RetrogeneDB ID: retro_cfam_1265

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 28:12694082..12694748(+)
• Located in intron of: ENSCAFG00000009536

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM147
• Ensembl ID: ENSCAFG00000006960
• Aliases: None
• Description: transmembrane protein 147 [Source:HGNC Symbol;Acc:30414]

Sequence

>retro_cfam_1265
ATGACCCTATTCCACTTTGGGAATGACTTCACCCTGGCCTACTTCCCCTACTTCATCACCTACAAACAAGTACAATGTCT
GAGTACAATGCCTTCTAGAAATGTGCACAAACCAGGGTCACCTACCTCTTCATGCAGCTGTGCAAGATGCTGTTCCTGAC
CACTTTTTTTCCTACCTGGGAAGGCAGCATCTATGACTTTTTTGGGGTGTTATGAAGGTCAGCATGGATGCGGCAGTCTG
GTAGGCCTAAACCTTGTCAGGTCCTGGAATGTGCGCGAAGGAGAGTATAAGATCATGGTTCTGCCTTGGGCTGGGCCACC
GCCAAGCTCATTATGTCCCACTGCATCCCCTCTGAGTTGGAGCCCAGGGCATTGAGTTTGACTGGAAGTACATCCAGAAG
AGCCTGGACACCAACATCAGCCTAGTTCATTACATCATCTCATATGCCCAGGTCTGGATGATAACATGCTACAACCTATA
CTGTACTTTTCAGCCAGCAATATTCCTACTGATGTTCTTTAACGTCCATGAGGCCTTCGTTATGGAGACCTTCATCTACC
TCTGTTCCCTGGGCAGCTGGACAGCACAGCTGGCCGAGCAATGGTGACAAGCCTGCTGGCCCTTAGCACCCTAGCTCTGT
GTGTCACCATTGTCAACATGCACTCC

Alignment

ORF - retro_cfam_1265 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.48 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MTLFHFGNCFALAYFPYFITYK-CSGLSEYNAFWKCVQAGVTYLFVQLCKMLFLATFFPTWEGGIYDFIG
          MTLFHFGN.F.LAYFPYFITYK..S..SEYNAF.KC.Q..VTYLF.QLCKMLFL.TFFPTWEG.IYDF.G
Retrocopy MTLFHFGNDFTLAYFPYFITYK<TSTMSEYNAF*KCAQTRVTYLFMQLCKMLFLTTFFPTWEGSIYDFFG

Parental  EF-MKASVDVA-DLIGLNLVMSRNAGKGEYKIMV-AALGWATAELIMSRCIP-LWVGARGIEFDWKYIQM
          ...MK.S.D.A..L.GLNLV.S.N...GEYKIMV..ALGWATA.LIMS.CIP.L.VGA.GIEFDWKYIQ.
Retrocopy VL<MKVSMDAA<SLVGLNLVRSWNVREGEYKIMV<SALGWATAKLIMSHCIP<L*VGAQGIEFDWKYIQK

Parental  SIDSNISLVHYIVASAQVWMITRYDLYHTFRPAVLLLMFLSVYKAFVMETFVHLCSLGSWTALLA-RAVV
          S.D.NISLVHYI...AQVWMIT.Y.LY.TF.PA..LLMF..V..AFVMETF..LCSLGSWTA.LA.RA.V
Retrocopy SLDTNISLVHYIISYAQVWMITCYNLYCTFQPAIFLLMFFNVHEAFVMETFIYLCSLGSWTAQLA<RAMV

Parental  TGLLALSTLALYVAVVNVHS
          T.LLALSTLAL.V..VN.HS
Retrocopy TSLLALSTLALCVTIVNMHS

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	67.70 RPM
SRP017611_brain	0.00 RPM	38.11 RPM
SRP017611_kidney	0.00 RPM	129.10 RPM
SRP017611_liver	0.00 RPM	23.57 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1265 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1265 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1265 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000010132	1 retrocopy	retro_acar_105,
Ailuropoda melanoleuca	ENSAMEG00000000375	1 retrocopy	retro_amel_1193,
Bos taurus	ENSBTAG00000015920	1 retrocopy	retro_btau_1546,
Canis familiaris	ENSCAFG00000006960	2 retrocopies	retro_cfam_1070, retro_cfam_1265 ,
Dasypus novemcinctus	ENSDNOG00000004059	1 retrocopy	retro_dnov_1123,
Felis catus	ENSFCAG00000006373	2 retrocopies	retro_fcat_1489, retro_fcat_224,
Myotis lucifugus	ENSMLUG00000016383	1 retrocopy	retro_mluc_1889,
Mustela putorius furo	ENSMPUG00000006709	1 retrocopy	retro_mputfur_588,
Tarsius syrichta	ENSTSYG00000008207	1 retrocopy	retro_tsyr_56,
Tursiops truncatus	ENSTTRG00000015114	2 retrocopies	retro_ttru_1406, retro_ttru_219,