RetrogeneDB ID: retro_cfam_1002

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 21:6833994..6834629(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CRLS1
• Ensembl ID: ENSCAFG00000005934
• Aliases: None
• Description: cardiolipin synthase 1 [Source:HGNC Symbol;Acc:16148]

Sequence

>retro_cfam_1002
TCTGCTACTGAAGCCCCAGATGGACAATGCGGCCTGACAAGCACCATCAAGCCTATATGAAAACCTGTAGACAATTCCAT
ATATGTTGTCAATGAGGAGAATCAATTTAGCCTCAGTTCGGGGCTCTTTGATTACTAGAGAAGATTTTGATATTGCACTA
GGAGTTTTTGCTCTAGTTGGGCTCACTGATTTGTTGCTTGGATTTATTGCTTGAAACTGGGACAATTGATAACCAGCTGT
GGGAAACATTCTTGGTCCACTTGCTGATGAAATCCCTATCAATGACCTATATATTAGCGTGCCCTAAACAGATCTTACTC
CAGTTTCACTTATTTATATGATAATTTTGAAGATGTAATATTGGTTGCTATCATCTTTATGTCAGATATCGAATTCTTCC
AACACTGAGAACACTTGCTAAGTATTTCAATCCTTGCTGTGTCACTGCTAAATTAAAACCAACATGTATCCACAAAGTAA
ACATAGCAGTCCAGTTAATCTTGGTGGTTTCTTTGGCAGCTGTGGTTTTCAATTATGCTGACAGTATTTATCTTCAGATA
CTGTGGTGTTTTATATTTTGCAGCACAGATGCATCAGCTTATAGTTACTATCATCATGCTCAGAATGCTGTCAGG

Alignment

ORF - retro_cfam_1002 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.81 %
• Parental protein coverage: 70.53 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AAAEARGGRWGQASA-ASLYENPWTIPNMLSMTRIGLAPVLGYLIIEEDFNIALGVFALAGLTDLLDGFI
          .A.EA..G..G..S...SLYEN..TIP.MLSM.RI.LA.V.G.LI..EDF.IALGVFAL.GLTDLL.GFI
Retrocopy SATEAPDGQCGLTST>SSLYENL*TIPYMLSMRRINLASVRGSLITREDFDIALGVFALVGLTDLLLGFI

Parental  ARNWANQKSALGSALDPLADKILISILYVSLTYADLIPVPLTYMIISR-DVMLIAAVF-YVRYRTLPTPR
          A.NW.N...A.G..L.PLAD.I.I..LY.S....DL.PV.L.YMII...DV.L.A..F.YVRYR.LPT.R
Retrocopy A*NWDN**PAVGNILGPLADEIPINDLYISVP*TDLTPVSLIYMIILK<DVILVAIIF<YVRYRILPTLR

Parental  TLSKYFNPCYATARLKPTFISKVNTAVQLILVAASLAAPVFNYADSIYLQILWCFTAFTTAASAYSYYHY
          TL.KYFNPC..TA.LKPT.I.KVN.AVQLILV..SLAA.VFNYADSIYLQILWCF....T.ASAYSYYH.
Retrocopy TLAKYFNPCCVTAKLKPTCIHKVNIAVQLILV-VSLAAVVFNYADSIYLQILWCFIFCSTDASAYSYYHH

Parental  GRKTVQ
          ....V.
Retrocopy AQNAVR

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	15.33 RPM
SRP017611_brain	0.00 RPM	11.83 RPM
SRP017611_kidney	0.00 RPM	48.14 RPM
SRP017611_liver	0.00 RPM	27.05 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1002 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1002 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1002 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010596	1 retrocopy	retro_amel_1758,
Bos taurus	ENSBTAG00000000065	1 retrocopy	retro_btau_1167,
Canis familiaris	ENSCAFG00000005934	1 retrocopy	retro_cfam_1002 ,
Equus caballus	ENSECAG00000023869	2 retrocopies	retro_ecab_247, retro_ecab_930,
Felis catus	ENSFCAG00000023647	1 retrocopy	retro_fcat_1393,
Microcebus murinus	ENSMICG00000011666	1 retrocopy	retro_mmur_751,
Mustela putorius furo	ENSMPUG00000006349	1 retrocopy	retro_mputfur_1021,
Rattus norvegicus	ENSRNOG00000021273	3 retrocopies	retro_rnor_2865, retro_rnor_2866, retro_rnor_2977,