RetrogeneDB ID: retro_cfam_963

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 20:37179589..37180042(+)
• Located in intron of: ENSCAFG00000009084

Retrocopy information

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

Parental gene information

• Parental gene symbol: CREG1
• Ensembl ID: ENSCAFG00000015414
• Aliases: None
• Description: cellular repressor of E1A-stimulated genes 1 [Source:HGNC Symbol;Acc:2351]

Sequence

>retro_cfam_963
CATATCTGTGACTGGGGTGCACTGGCTGCAGAGGAGGCTGTACACCACTAGGCCTTGATCAGTGTCTTCTTGCTCAGTGA
TGGGCTGGGCATGGGTAGTGGCATGCCCAACTACTACCTGAGCCCACTGCAGCAATTGGTGGGCAGCCTGCAGGAGAATC
CACATGCTATGCTGACCATGTCTTTGGCATAGACCTAACTTCTGCAGGAAGCACGTATTTGATCCCTAAAGTTCCCTCTC
TGCTCCCATGATACTGTCAGGAACTGTTAACAAGATGGATGAAACGGAAATGGATTTTGCCAAGCAATCACTGTTCATCC
AGCACCCTGAGATGAAAACCTGACCTTCCAGCCGTAATTGGTTCTCTGCCAAGTTGAATTAACCAACATCTGGGTCCTGG
ACTACTTTGGTGGGCCAAAAATAGTAACACCTGAACAATATTACAGTGTCACA

Alignment

ORF - retro_cfam_963 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.06 %
• Parental protein coverage: 70.45 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  HVCDWGALASLSTDPAVRGWAFADVLSLSDGPPGAGSGVPYFYLSPLQQSVGNLQENPHATLTMSLAQT-
          H.CDWGALA......AV...A...V..LSDG..G.GSG.P..YLSPLQQ.VG.LQENPHA.LTMSLA.T.
Retrocopy HICDWGALAA---EEAVHH*ALISVFLLSDGL-GMGSGMPNYYLSPLQQLVGSLQENPHAMLTMSLA*T>

Parental  NFCRKKGFDPQSPLCAHIILSGTVTKVNQTEMDFAKHSLFVRHPEMKTWPSSHNWFFAKLN-ITNIWVLD
          NFCRK..FDP.S.L.A..ILSGTV.K...TEMDFAK.SLF..HPEMKT.PSS.NWF.AKLN..TNIWVLD
Retrocopy NFCRKHVFDP*SSLSAPMILSGTVNKMDETEMDFAKQSLFIQHPEMKT*PSSRNWFSAKLN<LTNIWVLD

Parental  YFGGPKIVTPEEYYNVT
          YFGGPKIVTPE.YY.VT
Retrocopy YFGGPKIVTPEQYYSVT

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	0.21 RPM	53.59 RPM
SRP017611_brain	0.00 RPM	49.78 RPM
SRP017611_kidney	0.13 RPM	206.04 RPM
SRP017611_liver	0.00 RPM	137.70 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_963 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_963 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_963 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000024	1 retrocopy	retro_amel_792,
Canis familiaris	ENSCAFG00000015414	1 retrocopy	retro_cfam_963 ,
Monodelphis domestica	ENSMODG00000027768	1 retrocopy	retro_mdom_1918,