RetrogeneDB ID: retro_cfam_1876

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 7:37272711..37273642(-)
• Located in intron of: ENSCAFG00000032694

Retrocopy information

• Ensembl ID: ENSCAFG00000015869
• 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_1876
CATAGTAACTTTGAGTTAAAGACAATTGAACTCCTGTCCTTAAAAAATGGAGAGGTCCTGCTGGAAGCTTTGTTCCTTAC
TGTGGATCCTTAACATGAGAGTGGCAGCCAAAAGGTTGAAGGAGGGTGATATGATGATAGGGCAGCAAGTGGCCAGAGTT
GTGAAAAATAAAAACTCAGCCTTCCCAGCAGGAACTGTGGTAGTGGCTTCTCCAGGCTGGACATTGCACTGTATTTCTGA
TGGGAAAGATCTGGAAAGCTGCCTGCAGAGTGGCCGGACACGGTACCAGGGTCTTTGGCTCTGGGAACAATTGGCATGAC
AGGTCTAATGGCCTACTTTGGCCTCCTTGACATCTGTGATGTGAAGGGTGGAGAAACAGTGATGGTTAATGCAGCAGCAG
GGGCAGTGGGCTCTGTGGTGGGGCAGATTGCTGAGCTCAAGGGCTGCAAAGTTGTTGGAGCAGCAGGGTCTGATGAAAAG
GTTGGGTACCTTAAAAAGCTTGGATATGATGTTGCTTTTAACTACAAAACCGTGGAGTCTTTGGAAGAAACTGAAAAAAG
CCTTTTCTGATGGTTATGATTGTTACTTTGATAATGTAGGTGGAAAGTTTTCAAACATTGTTATTCCCCAGATGAAGAAA
TTTGGAAGAATTTCTATTTGTGGGGCCATCATGAGGTATAATATTACTCGCCCACTTCCCCCAGGCCCACCCCAAGAGAA
TATTATCTATCAGCAGCTCTGCTTGGAAGGGTTCATCGTTTATCGCTGGCAAGGAGAGGTCCGCCAGATTGAAAGGCTTT
TTTTGCTGACATGGGTCATAGAGGGTAAAATCCAGTACCACGAATACATCATTGAAGGATTTGAAAACATGCCAGCTGCA
TTTATGGGAATGCTGAAAGGAGATAATTTGGGAAAAACAATAGTGAAAGCA

Alignment

ORF - retro_cfam_1876 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.44 %
• Parental protein coverage: 94.53 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  HSNFELKTVELPSLKNGEVLLEALFLTVDP-YMRVAAKRLKEGDMMMGQQVARVVESKNSAFPAGTVVVA
          HSNFELKT.EL.SLKNGEVLLEALFLTVDP..MRVAAKRLKEGDMM.GQQVARVV..KNSAFPAGTVVVA
Retrocopy HSNFELKTIELLSLKNGEVLLEALFLTVDP>NMRVAAKRLKEGDMMIGQQVARVVKNKNSAFPAGTVVVA

Parental  SSGWTSHSISDGKDLE-KLPAEWPDTVPVSLALGTIGMTGLTAYFGLLDICGVKGGETVMVNAAAGAVGS
          S.GWT.H.ISDGKDLE.KLPAEWPDTVP.SLALGTIGMTGL.AYFGLLDIC.VKGGETVMVNAAAGAVGS
Retrocopy SPGWTLHCISDGKDLE<KLPAEWPDTVPGSLALGTIGMTGLMAYFGLLDICDVKGGETVMVNAAAGAVGS

Parental  VVGQIAKLKGCKVVGAAGSDE-KVAYLKKLGYDVAFNYKTIKSLEETLKKASPDGYDCYFDNVGGEFSNI
          VVGQIA.LKGCKVVGAAGSDE.....LK.L........K...SL...LKKA..DGYDCYFDNVGG.FSNI
Retrocopy VVGQIAELKGCKVVGAAGSDE>RLGTLKSLDMMLLLTTKPW-SLWKKLKKAFSDGYDCYFDNVGGKFSNI

Parental  VIPQMKKFGRIAICGAISTYNSTRPLPPGPPPENIIYQQLRMEGFIVNRWQGDVRQKALKDLLTWVIEGK
          VIPQMKKFGRI.ICGAI..YN.TRPLPPGPP.ENIIYQQL..EGFIV.RWQG.VRQ.....LLTWVIEGK
Retrocopy VIPQMKKFGRISICGAIMRYNITRPLPPGPPQENIIYQQLCLEGFIVYRWQGEVRQIERLFLLTWVIEGK

Parental  IQYHEYIIEGFENMPAAFMGMLKGDNLGKTIVKA
          IQYHEYIIEGFENMPAAFMGMLKGDNLGKTIVKA
Retrocopy IQYHEYIIEGFENMPAAFMGMLKGDNLGKTIVKA

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	0.17 RPM	19.24 RPM
SRP017611_brain	0.00 RPM	13.42 RPM
SRP017611_kidney	0.20 RPM	21.40 RPM
SRP017611_liver	0.07 RPM	29.22 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1876 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1876 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1876 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,