RetrogeneDB ID: retro_mdom_45

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:131828611..131829124(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000024678
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

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_45
ATGACGGAGCTGCAGTCGGCACTGCTTCTGCGAAGACAGCTGACAGAGCTCAACAAAAACCCCGTGGAAGGCTTCTCGGC
GGGTTTGATAGACGGCAATGACCTCTATCGATGGGAAGTGCTCATCATTGGTCCTCCTGACACCCTGTACGAGGGCGGCG
TTTTCAAAGCTCATCTCACTTTCCCTAAAGACTATCCCCTCCGTCCTCCAGAAATGAAATTCATCACCGAAATCTGGCAC
CCAAATGTTGACAAAAACGGAGACGTGTGCATTTCCATTCTCCACGAACCTGGAGAGGACAAATATGGCTATGAGAAACC
AGAAGAACGCTGGCTGCCCATTCACACCGTGGAGACCATCATGATCAGTGTCATTTCTATGCTGGCCGACCCTAACGGAG
ACTCACCGGCTAATGTGGACGCAGCCAAAGAATGGAGGGAAGACCGAAATGGAGAATTCAAAAGGAAAGTTGCTCGCTGT
GTAAGAAGAAGCCAGGAGACTGCTTTTGAGTGA

Alignment

ORF - retro_mdom_45 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.57 %
• Parental protein coverage: 69.75 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTSSQKALML--ELKSLQEEPVEGFRITLVDESDLYNWEVAIFGPPNTLYEGGYFKAHIKFPIDYPYSPP
          MT..Q.AL.L...L..L...PVEGF...L.D..DLY.WEV.I.GPP.TLYEGG.FKAH..FP.DYP..PP
Retrocopy MTELQSALLLRRQLTELNKNPVEGFSAGLIDGNDLYRWEVLIIGPPDTLYEGGVFKAHLTFPKDYPLRPP

Parental  TFRFLTKMWHPNIYENGDVCISILHPPVDDPQSGELPSERWNPTQNVRTILLSVISLLNEPNTFSPANVD
          ...F.T..WHPN...NGDVCISILH.P..D....E.P.ERW.P...V.TI..SVIS.L..PN..SPANVD
Retrocopy EMKFITEIWHPNVDKNGDVCISILHEPGEDKYGYEKPEERWLPIHTVETIMISVISMLADPNGDSPANVD

Parental  ASVMFRKWRDSKGKDKEYAEIIRKQVLA
          A....R..R....K.K......R.Q..A
Retrocopy AAKEWREDRNGEFKRKVARCVRRSQETA

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	0.40 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	16.50 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_45 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_45 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,