RetrogeneDB ID: retro_itri_1619

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393577.1:511605..511917(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PGRMC1
• Ensembl ID: ENSSTOG00000024047
• Aliases: None
• Description: progesterone receptor membrane component 1 [Source:HGNC Symbol;Acc:16090]

Sequence

>retro_itri_1619
CCGAGCATCCTGCTCGAGGTCAATGGGAAAGTCTTCGATGTGACCAAAGGCAGCAAGTTCTACAGCCCCGCGGGTCCATA
TGGAATATTTGCTGGTAGGGATGCCTCCAGAGGACTGGCAACATTTTACCTAGATAAGGATGCACTTAGAGACGAATATG
ATGATCTCTCAGATTTGAATGCAGTACAAATGGAGAGTGTTCGAGCATGGGAAATGCAGTTTAAAGAAAAATATGATTAT
GTAGGCAGACTCCTAAAACCAGGGGAAGAACCTTCAGAATGTACAGATAAAGAAGATACCAAGGATCACAAT

Alignment

ORF - retro_itri_1619 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.35 %
• Parental protein coverage: 53.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PRILMAINGKVFDVTKGRKFYGPEGPYGVFAGRDASRGLATFCLDKEALKDEYDDLSDLTPAQQETLSDW
          P.IL...NGKVFDVTKG.KFY.P.GPYG.FAGRDASRGLATF.LDK.AL.DEYDDLSDL...Q.E....W
Retrocopy PSILLEVNGKVFDVTKGSKFYSPAGPYGIFAGRDASRGLATFYLDKDALRDEYDDLSDLNAVQMESVRAW

Parental  DSQFTFKYHHVGKLLKEGEEPTVYSDDEEPKDEN
          ..QF..KY..VG.LLK.GEEP....D.E..KD.N
Retrocopy EMQFKEKYDYVGRLLKPGEEPSECTDKEDTKDHN

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_1619 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1619 was not experimentally validated.

Homology

Retrocopy orthology:

Ictidomys tridecemlineatus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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 ,