RetrogeneDB ID: retro_cfam_639

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 14:45246393..45246745(-)
• Located in intron of: ENSCAFG00000003161

Retrocopy information

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

Parental gene information

• Parental gene symbol: GABARAPL2
• Ensembl ID: ENSCAFG00000031455
• Aliases: None
• Description: GABA(A) receptor-associated protein-like 2 [Source:HGNC Symbol;Acc:13291]

Sequence

>retro_cfam_639
ATGGAGTGGATGTTCAAGGAGGACCACTTGCTGGAACACAGATGCATGGAATCTGTGAAGATCCCAGCAAAAATATCCCA
ACTGGGTTCCAGTGATTGTGGAAAAAGTCTTAGGCTCTCAGATTATTGACACTGACAAATGGAAGTATCTGGTTCCATCT
GATAACCCTGTGGTTCAGTTTACATGGATCATTAGGGAAAGGATCCAGCTTTCTTCTGAAAAGGCAATCTTCCTGTTTTG
TGGATAAGACAGTCCCACAGTCCAGCCTAACTATGGGACAGCTTTACACGAAGGAAAAGATGAAAATAGATTCTTGTATG
TGGCCTACAATGGAGAGAACACTTTTGGTTTC

Alignment

ORF - retro_cfam_639 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80. %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MKWMFKEDHSLEHRCVESAKIRAK-YPDRVPVIVEKVSGSQIVDIDKRKYLVPSDITVAQFMWIIRKRIQ
          M.WMFKEDH.LEHRC.ES.KI.AK.YP..VPVIVEKV.GSQI.D.DK.KYLVPSD..V.QF.WIIR.RIQ
Retrocopy MEWMFKEDHLLEHRCMESVKIPAK>YPNWVPVIVEKVLGSQIIDTDKWKYLVPSDNPVVQFTWIIRERIQ

Parental  LPSEKAIFL-FVDKTVPQSSLTMGQLYEKE-KDEDGFLYVAYSGENTFGF
          L.SEKAIFL.FVDKTVPQSSLTMGQLY.KE.KDE..FLYVAY.GENTFGF
Retrocopy LSSEKAIFL>FVDKTVPQSSLTMGQLYTKE<KDENRFLYVAYNGENTFGF

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	209.32 RPM
SRP017611_brain	0.00 RPM	80.66 RPM
SRP017611_kidney	0.00 RPM	119.66 RPM
SRP017611_liver	0.00 RPM	14.79 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_639 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_639 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_639 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005453	2 retrocopies	retro_amel_1054, retro_amel_1238,
Canis familiaris	ENSCAFG00000019909	1 retrocopy	retro_cfam_1578,
Canis familiaris	ENSCAFG00000031455	1 retrocopy	retro_cfam_639 ,
Callithrix jacchus	ENSCJAG00000014253	1 retrocopy	retro_cjac_146,
Dasypus novemcinctus	ENSDNOG00000002240	2 retrocopies	retro_dnov_1755, retro_dnov_2332,
Microcebus murinus	ENSMICG00000011981	1 retrocopy	retro_mmur_1473,
Mustela putorius furo	ENSMPUG00000009894	1 retrocopy	retro_mputfur_993,
Mus musculus	ENSMUSG00000031950	5 retrocopies	retro_mmus_2637, retro_mmus_2655, retro_mmus_3240, retro_mmus_456, retro_mmus_506,
Rattus norvegicus	ENSRNOG00000019425	1 retrocopy	retro_rnor_57,