RetrogeneDB ID: retro_cfam_1492

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 32:6395055..6395565(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MED20
• Ensembl ID: ENSCAFG00000001613
• Aliases: None
• Description: mediator complex subunit 20 [Source:HGNC Symbol;Acc:16840]

Sequence

>retro_cfam_1492
GTGACCTGTGTGTCCCAGATGCCTGTGGCTGAGGGCAAGAGTGTCCAGCAGACTGTGGAGCTCCTCACCCAGAAATTGGA
GATGCTTGAGGCAGAGAAGCAAGGAATATTTTGTGTGGATTGTGAAACGTGCCATGCAGCTGCCTCTATTTTTGGCAGCC
AAGGTCAGGCCAGAAAGCTGATGTAAGTGATGCACAACTCAGCGTACCCTTTGAGCTGCTTGGTCCTCTTTGAGAATGGC
CCTCGCCTTATTGCCGACACCAACTCTGATGTGCTCATGGTGAAGCTCAAGGGCTTTTTCCAGAGTGCCAAGGCCATCAA
GACTGAGACCCGGGGTACCTGTTACCAGTACCGTGACTTCCTAGTGAAGGGGGGCACAGTCACCAGGGGACCCAGTTCCT
GAAGCATCTCCATTGCCGTGGAGTATGGCCCCTTTGTGGTAGCTAGCGGCATCTGGAGCTTGCTGCTCAAGTTCCTACAG
AGTTTTCTGGGCAGCAGCTATACACCAGGG

Alignment

ORF - retro_cfam_1492 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.59 %
• Parental protein coverage: 79.72 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VVGVSQMPVAEGKSVQQTVELLTRKLEMLGAEKQGTFCVDCETYHTAASTLGSQGQAGKLMYVMHNSEYP
          V..VSQMPVAEGKSVQQTVELLT.KLEML.AEKQG.FCVDCET.H.AAS..GSQGQA.KLM.VMHNS.YP
Retrocopy VTCVSQMPVAEGKSVQQTVELLTQKLEMLEAEKQGIFCVDCETCHAAASIFGSQGQARKLM*VMHNSAYP

Parental  LSCFALFENGPCLIADTNFDVLMVKLKGFFQSAKASKIETRGTRYQYCDFLVKVGTVTMGPSARGISVEV
          LSC..LFENGP.LIADTN.DVLMVKLKGFFQSAKA.K.ETRGT.YQY.DFLVK.GTVT.GPS...IS..V
Retrocopy LSCLVLFENGPRLIADTNSDVLMVKLKGFFQSAKAIKTETRGTCYQYRDFLVKGGTVTRGPSS*SISIAV

Parental  EYGPCVVASDCWSLLLEFLQSFLG-SHTPG
          EYGP.VVAS..WSLLL.FLQSFLG.S.TPG
Retrocopy EYGPFVVASGIWSLLLKFLQSFLGSSYTPG

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	0.08 RPM	6.64 RPM
SRP017611_brain	0.00 RPM	1.83 RPM
SRP017611_kidney	0.00 RPM	6.47 RPM
SRP017611_liver	0.00 RPM	2.90 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1492 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1492 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1492 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001613	1 retrocopy	retro_cfam_1492 ,
Dasypus novemcinctus	ENSDNOG00000016666	1 retrocopy	retro_dnov_533,
Microcebus murinus	ENSMICG00000011326	1 retrocopy	retro_mmur_972,
Myotis lucifugus	ENSMLUG00000014024	1 retrocopy	retro_mluc_2117,