RetrogeneDB ID: retro_cfam_1070

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 22:18032077..18032661(-)
• Located in intron of: None

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_1070
GAGTACAACACCTTCTGGAAGCATGTGCAGGCCAGAGGCACCCACCTCTTCACACTGCTGCGAAAGATGCTGCTCCTGGC
CATTTTTCTCCCACCAGGAAAGGTGGCATCTATGACTTCATTGGGGATTTTGTGAAGGCCACAGTGGATGTGATAGACCT
GATAGACCTAAACCTTGTCACATCCTGGAATGCAGGCAAGGCGGGGTACGAGATCATGGCTGCTGCCTTGGGCTACCCAC
CACCAAGCTCATTGTGTCCTGCTGAATCCCCTTTTGGTTTGGAGCCCCGGATTTGAGTTTGACTGAAGTATATCCAGATG
GGCAATGACTCCAATATCAGTCTGGTCCATTACATCGTTTCATCTGCCCAGGTCTGGATCACAAGGTGCTATGACCTGTG
CCACAGTTTTCAGCCAGTAGTACTTCTACTGGCGTTCCTTAGCATCTACGAGGCCTTAGTCAGGGAGACCTTCATCCCCC
TCTGTTCCCTGGGCAGCTGGACAGCATTGTCCAGAGCAGTGGTGACAGGGCTGCTGGCTCTCAGTACCCTGGTGCTCCAT
GTCACTGCTATCAGCATACACTCT

Alignment

ORF - retro_cfam_1070 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 87.95 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  EYNAFWKCVQAGVTYLFVQLCKMLFLATFFP-TWEGGIYDFIGEFMKASVDVADLIGLNLVMSRNAGKGE
          EYN.FWK.VQA..T.LF..L.KML.LA.F.P.T..GGIYDFIG.F.KA.VDV.DLI.LNLV.S.NAGK..
Retrocopy EYNTFWKHVQARGTHLFTLLRKMLLLAIFLP<TRKGGIYDFIGDFVKATVDVIDLIDLNLVTSWNAGKAG

Parental  YKIMVAALGWA-TAELIMSRCIPLWVGAR-GIEFD-WKYIQMSIDSNISLVHYIVASAQVWMITRYDLYH
          Y.IM.AALG...T..LI.S..IP.W.GA..G.EFD..KYIQM..DSNISLVHYIV.SAQVW....YDL.H
Retrocopy YEIMAAALGYP<TTKLIVSC*IPFWFGAP<GFEFD<LKYIQMGNDSNISLVHYIVSSAQVWITRCYDLCH

Parental  TFRPAVLLLMFLSVYKAFVMETFVHLCSLGSWTALLARAVVTGLLALSTLALYVAVVNVHS
          .F.P.VLLL.FLS.Y.A.V.ETF..LCSLGSWTA.L.RAVVTGLLALSTL.L.V.....HS
Retrocopy SFQPVVLLLAFLSIYEALVRETFIPLCSLGSWTA-LSRAVVTGLLALSTLVLHVTAISIHS

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_1070 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1070 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1070 has 0 orthologous retrocopies within eutheria group .

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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,