RetrogeneDB ID: retro_cfam_596

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 14:19730178..19730385(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: POLR2F
• Ensembl ID: ENSCAFG00000001437
• Aliases: None
• Description: polymerase (RNA) II (DNA directed) polypeptide F [Source:HGNC Symbol;Acc:9193]

Sequence

>retro_cfam_596
CCATATATGGGCATATACATGCTGGGCACCTGAGCCCTCCAGATAGCAATGTGTACACCTGTGATGGTGGAGCTAGAGGG
GGATTCAGATCCCTTGCTCATTACCATGAAAAAGCTCAAAGTCCAAAAGATCCCTGTCACCATTTGCCACTACCTGCCAG
ATGAGAGCTATGAAGACTGCAGGGTAGACAAGGTCATCATCACCAAC

Alignment

ORF - retro_cfam_596 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.75 %
• Parental protein coverage: 57.48 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDWGVDELI
          PYM..Y.....LGT.ALQIAMC.PVMVELEG..DPLLI.MK.LK..KIP..I..YLPD.SYED..VD..I
Retrocopy PYMGIY----MLGT*ALQIAMCTPVMVELEGDSDPLLITMKKLKVQKIPVTICHYLPDESYEDCRVDKVI

Parental  ITD
          IT.
Retrocopy ITN

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	30.87 RPM
SRP017611_brain	0.00 RPM	8.81 RPM
SRP017611_kidney	0.00 RPM	63.53 RPM
SRP017611_liver	0.00 RPM	9.64 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_596 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_596 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_596 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010331	1 retrocopy	retro_amel_716,
Bos taurus	ENSBTAG00000004820	1 retrocopy	retro_btau_1648,
Canis familiaris	ENSCAFG00000001437	1 retrocopy	retro_cfam_596 ,
Myotis lucifugus	ENSMLUG00000014315	1 retrocopy	retro_mluc_199,
Monodelphis domestica	ENSMODG00000019063	2 retrocopies	retro_mdom_1276, retro_mdom_2015,
Mustela putorius furo	ENSMPUG00000012997	1 retrocopy	retro_mputfur_1158,
Otolemur garnettii	ENSOGAG00000025463	1 retrocopy	retro_ogar_1639,