RetrogeneDB ID: retro_cfam_1985

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 9:38095294..38095837(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPT1
• Ensembl ID: ENSCAFG00000003004
• Aliases: None
• Description: Canis lupus familiaris palmitoyl-protein thioesterase 1 (PPT1), mRNA. [Source:RefSeq mRNA;Acc:NM_001010944]

Sequence

>retro_cfam_1985
GTGGCGTCGCCCAGCTGCTTGTGGCTCCTGGTCGTCACTCTCCTGCCGGGATCCGGCACTGCCCGGGTGCCGTGGCGTGT
GGACCCAGCCACGCCGCTGCCGCTGGTGATCTGGCATGGGATGGAAGACAGCTGTTATAACCCCTTAAGCATGGGAGCTA
TCAAAAAAATGGTTGAGAAGAAAATACCCGGAATTTACATCTTATCTTTAAAGATTGGGAAGACCCTGATGGAGGATGTG
GAGAACAGCTTCTTCTTGAATGTCAATTCCCAAGTAACAACAGTGTGTCAGATTCTTGCTAAGGATCCTAAATTGCAGCA
TGGCTACGATGCTATGGGATTCTCCCAAGGAGGCCAATTTCTGAGGGCAGTGGCTTAGAGATGCCCATCACCTCCCATGA
TCAATCTGATCTCGATTGGGAGACAACATCAAAGTGTATATGGACTCCCTTGGTGCCCAGGGGAGAGCTCTCACATCTGT
GACTTGATCAGAAAAGCACTGAACGCTGGGGCTTACAACAAAGCTATTCAAGAAACCCTGGTG

Alignment

ORF - retro_cfam_1985 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.4 %
• Parental protein coverage: 59.15 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASPSCLWLLAVALLPGSGAARAPWRLDPAAPLPLVIWHGMGDSCCNPLSMGAIKKMVEEKIPGIYVLSL
          .ASPSCLWLL.V.LLPGSG.AR.PWR.DPA.PLPLVIWHGM.DSC.NPLSMGAIKKMVE.KIPGIY.LSL
Retrocopy VASPSCLWLLVVTLLPGSGTARVPWRVDPATPLPLVIWHGMEDSCYNPLSMGAIKKMVEKKIPGIYILSL

Parental  EIGKTLMEDVENSFFLNVNSQVTTVCQILAKDPKLHQGYNAMGFSQGGQFLRAVAQRCPSPPMINLISIG
          .IGKTLMEDVENSFFLNVNSQVTTVCQILAKDPKL..GY.AMGFSQGGQFLRAVA.RCPSPPMINLISIG
Retrocopy KIGKTLMEDVENSFFLNVNSQVTTVCQILAKDPKLQHGYDAMGFSQGGQFLRAVA*RCPSPPMINLISIG

Parental  GQHQGVYGLPRCPGESSHICDLIRKTLNAGAYNKAIQERLV
          .QHQ.VYGLP.CPGESSHICDLIRK.LNAGAYNKAIQE.LV
Retrocopy RQHQSVYGLPWCPGESSHICDLIRKALNAGAYNKAIQETLV

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	116.71 RPM
SRP017611_brain	0.00 RPM	204.04 RPM
SRP017611_kidney	0.00 RPM	125.73 RPM
SRP017611_liver	0.00 RPM	19.29 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1985 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1985 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1985 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013367	1 retrocopy	retro_btau_348,
Canis familiaris	ENSCAFG00000003004	1 retrocopy	retro_cfam_1985 ,
Loxodonta africana	ENSLAFG00000022663	2 retrocopies	retro_lafr_199, retro_lafr_422,
Procavia capensis	ENSPCAG00000002429	1 retrocopy	retro_pcap_94,
Tursiops truncatus	ENSTTRG00000004339	1 retrocopy	retro_ttru_659,