RetrogeneDB ID: retro_cfam_1766

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 5:47893238..47893815(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000018812
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_1766
GACTCGCACTACGAGGAGAAGAAGTACACGATGGGGGACGCTCCCGGCTATGACAGAAGCCAGTGGCTGAATGAAAAATT
CAAGCTGGGCCTGGACTTCCCCAATCTGCCCTACTTAATTGATGGGGCTCACAAGATCACCCAGAGCAACGCCATCCTTC
GCTACATTGCTCGCAAACACAACCTATGGGGAGACGGAAGAGGAGAAGATTCGTGTGGACGTTTTGGAGAATGAGGTTAT
GACACCGCATATACTTTGCCAGGATCTGCTACAGCCCTGATTTTGAGAAACTGAAGCCTGAGTACGTGAAGGCAAACCCT
GACAAGATGAAGCTCTACTCACAGCTCCTGGGGAAGAGGCCCTGGTTTGCAGGGGAGAAACTCACCTACGTGGATTTCCC
GGTTTCCGACATCCTTGACCTGCCCCGCATAGTTGAGCCCACTTCCCTGGACGCGCTCCCCAACCTGAAGGAGTCAAGGC
TCCCTTTGAGGGCTTGAAGAGCATTTGTGCCTACATGAAGTCCAGCCGCTTGGTCCCAGGCCCTCTGTTTCTAAAGATTG
CCACGTGGGGCGACAAG

Alignment

ORF - retro_cfam_1766 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.37 %
• Parental protein coverage: 86.22 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  DSHYEEKKYTMGDAPDYDRSQWLNEKFKLGLDFPNLPYLIDGAHKITQSNAILRYIARKHNLCGE-TEEE
          DSHYEEKKYTMGDAP.YDRSQWLNEKFKLGLDFPNLPYLIDGAHKITQSNAILRYIARKHNL.G...EE.
Retrocopy DSHYEEKKYTMGDAPGYDRSQWLNEKFKLGLDFPNLPYLIDGAHKITQSNAILRYIARKHNLWGD>EEE-

Parental  KIRVDILENEVM-DT-RIYFARICYSPDFEKLKPEYVKAIPDKMKLYSQFLGKRPWFAGEKLTYVDFLVY
          KIRVD.LENEVM.DT.RIYFARICYSPDFEKLKPEYVKA.PDKMKLYSQ.LGKRPWFAGEKLTYVDF.V.
Retrocopy KIRVDVLENEVM<DT<RIYFARICYSPDFEKLKPEYVKANPDKMKLYSQLLGKRPWFAGEKLTYVDFPVS

Parental  DILDLHRIFEPTSLDAFPNLKE-FMARFEGLKNISAYMKSSRFVPGPLFLKIAMWGNK
          DILDL.RI.EPTSLDA.PNLKE...A.FEGLK.I.AYMKSSR.VPGPLFLKIA.WG.K
Retrocopy DILDLPRIVEPTSLDALPNLKE<VKAPFEGLKSICAYMKSSRLVPGPLFLKIATWGDK

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	0.08 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_1766 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1766 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1766 has 0 orthologous retrocopies within eutheria group .

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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,