RetrogeneDB ID: retro_cfam_1290

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 29:17165454..17166258(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000007577
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PTGR1
• Ensembl ID: ENSCAFG00000003000
• Aliases: None
• Description: prostaglandin reductase 1 [Source:HGNC Symbol;Acc:18429]

Sequence

>retro_cfam_1290
GATATGATGATGGGGCAACAAGTGGCCAGAGTTCTGGAAAGTAAAATCTCAGCCTTCCCAGCAGGAACTGTGGTAGTGGC
TTCTTCAGGCTGGACATCGCATTCTATTTCTGATGGGAAAGATTTGGAAAAGCTGCCTGCAGAGTGGCCAAACACAGTAC
CAGTGTCTTTGGCTCTGGGAACAATGGGCATGAAAGGACTAACAGCCTACTTTGGCCTCCCTGACACCTGTGGTGTGAAG
GGTGGAGAAACAGTGATGGTTAATGCAGCAGCAGGGGCAGTGGGTTCTGTGGTGGGGCAGATTGCTAAGCTCAAGGACTG
CAAAGTAGTTGGAGCAGCAGGGTCTGACGAAAAGCTTGCCTACCTTAAAAAACTTGGATAGGATGTTGACTTTAACTACA
AAAACCATAGAGTCTTCAGAAGAAACTTTGAAAAAAACCTCTCCTGATGGTTATGATTGTTACTTTGATAATGTAGGTGG
AGAGTTTTCAAACATTGTTATTCCCCAGATGAGGAAATTTGGAAGAATTGCTGTTTGTGGCGCCATCCCGACACATAATA
GTACTTGCCCACTTCCCCCAGGCCCACCCCCAGAGAATATTATCAGCAGCTCCACACAGAAGGGTTCATCGTTTATCGCT
GGCAAGGAGAGGTCCGCCAGAACGCTCTGAAAGACTTGCTGACATGGGTCATAGAGGGTAAAATCCAGTACCATGAATAC
ATCATTGAAGGATTTGAAAACATGCCAGCTGCATTTATGGGAATGCTGAAAGGAGATAATTTGGGAAAAACAATAGTGAA
AGCA

Alignment

ORF - retro_cfam_1290 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.93 %
• Parental protein coverage: 81.76 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DMMMGQQVARVVESKNSAFPAGTVVVASSGWTSHSISDGKDLEKLPAEWPDTVPVSLALGTIGMTGLTAY
          DMMMGQQVARV.ESK.SAFPAGTVVVASSGWTSHSISDGKDLEKLPAEWP.TVPVSLALGT.GM.GLTAY
Retrocopy DMMMGQQVARVLESKISAFPAGTVVVASSGWTSHSISDGKDLEKLPAEWPNTVPVSLALGTMGMKGLTAY

Parental  FGLLDICGVKGGETVMVNAAAGAVGSVVGQIAKLKGCKVVGAAGSDEKVAYLKKLGYDVAFNYK-TIKSL
          FGL.D.CGVKGGETVMVNAAAGAVGSVVGQIAKLK.CKVVGAAGSDEK.AYLKKLG.DV.FNYK.TI.S.
Retrocopy FGLPDTCGVKGGETVMVNAAAGAVGSVVGQIAKLKDCKVVGAAGSDEKLAYLKKLG*DVDFNYK>TIESS

Parental  EETLKKASPDGYDCYFDNVGGEFSNIVIPQMKKFGRIAICGAISTYNSTRPLPPGPPPENII-YQQLRME
          EETLKK.SPDGYDCYFDNVGGEFSNIVIPQM.KFGRIA.CGAI.T.NST.PLPPG.PP...I.YQQL..E
Retrocopy EETLKKTSPDGYDCYFDNVGGEFSNIVIPQMRKFGRIAVCGAIPTHNSTCPLPPG-PPPENI<YQQLHTE

Parental  GFIVNRWQGDVRQKALKDLLTWVIEGKIQYHEYIIEGFENMPAAFMGMLKGDNLGKTIVKA
          GFIV.RWQG.VRQ.ALKDLLTWVIEGKIQYHEYIIEGFENMPAAFMGMLKGDNLGKTIVKA
Retrocopy GFIVYRWQGEVRQNALKDLLTWVIEGKIQYHEYIIEGFENMPAAFMGMLKGDNLGKTIVKA

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	19.24 RPM
SRP017611_brain	0.00 RPM	13.42 RPM
SRP017611_kidney	0.00 RPM	21.40 RPM
SRP017611_liver	0.00 RPM	29.22 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1290 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1290 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1290 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003000	2 retrocopies	retro_cfam_1290 , retro_cfam_1876,
Callithrix jacchus	ENSCJAG00000017571	1 retrocopy	retro_cjac_1653,
Echinops telfairi	ENSETEG00000006136	1 retrocopy	retro_etel_358,
Felis catus	ENSFCAG00000004339	1 retrocopy	retro_fcat_1898,
Homo sapiens	ENSG00000106853	1 retrocopy	retro_hsap_219,
Nomascus leucogenys	ENSNLEG00000017487	1 retrocopy	retro_nleu_2424,
Otolemur garnettii	ENSOGAG00000011144	1 retrocopy	retro_ogar_2834,
Pongo abelii	ENSPPYG00000019499	1 retrocopy	retro_pabe_283,