RetrogeneDB ID: retro_cfam_1237

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 27:5910207..5910609(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000008954
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PGRMC1
• Ensembl ID: ENSCAFG00000018372
• Aliases: None
• Description: Canis lupus familiaris progesterone receptor membrane component 1 (PGRMC1), mRNA. [Source:RefSeq mRNA;Acc:NM_001195148]

Sequence

>retro_cfam_1237
GACCAGCCGCCCCCCTGCCCCGCCTTAAGCCGCCTGACTTCACCCCAGTCTAGCTGCGGCACTCGACGGCATCCAGGACC
CACACATACTCATGACCATCAACTGCAAGGTGTTCATCGTGACCAAAGGCTGCAAGTTCTACGGGCCCGAGGGGCCATAC
GGGGTCTTTGCTGGAAGAGATGCATCCCGGGGCCTTGCCACATTTTGCCTGGATAAGGAAGCACTGAAGGACGAGTACGA
TGACCTTTCTGACCTCACCCCTGCCCAGTAGGGAGACCCCGAGTGACTGGGACTCTCAGTTCACTTTCAAGTATCATCGT
GGGCAAACTGCTGAAGGAGGGGGAGGAGCCCACTGCGTACTCTGATGAGGAAGAAGCAAAAGATGAGAATGCTCGGAAAA
AT

Alignment

ORF - retro_cfam_1237 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.86 %
• Parental protein coverage: 69.23 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  DEPPP-LPRLKRRDFTPAELRR-FDGVQDPRILMAINGKVFDVTKGRKFYGPEGPYGVFAGRDASRGLAT
          D.PPP.LPRLK..DFTP..LR...DG.QDP.ILM.IN.KVF.VTKG.KFYGPEGPYGVFAGRDASRGLAT
Retrocopy DQPPP<LPRLKPPDFTPV*LRH<LDGIQDPHILMTINCKVFIVTKGCKFYGPEGPYGVFAGRDASRGLAT

Parental  FCLDKEALKEEYDDLSDLTPAQ-QETLSDWDSQFTFKYHHVGKLLKEG-EEPTVYSDEEEAKDENARKN
          FCLDKEALK.EYDDLSDLTPAQ..ET.SDWDSQFTFKYH..G.....G.EEPT.YSDEEEAKDENARKN
Retrocopy FCLDKEALKDEYDDLSDLTPAQ>RETPSDWDSQFTFKYHR-GQTAEGG>EEPTAYSDEEEAKDENARKN

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	109.49 RPM
SRP017611_brain	0.00 RPM	110.51 RPM
SRP017611_kidney	0.13 RPM	432.74 RPM
SRP017611_liver	0.00 RPM	353.21 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1237 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1237 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1237 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018372	1 retrocopy	retro_cfam_1237 ,
Homo sapiens	ENSG00000101856	1 retrocopy	retro_hsap_1824,
Macaca mulatta	ENSMMUG00000014466	1 retrocopy	retro_mmul_1252,
Nomascus leucogenys	ENSNLEG00000014842	1 retrocopy	retro_nleu_2797,
Pongo abelii	ENSPPYG00000020666	1 retrocopy	retro_pabe_1491,
Rattus norvegicus	ENSRNOG00000012786	1 retrocopy	retro_rnor_1461,
Ictidomys tridecemlineatus	ENSSTOG00000024047	1 retrocopy	retro_itri_1619,