RetrogeneDB ID: retro_mdom_533

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:187705346..187706290(-)
• Located in intron of: ENSMODG00000001626

Retrocopy information

• Ensembl ID: ENSMODG00000024244
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RBKS
• Ensembl ID: ENSMODG00000015586
• Aliases: None
• Description: ribokinase [Source:HGNC Symbol;Acc:30325]

Sequence

>retro_mdom_533
ATGGCAGTCTGTGTGATGGGGCTGCAGCCAGACTCGGCAATGGTAGTGGTGGGCTCCTGCAAGACCGACCTGGTCAGCCT
TACATCACATCTGCCCAAAACTGGAGAAACCATCTGTGGACATAAGTTTTTATTGGCTTTGGAGGAAAAGGTGCTAACCA
ATGTGCCCAAGACGTCTGGTTTGGAGCCAAGACTTCTTTAACGTGCAAGGTTGGCAAAGATTCTTTTGGCAGTGATTATA
TAGAAAACTTAAAGCAGAATGACATTTCTACAGAATTTATGTATCAGACCAAAGATGCCACTACAGGAGCTGCTTCAATA
ATTGTCAATAATGGACAGAATATTTTTGTCATTATGGCCAGAGCAAACTTGCTGTTGAATTCTGATGACCTGAAGAAGGC
AGGCGATATCATTAGCAGAGCCAAAGTAAATGTCTGCCAGCTAGAAATATCTCCAGCTACTTCTCTGGAAGCCCTGACAA
TGGCCCTCAAGAGCAGAGTGGAGACAGTGTTTAATTCCACTCCTGCCACAACTGATCTTGATGCACAATTCTATTCTGAT
TCTGATGTGTACTGCTGCAATGAGAGTGAGGCTGAGATTTTTAACTGGACTAAAAATTAGCAGCCCTGCAGCTGCTGGAT
CAGTGCTGATTGAAAGGGGTTGCAAAATAGTCATCATTACATTGGATTCTGAAGGATGTGTGTTTGTATCAGCTGAAGAA
CCTTTCCCAAAGCATATTCCCTCACAGAAGATCCTCGAGCCTGTAGATACTACAGGAGCTGGAGATAGTTTTGTGGGAGC
ATTGGCCTTCTACCTGGCTTAGTATCCTAACCTGCCTATGGAAGAAATGATCAAGAGAGCCAGCTTCATTTATCAGTCAG
TGTCCAAACCTCAGGAACCCAGTCTTCTTTCCCTTACAAAAAGGACCTGCCACTTCATCTGTTT

Alignment

ORF - retro_mdom_533 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.02 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAACVAGLQPDSAVVVVGSCMTDLVSLTSRLPKTGETIHGHKF-FIGFGGKGANQCVQAARLGAKTSLVC
          MA.CV.GLQPDSA.VVVGSC.TDLVSLTS.LPKTGETI.GHKF.FIGFGGKGANQC.Q....GAKTSL.C
Retrocopy MAVCVMGLQPDSAMVVVGSCKTDLVSLTSHLPKTGETICGHKF<FIGFGGKGANQCAQDVWFGAKTSLTC

Parental  KVGKDSFGSDYIENLKRNDISTEFMYQTKDAATGAASIIVNNEGQNIIVIVAGANLLLNSDDLRKAADII
          KVGKDSFGSDYIENLK.NDISTEFMYQTKDA.TGAASIIVNN.GQNI.VI.A.ANLLLNSDDL.KA.DII
Retrocopy KVGKDSFGSDYIENLKQNDISTEFMYQTKDATTGAASIIVNN-GQNIFVIMARANLLLNSDDLKKAGDII

Parental  SRAKVIICQLEISPATSLEALTMARKSGVKTVFNPAPATADLDAQFYSVSDVFCCNESEAEI-LTGLKIS
          SRAKV..CQLEISPATSLEALTMA.KS.V.TVFN..PAT.DLDAQFYS.SDV.CCNESEAEI.LTGLKIS
Retrocopy SRAKVNVCQLEISPATSLEALTMALKSRVETVFNSTPATTDLDAQFYSDSDVYCCNESEAEI>LTGLKIS

Parental  SPAVAGKAGSVLIERGCKIVIITLGSEGCVFVSAEEPGPKHIPTQKILKPVDTTGAGDSFVGALAFYLAY
          SPA.AG...SVLIERGCKIVIITL.SEGCVFVSAEEP.PKHIP.QKIL.PVDTTGAGDSFVGALAFYLA.
Retrocopy SPAAAG---SVLIERGCKIVIITLDSEGCVFVSAEEPFPKHIPSQKILEPVDTTGAGDSFVGALAFYLA*

Parental  YPNLTMEEMIKRASFV-ASVSVQTSGTQSSFPYKKDLPLHLF
          YPNL.MEEMIKRASF...SVSVQTSGTQSSFPYKKDLPLHLF
Retrocopy YPNLPMEEMIKRASFI<LSVSVQTSGTQSSFPYKKDLPLHLF

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	11.20 RPM
SRP007412_cerebellum	0.00 RPM	12.73 RPM
SRP007412_heart	0.00 RPM	5.98 RPM
SRP007412_kidney	0.00 RPM	114.56 RPM
SRP007412_liver	0.00 RPM	185.28 RPM
SRP007412_testis	0.20 RPM	11.39 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_533 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_533 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000015586	1 retrocopy	retro_mdom_533 ,
Otolemur garnettii	ENSOGAG00000000511	1 retrocopy	retro_ogar_1747,