RetrogeneDB ID: retro_mdom_1224

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:19809595..19810393(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRKX
• Ensembl ID: ENSMODG00000000005
• Aliases: None
• Description: protein kinase, X-linked [Source:HGNC Symbol;Acc:9441]

Sequence

>retro_mdom_1224
CCTCCTCCTCCTCCTCTGTTTCCTACAGGGTCCTCCGAGTCTGGGCATTCAGAGCCCACCCATTCCTTGAGCCCTGTTGT
GGGCCCAGGCTCTTCAGCTCCTTTGACCAAGCTTCCAGCTTACAAGCTTCATGACTTCGATATCCTGGCTTTTGTGGGCA
TTGGTACCTTTGGGTGAGTTTAGCTAGTCAAAGAAAGAACAGCCAAGCATTATTTTTCATTGAAGGTAATGAGCATTCCA
GATGTCATTCAGCTAAAGGAAGAGCAGCATGTACACAATGAAAAGTCAGTTCTGAAAGAAGTCAGCCATCCATTTCTGAT
CAGATTGTACCGGACCTATCATGATGAAAGATTTTTATACATGTTAATGGAATATGTTCCTGGAGGAGAACTTTTCAACT
ACTTGAGAAACATGGGATGGTTCAATAACAGCACAGGACTATTTTATTCTGTAGAGATTATCTGTGAATAGAATATCTGC
ACTCCAAAGAAATAGTTTACAGAGATCTAAAACCTGAAAATATATTGTTCGATAAAGAAGGCCATATTAAGCTCATAGAT
TTTGGATTTGTTAAAAAGCTAATAGACAGGACATGGACACTCTGTGTGACATCAGAATACCTGGCTCCAGAAGTCATACA
AAGTAAAGGTGATGAAAGAGCAGTAGATTGGTGGGCTCTGGGGATTCTGATCTTTGAGATGCTCTGTGGGTTTCCTCCAT
TTTTTTGATGACAACCCATTTGGCATCTATCAAAAAATTCTTGTAGGTAAAATAGATTTCCCTAGGCATTTGGATCTC

Alignment

ORF - retro_mdom_1224 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.96 %
• Parental protein coverage: 69.27 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PPPPPPAPPGSSGSGDSEPAHSSSPAVGPGSPAPSPELPAYKLQDFDTLATVGTGTFGRVHLVKERTAKH
          PPPPP..P.GSS.SG.SEP.HS.SP.VGPGS.AP...LPAYKL.DFD.LA.VG.GTFG.V.LVKERTAKH
Retrocopy PPPPPLFPTGSSESGHSEPTHSLSPVVGPGSSAPLTKLPAYKLHDFDILAFVGIGTFG*V*LVKERTAKH

Parental  YFALKVMSIPDVIRLKQEQHVHNEKSVLKEVSHPFLIRLYWTYHDERFLYMLMEYDPGEYLFSYVRDMGR
          YF.LKVMSIPDVI.LK.EQHVHNEKSVLKEVSHPFLIRLY.TYHDERFLYMLMEY.PG..LF.Y.R.MG.
Retrocopy YFSLKVMSIPDVIQLKEEQHVHNEKSVLKEVSHPFLIRLYRTYHDERFLYMLMEYVPGGELFNYLRNMGW

Parental  FNNSTGLFYSAEIICA-IEYLHSKEIVYRDLKPENILLDKEGHIKLTDFGFAKKLLDRTWTLCGTPEYLA
          FNNSTGLFYS.EIIC..IEYLHSKEIVYRDLKPENIL.DKEGHIKL.DFGF.KKL.DRTWTLC.T.EYLA
Retrocopy FNNSTGLFYSVEIICE<IEYLHSKEIVYRDLKPENILFDKEGHIKLIDFGFVKKLIDRTWTLCVTSEYLA

Parental  PEVIQSKGHGRAVDWWALGILIFEMLSGFPP-FFDDNPFGIYQKILAGKIDFPRHLDL
          PEVIQSKG..RAVDWWALGILIFEML.GFPP.FFDDNPFGIYQKIL.GKIDFPRHLDL
Retrocopy PEVIQSKGDERAVDWWALGILIFEMLCGFPP>FFDDNPFGIYQKILVGKIDFPRHLDL

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
SRP007412_brain	0.00 RPM	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1224 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1224 was not experimentally validated.

Homology

Retrocopy orthology:

Monodelphis domestica does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000000005	1 retrocopy	retro_mdom_1224 ,
Monodelphis domestica	ENSMODG00000012087	1 retrocopy	retro_mdom_1978,
Nomascus leucogenys	ENSNLEG00000008541	1 retrocopy	retro_nleu_1293,
Drosophila melanogaster	FBgn0000489	1 retrocopy	retro_dmel_60,