RetrogeneDB ID: retro_cfam_1999

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 9:24270298..24270764(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPIB
• Ensembl ID: ENSCAFG00000017053
• Aliases: None
• Description: peptidylprolyl isomerase B (cyclophilin B) [Source:HGNC Symbol;Acc:9255]

Sequence

>retro_cfam_1999
GTGGTCATTGGTCTCTTTGGAAAGACTGTTCCAAAAACAGTGGATAATTTTGTGGCCTTAGCCATGGGGGAGAAAGGATT
TGGCTACAAAGACAGCAAATTCCATCGTGTGATCAAGGACTTCATGATCCAGAGTGGAGACTTTACCCGGGGAGATGGCG
CTAGAGGAAAGAGCATCTATGGTGAATGCTTCCCTGGTGAGAGCTTCAAGCTGAAACACTATGGGCCTGGCTGGGTGAGC
ATGGCCAATGCAGGCAAAGACACCAACGGCTCCTAGTTCTTTATCACGAGGGTTAAGACCGCCTGGCTAGATGGCAAGCA
CGTGGCGTTGGCAAAGTTTTGGAAGGCATGGAGGTAGTACAGAAGGTGGAGAGCACGAAAACAGACAGGACAAGCCCCTG
CAGGATGTGACGATTGCAGACGGTGGCAAGATTGAGGTGGAGAAGCCCTTCGCCAACGCCAAGGAA

Alignment

ORF - retro_cfam_1999 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.42 %
• Parental protein coverage: 72.69 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VVIGLFGKTVPKTVDNFVALATGEKGFGYKDSKFHRVIKDFMIQGGDFTRGDGTGGKSIYGERFPDENFK
          VVIGLFGKTVPKTVDNFVALA.GEKGFGYKDSKFHRVIKDFMIQ.GDFTRGDG..GKSIYGE.FP.E.FK
Retrocopy VVIGLFGKTVPKTVDNFVALAMGEKGFGYKDSKFHRVIKDFMIQSGDFTRGDGARGKSIYGECFPGESFK

Parental  LKHYGPGWVSMANAGKDTNGSQFFITTVKTAWLDGKHVVF-GKVLEGMEVVRKVESTKTDSRDKP-LKDV
          LKHYGPGWVSMANAGKDTNGS.FFIT.VKTAWLDGKHV...GKVLEGMEVV.KVESTKTD.R..P.L.DV
Retrocopy LKHYGPGWVSMANAGKDTNGS*FFITRVKTAWLDGKHVAL<GKVLEGMEVVQKVESTKTD-RTSP<LQDV

Parental  TIADCGKIEVEKPFAIAKE
          TIAD.GKIEVEKPFA.AKE
Retrocopy TIADGGKIEVEKPFANAKE

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	145.36 RPM
SRP017611_brain	0.00 RPM	71.37 RPM
SRP017611_kidney	0.00 RPM	183.52 RPM
SRP017611_liver	0.00 RPM	96.37 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1999 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1999 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1999 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017053	1 retrocopy	retro_cfam_1999 ,
Canis familiaris	ENSCAFG00000032245	1 retrocopy	retro_cfam_180,
Equus caballus	ENSECAG00000017164	1 retrocopy	retro_ecab_617,
Echinops telfairi	ENSETEG00000012671	1 retrocopy	retro_etel_1493,
Loxodonta africana	ENSLAFG00000018698	1 retrocopy	retro_lafr_521,
Oryctolagus cuniculus	ENSOCUG00000012012	1 retrocopy	retro_ocun_413,