RetrogeneDB ID: retro_mdom_923

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:454396064..454396573(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2R2
• Ensembl ID: ENSMODG00000003686
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2R 2 [Source:HGNC Symbol;Acc:19907]

Sequence

>retro_mdom_923
GTGGATTATTCTGATGTACATAGTCAACAATTACAAATGGGAAGTAGCCACACTCCCTTCCAAAAGGGCTATTTCAAACA
CCATATTGAATTTCCCCTTGGCTAATCATTTTCGACACTCACCTTCAGATTTCTGTCTAAAATGTGGCAGCCCATTTCTG
AAAATGGAAATATGGTCATTTTGATTCTTCAGCTTGCTTTAGATGACCCAAAGAGAGAATTGTTTCTAGATAAGTGGCAT
ATGGCTCATAATGTGAGTACTCTCTTGTTGAATGTAATTTTGATACTTATTGAGCCCAATATTTCTCTCCTGCCAATGTG
GATGTTTCAGTTATGTTCAGGAAATGGAAGGATTATGAAGGAAAAGGAAAGGAATATGCTAAAATCATTAGGCAATAGAT
TTTGGCTTTCATGAGTAAAACAGAGAGTGAAGGTCCTACAATAGTAGCCAAATACTCCATAAAAAGTCAAGTTCCCTCCA
ATGACAACAGTTTAGATTTATTTTATGAT

Alignment

ORF - retro_mdom_923 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.54 %
• Parental protein coverage: 73.95 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VDESDLYNWEVAIFGPPNTLYEGGYFKAHIKFPIDYPYSPPTFRFLTKMWHPNIYENGDVCISILHPPVD
          VD.SD.........G...T....GYFK.HI.FP.....S..TFRFL.KMW.P.I.ENG...I.IL....D
Retrocopy VDYSDVHSQQLQM-GSSHTPFQKGYFKHHIEFPLG*SFSTLTFRFLSKMWQP-ISENGNMVILILQLALD

Parental  DPQSGELPSERWNPTQNVRTILLSVISLLNEPNT-FSPANVDASVMFRKWRDSKGKDKEYAEIIRKQVLA
          DP...EL....W....NV.T.LL.VI..L.EPN..FSPANVD.SVMFRKW.D..GK.KEYA.IIR...LA
Retrocopy DPKR-ELFLDKWHMAHNVSTLLLNVILILIEPNI<FSPANVDVSVMFRKWKDYEGKGKEYAKIIRQ*ILA

Parental  TKAEAEKDGVKVPTTLAEYCIKTKVPSNDNSSDLLYD
          .....E..G...PT..A.Y.IK..VPSNDNS.DL.YD
Retrocopy FMSKTESEG---PTIVAKYSIKSQVPSNDNSLDLFYD

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_923 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_923 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 3 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000006793	1 retrocopy	retro_mluc_2175,
Monodelphis domestica	ENSMODG00000003686	2 retrocopies	retro_mdom_45, retro_mdom_923 ,
Nomascus leucogenys	ENSNLEG00000005052	3 retrocopies	retro_nleu_1451, retro_nleu_2245, retro_nleu_2987,