCACTCCTGGAGCCCTTGC
TGGCCACTGTGTGCCCTGTACATAATACCTATGCCCAGCAGAGCTCCTATGTGCAACAGGCACATAGGATACACAGCCCC
TGTGCACAGTTGACCCTCATGTCATCACCACACCACAGTGGGGCAGCCCAACGACATGCCAGTGACGATGTAGACTCCTC
CCATCCCTCCACCTAGAGGCAATGGCATCAGCATGGGCATGGCTATAACCACCACGGCCATGTCAGTAGGTACCCTGCTG
ACCAACCACTTCTCAGCTCCTGTTGCATGCCACCCAGCCACTGTGCCCACGTATTGGGCCCCAGGAATGCCCACCTCCAG
TTAAGTGTCCCTTCAGTGG

Alignment

ORF - retro_cfam_344 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.14 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MNPVYSPGSSGVPYANAKGIGYPAGFPMGYAAAAPAYSPNMYPGANPTFQTGYTPGTPYKVSCSPTSGAV
          M..VYSP.SSGVPYANAKGI.YPA.F...YAA..PA.SPNMY.GANP.FQTG.TPGT....SCS..S...
Retrocopy MSWVYSPSSSGVPYANAKGIAYPADFSLCYAATTPACSPNMYFGANPNFQTG*TPGTLCTASCSSNSRVA

Parental  PPYSSS-PNPYQTAVYPVRSAYPQQSPYAQQ-GTYYTQPLYAAPPHVI-HHTTVVQPNGMPATVYPAPIP
          PPYS.S...P....V.PV...Y.QQS.Y.QQ.GT..TQPL....PHVI.HHTTV.QPN.MP.T....PIP
Retrocopy PPYSHS<LEPLLATVCPVHNTYAQQSSYVQQ<GT*DTQPLCTVDPHVI<HHTTVGQPNDMPVTM*TPPIP

Parental  PPRGNGVTMGMVAGTTMAMSAGTLLTAHSPTPVAPHPVTVPTYRAPGTPTYSYVPPQW
          PPRGNG..MGM.A.TT.AMS.GTLLT.H...PVA.HP.TVPTY.APG.PT.S.V..QW
Retrocopy PPRGNGISMGM-AITTTAMSVGTLLTNHFSAPVACHPATVPTYWAPGMPTSS*VSLQW

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_344 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_344 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_344 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,