RetrogeneDB ID: retro_cfam_544

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 13:19830176..19830766(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FTSJ1
• Ensembl ID: ENSCAFG00000015339
• Aliases: None
• Description: FtsJ RNA methyltransferase homolog 1 (E. coli) [Source:HGNC Symbol;Acc:13254]

Sequence

>retro_cfam_544
GCTGTGGATCATCAGGCTATGGCTTCATTACTAGGTGTATTATAGATCCAAGGGGACATCACCCAGTCATCCACTGCCAG
GATCATCCAGACTTTGAGGGCTGCCCTGTGGACCTAATGGTGTGTGATGGGGCTCCCAATGTAACCAGCTCCATGATGTG
GATAAGTATATGTAGGCCTAGATCCCCCTAGTACCTCTGAACATTGCTATACACATCTTGCAGCCAAGGGGCTGCTCTAT
AGCCAAGATCTTTGGAGTTCAGGATGTGACCCTGAGCTATAGCCAGCTGCATCTCTTCATCTCCAGTGTGCTGTGTGCCA
AGCCCAGGAGCAGCCCTCACTCCAGCACAGGGGCCTTCACTGTCTGTCAGGGTTATGACCCCACTGAGGGCTTCCTTCTG
GACCTGACCTTCTGGACCAAACTCTTGTGGGACTACTCTTACAATCCATTATTTCAGCAAGTTAGGTGATCCTACTCACA
TCACTGTGCCATTTGTGACCTGTAGGGACCTGAGCTATTGTTTGGGAGGCAGTTACCCACTGGCCCTAGAGGAAGGATCA
GAGTACAAGTACACTCCACCACTCCATCCA

Alignment

ORF - retro_cfam_544 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.33 %
• Parental protein coverage: 59.57 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AVDLQAMAPLPGVLQIQGDITQLSTAKEIIQ-HFEGCPADLVVCDGAPDVTG-LHDVDEYMQAQLLLAAL
          AVD.QAMA.L.GVL.IQGDITQ.STA..IIQ..FEGCP.DL.VCDGAP.VT..LHDVD.YM.A...L..L
Retrocopy AVDHQAMASLLGVL*IQGDITQSSTAR-IIQ<DFEGCPVDLMVCDGAPNVTS<LHDVDKYM*A*IPLVPL

Parental  NIATHVLKPGGCFVAKIFRGRDVTLIYSQLRVFFSNVLCAKPRSSRNSSIEAFAVCQGYDPPEGFLPDLT
          NIA.H.L.P.GC..AKIF...DVTL.YSQL..F.S.VLCAKPRSS..SS..AF.VCQGYDP.EGFL.DLT
Retrocopy NIAIHILQPRGCSIAKIFGVQDVTLSYSQLHLFISSVLCAKPRSSPHSSTGAFTVCQGYDPTEGFLLDLT

Parental  ---KPLLDHSYDPDFNQ-LDGPTRIIVPFVTCGDLSSYDSDRSYPLDLEDGSEYKYTPPTQP
          ...K.L.D.SY.P.F.Q.L..PT.I.VPFVTC.DL.SY....SYPL.LE.GSEYKYTPP..P
Retrocopy FWTKLLWDYSYNPLFQQ>LGDPTHITVPFVTCRDL-SYCLGGSYPLALEEGSEYKYTPPLHP

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	50.52 RPM
SRP017611_brain	0.00 RPM	32.63 RPM
SRP017611_kidney	0.00 RPM	23.91 RPM
SRP017611_liver	0.00 RPM	12.62 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_544 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_544 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_544 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
Bos taurus	ENSBTAG00000031829	1 retrocopy	retro_btau_27,
Canis familiaris	ENSCAFG00000015339	1 retrocopy	retro_cfam_544 ,
Erinaceus europaeus	ENSEEUG00000001469	1 retrocopy	retro_eeur_222,
Echinops telfairi	ENSETEG00000014092	3 retrocopies	retro_etel_1697, retro_etel_1803, retro_etel_1928,
Myotis lucifugus	ENSMLUG00000003977	1 retrocopy	retro_mluc_1329,
Oryctolagus cuniculus	ENSOCUG00000008009	1 retrocopy	retro_ocun_870,
Otolemur garnettii	ENSOGAG00000016174	1 retrocopy	retro_ogar_180,
Sorex araneus	ENSSARG00000007091	1 retrocopy	retro_sara_26,