RetrogeneDB ID: retro_cfam_2062

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:39227181..39227741(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GSTM4
• Ensembl ID: ENSCAFG00000019812
• Aliases: GSTM1, GSTM4
• Description: glutathione S-transferase mu 4 [Source:HGNC Symbol;Acc:4636]

Sequence

>retro_cfam_2062
GAAAGCTGAACGGTGGCCATGACCTTGGCTCCCTGGGGCACCCATGGGCTGGCTTATACCATCCACCTGCTTCTGGACCA
CACAGACTCAAGGCTATGAGGAGAAGAAATATGTGATGGGGATACTCCAAGTATGACAGAAGCCAGTGGCTGAATGAAAC
ATTCAAGTTGAGCCTCGACTTTCTCAGTCTGCCCTACTTCATTAATAAAGTTCACAAGATCACCCAGAGCAATGCCACCC
TTTACTGCATTGCTCACAAGCACAATCTATGAGGAGAAACAAGAGAGAAGATTCATGTGGACAATTTGAAGAACTAGGTT
ACAGACACTTCCAATCAGCTGGCCAGTGTTTGCTACAGCCCTGACTTCGAGAAACAAAGCATGAGTCCTTGGAGGGGCTC
CCTAAAAAGATGAAGGTCTCACAGACAGTTTCTATGGAAGAGGTCACCATTTGCGGGGGACAAGATCACCTTTGCAGATC
TCCTTGCTTATGGCATCCTTGACCTGCACCATATATTTGAGCCCAAGTGCCTGAATGCAAGAAACATGAAAGACTTTATC

Alignment

ORF - retro_cfam_2062 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.73 %
• Parental protein coverage: 84. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  KSGTMVMIFGYWDIRGLAHAVRLLLEYTDSH-YEEKKYTMG-DAPD-YDRSQWLNEKFKLGLDFPNLPYL
          .S.T..M....W...GLA....LLL..TDS..YEEKKY.MG.D.P..YDRSQWLNE.FKL.LDF..LPY.
Retrocopy ES*TVAMTLAPWGTHGLAYTIHLLLDHTDSR>YEEKKYVMG<DTPS<YDRSQWLNETFKLSLDFLSLPYF

Parental  IDGAHKITQSNAILRYIARKHNLCGETEEEKIRVDILENEVMDTRIYFARICYSPDFEK-LKPEYVKAIP
          I...HKITQSNA.L..IA.KHNL.GET.E.KI.VD.L.N.V.DT....A..CYSPDFEK..K.E.....P
Retrocopy INKVHKITQSNATLYCIAHKHNL*GETRE-KIHVDNLKN*VTDTSNQLASVCYSPDFEK<TKHESLEGLP

Parental  DKMKL-YSQFLGKRPWFAGEKLTYVDFLVYDILDLHRIFEPTSLDAFPNLKEFM
          .KMK....QFL.KR..FAG.K.T..D.L.Y.ILDLH.IFEP..L.A..N.K.F.
Retrocopy KKMKV>HRQFLWKRSPFAGDKITFADLLAYGILDLHHIFEPKCLNA-RNMKDFI

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	49.18 RPM
SRP017611_brain	0.00 RPM	55.02 RPM
SRP017611_kidney	0.00 RPM	30.71 RPM
SRP017611_liver	0.00 RPM	283.24 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2062 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2062 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2062 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Equus caballus	retro_ecab_1058

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004970	1 retrocopy	retro_amel_1548,
Bos taurus	ENSBTAG00000016472	1 retrocopy	retro_btau_1181,
Canis familiaris	ENSCAFG00000011349	4 retrocopies	retro_cfam_143, retro_cfam_2043, retro_cfam_46, retro_cfam_617,
Canis familiaris	ENSCAFG00000019812	2 retrocopies	retro_cfam_1766, retro_cfam_2062 ,
Mustela putorius furo	ENSMPUG00000003658	1 retrocopy	retro_mputfur_758,
Mus musculus	ENSMUSG00000027890	1 retrocopy	retro_mmus_204,