RetrogeneDB ID: retro_cfam_2164

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:51444537..51445371(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GPR137
• Ensembl ID: ENSCAFG00000014472
• Aliases: None
• Description: G protein-coupled receptor 137 [Source:HGNC Symbol;Acc:24300]

Sequence

>retro_cfam_2164
TTTGCCCAGGTTGTGTTCAAGGCCAAGGCGAAGCGCTGAGATGAGCTGAGGCTTGCTGGCTGTCCAAGAGGCCTTCGTGG
GGGCCTCGCTGCTCGTTTTGCGGGTGAATGTGCTGTGTGCTGTGCTGTCCCACTGGCCCCGGGCACAGCCCTGGGCCCTC
CTGCTGGTATGAGTCCTGGTGAGTGACTCTCTCTTTGTTATCTGTGCCCTCTCTCTTGCTGCCTGCCTCTGCCTTGTTGC
CCTGCATGCATCCTCCACCAGCATCTACCTGGAGGCCAAGGGGACCAGTGCGTGCCAGGCAGCTGTGATGAGTGGTGCCA
TGTTCCTGCTGTATGCCAGCTGGGCCTGCTACAACCTGGCAACCCTGGCCTTGGCCCCCCAGAGCCAGCTGGATGCCTTT
GATTATGACTGGTATGTCTCTGACCAGGCAGACCTGGTGAATGATTTGGGGGAACAAAGGCTACCTGGTATTTGGCCTCA
TCCTCTTTGTGTGGGAGCTGCTGCCCACCACCCTGCTGGTGGGCTTTTTCCGGGTCCACCGGCCCCCACAGGACCTGAGC
ACCAGTCACATCCTCAATGGGCAGGCCTTTGTTTCCCGTTCTTACTTCTTTGACCAGGCTGGAACATTGTGAGGATGAGG
GCTGCTCCTGGGAGCATGATCGCTGTGAAAGCACCAGCATGTCAGGCAGCCTAGGTTCTGGCAGCTGGTATGACGCCATT
GGGTGGGAGCCAGGCAAATGTGGGGGCAGCCAGACACAGACCACTCTTCTGCTCTTCTCCCAGGTGCTGGGACCAAGTGG
CCACCACCACAGTCTCTATTCCACCCCACAGACA

Alignment

ORF - retro_cfam_2164 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.51 %
• Parental protein coverage: 70.71 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  FAQVVFKAKAK-RRPEMSRGLLAVRGAFVGASLLFLLVNVLCAVLSRRRRAQPWALLLVRVLVSDSLFVI
          FAQVVF..KAK.R..EMS.GLLAV..AFVGASLL.L.VNVLCAVLS...RAQPWALLLV.VLVSDSLFVI
Retrocopy FAQVVF--KAK>RSAEMS*GLLAVQEAFVGASLLVLRVNVLCAVLSHWPRAQPWALLLV*VLVSDSLFVI

Parental  CALSLAACLCLVARRAPSTSIYLEAKGTSVCQAAAMGGAMVLLYASRACYNLAALALAPRSRLDAFDYDW
          CALSLAACLCLVA..A.STSIYLEAKGTS.CQAA.M.GAM.LLYAS.ACYNLA.LALAP.S.LDAFDYDW
Retrocopy CALSLAACLCLVALHASSTSIYLEAKGTSACQAAVMSGAMFLLYASWACYNLATLALAPQSQLDAFDYDW

Parental  YNVSDQADLVNDL-GNKGYLVFGLILFVWELLPTTLLVGFFRVHRPPQDLSTSRILNGQVFGSRSYFFDR
          Y.VSDQADLVNDL.GNKGYLVFGLILFVWELLPTTLLVGFFRVHRPPQDLSTS.ILNGQ.F.SRSYFFD.
Retrocopy Y-VSDQADLVNDL>GNKGYLVFGLILFVWELLPTTLLVGFFRVHRPPQDLSTSHILNGQAFVSRSYFFDQ

Parental  AG-HCEDEGCSWEHGHSESTSMSGSLGSGSWYGAIGREPGWCGGSQTRTTPLLFSQVLGPGGHHHSLYST
          AG.HCEDEGCSWEH...ESTSMSGSLGSGSWY.AIG.EPG.CGGSQT.TT.LLFSQVLGP.GHHHSLYST
Retrocopy AG>HCEDEGCSWEHDRCESTSMSGSLGSGSWYDAIGWEPGKCGGSQTQTTLLLFSQVLGPSGHHHSLYST

Parental  PQT
          PQT
Retrocopy PQT

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	29.57 RPM
SRP017611_brain	0.00 RPM	33.19 RPM
SRP017611_kidney	0.00 RPM	26.61 RPM
SRP017611_liver	0.00 RPM	20.23 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2164 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2164 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2164 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014472	1 retrocopy	retro_cfam_2164 ,