RetrogeneDB ID: retro_cfam_992

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 20:41183123..41183500(-)
• Located in intron of: ENSCAFG00000013136

Retrocopy information

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

Parental gene information

• Parental gene symbol: TAF10
• Ensembl ID: ENSCAFG00000006498
• Aliases: None
• Description: TAF10 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 30kDa [Source:HGNC Symbol;Acc:11543]

Sequence

>retro_cfam_992
GGCTGAGCACCCCCAGAGGGAGCCATGTCTAAGGGGGTTTACATACTGCTGAGCGCCGCCAACAGAGACCTGAACCCGGT
GGTGTCCAGCACACCTCTAGTGGACTTCCAGATGCAGCTGGAGGACTATACATCTAGGATCCCAGATGCAGTGACTGGTT
ACTACCTGAATCATGCTGGCTTTGAGGCCTCGGACCCGCGCATAATTTGGCTCATCTTCCTAGCTGCCCAGAAATTCATC
TCAGATATTGCCAACGATGCCCTACAGCACTGCAAAATGAAGGGCACAGCTTCTGGCAGCTCCTGAAGCAAGCGCAAGGA
CCACAAGTACACTCTACCATGGAGGACTTGACCCCTGCCCTCAGCGAATATGGCATA

Alignment

ORF - retro_cfam_992 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.61 %
• Parental protein coverage: 57.8 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GAAPPEGAMSNGVYVLPSAANGDVKPVVSSTPLVDFLMQLEDYTPTIPDAVTGYYLNRAGFEASDPRIIR
          G.APPEGAMS.GVY.L.SAAN.D..PVVSSTPLVDF.MQLEDYT..IPDAVTGYYLN.AGFEASDPRII.
Retrocopy G*APPEGAMSKGVYILLSAANRDLNPVVSSTPLVDFQMQLEDYTSRIPDAVTGYYLNHAGFEASDPRIIW

Parental  LISLAAQKFISDIANDALQHCKMKGTASGSSRSKSKDRKYTL-TMEDLTPALSEYGI
          LI.LAAQKFISDIANDALQHCKMKGTASGSS.SK.KD.KYTL.TMEDLTPALSEYGI
Retrocopy LIFLAAQKFISDIANDALQHCKMKGTASGSS*SKRKDHKYTL<TMEDLTPALSEYGI

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	0.00 RPM
SRP017611_brain	0.00 RPM	0.00 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_992 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_992 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_992 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000006498	2 retrocopies	retro_cfam_1041, retro_cfam_992 ,
Dasypus novemcinctus	ENSDNOG00000000814	1 retrocopy	retro_dnov_592,
Equus caballus	ENSECAG00000007794	1 retrocopy	retro_ecab_525,
Erinaceus europaeus	ENSEEUG00000008412	3 retrocopies	retro_eeur_542, retro_eeur_692, retro_eeur_709,
Echinops telfairi	ENSETEG00000008886	1 retrocopy	retro_etel_2090,
Felis catus	ENSFCAG00000015390	1 retrocopy	retro_fcat_1458,
Macropus eugenii	ENSMEUG00000008216	2 retrocopies	retro_meug_1645, retro_meug_992,
Myotis lucifugus	ENSMLUG00000024459	1 retrocopy	retro_mluc_1960,
Macaca mulatta	ENSMMUG00000007743	1 retrocopy	retro_mmul_1144,
Mus musculus	ENSMUSG00000043866	1 retrocopy	retro_mmus_35,
Tursiops truncatus	ENSTTRG00000004894	1 retrocopy	retro_ttru_1113,