RetrogeneDB ID: retro_mdom_1162

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:297749337..297750124(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000021392
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: UBFD1
• Ensembl ID: ENSMODG00000006727
• Aliases: None
• Description: ubiquitin family domain containing 1 [Source:HGNC Symbol;Acc:30565]

Sequence

>retro_mdom_1162
ATGGCGGCAGCCCGAGCCACGAATGACGACAGGGACTCAGGCATGGAACAAGATGCCCAGAAGCTACAGCTCAACTGTGT
AAACACCAAGGCTGAGACCACCTCCCTCGCCTCCTCATCGCCCTCTGCCTCAGCGACCAAGAGCAGCCTGCAGGCGGACC
AGTTGCTGGAGAATATAGCCAGTACCCAGGCCTCAGTCAGCAATGGCGACAACGCTGAATTGGAGAAGGAGCTGGTGGAT
CTGAAGATCATCTGGAACAAAAACAAGTATGACCTGCGAGTGCCTCTGGACAGCACCGGGGCGGAGCTGAAGCGCAGGAT
CCACTCCATTACAGGACTACCACCTGCCATGCAGAAAGTTATGTTTAAGAGACTTCTACCTGAGGAGAAAACATTACGGG
AAATCAAAGTGACCAGTGGTGCCAAGATTATGGTGGTTGGATCTACAATAAACGATGTTTTACACCCAAAGAGGCAGCAC
AGCAAGAAGCGAAAGCTGAAGAGAGTAAAAAGAAGCCACTTTGTAGGCAAAAGCAACACAGAACAGTATTAGATAAAGGG
AAACTTGAAGATTGATGCCTTCTGCTAAGAGTGCCCAGGAACAACTGCCAACAGTACCTTTATCAGGCATGTACAACGAG
AGAGGAGGAAAAGTAAGACTCACCTTTAAATTAGAACAAGACCAATTGTGGATTGTCCCTAAAGAGGGAGCTGAAAAATT
ATCCAGATGCTCCATTCAAAATTTGGTCAGTGAACCTATTGAAAGACATGAAGATCACCACATGATG

Alignment

ORF - retro_mdom_1162 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.37 %
• Parental protein coverage: 82.35 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAAAGAPDEVEEPGMETDAQKLQLNCVDAEAETSSCTSSSSSAPADKGSLQTDQPQENIATAQASVSNGD
          MAAA.A.......GME.DAQKLQLNCV...AET.S..SSS.SA.A.K.SLQ.DQ..ENIA..QASVSNGD
Retrocopy MAAARATNDDRDSGMEQDAQKLQLNCVNTKAETTSLASSSPSASATKSSLQADQLLENIASTQASVSNGD

Parental  DAETEKELVDLKIIWNKNKYDVRVPLDSSGAELKRRIHSITGLPPAMQKVMFKGLLPEEKTLREIKVTSG
          .AE.EKELVDLKIIWNKNKYD.RVPLDS.GAELKRRIHSITGLPPAMQKVMFK.LLPEEKTLREIKVTSG
Retrocopy NAELEKELVDLKIIWNKNKYDLRVPLDSTGAELKRRIHSITGLPPAMQKVMFKRLLPEEKTLREIKVTSG

Parental  AKIMVVGSTINDVLAVNTPKDAAQQEAKAEESK-KEPLCRQKQHRKVLDKGKPED-VMPSVKGAQERLPT
          AKIMVVGSTINDVL....PK.......K....K.K.PLCRQKQHR.VLDKGK.ED..MPS.K.AQE.LPT
Retrocopy AKIMVVGSTINDVL---HPKRQHSKKRKLKRVK<KKPLCRQKQHRTVLDKGKLED<LMPSAKSAQEQLPT

Parental  VPLSGMYNKTGGKVRLTFKLEQDQLWIGTKERTEKLPMGSIKNVVSEPIEGHEDYHMM
          VPLSGMYN..GGKVRLTFKLEQDQLWI..KE..EKL...SI.N.VSEPIE.HED.HMM
Retrocopy VPLSGMYNERGGKVRLTFKLEQDQLWIVPKEGAEKLSRCSIQNLVSEPIERHEDHHMM

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_1162 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1162 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 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000029331	2 retrocopies	retro_acar_106, retro_acar_204,
Canis familiaris	ENSCAFG00000017670	1 retrocopy	retro_cfam_1952,
Callithrix jacchus	ENSCJAG00000020614	1 retrocopy	retro_cjac_372,
Cavia porcellus	ENSCPOG00000006872	2 retrocopies	retro_cpor_292, retro_cpor_635,
Monodelphis domestica	ENSMODG00000006727	2 retrocopies	retro_mdom_1162 , retro_mdom_1298,
Oryctolagus cuniculus	ENSOCUG00000008444	1 retrocopy	retro_ocun_666,
Pongo abelii	ENSPPYG00000007191	1 retrocopy	retro_pabe_2528,