RetrogeneDB ID: retro_mdom_1459

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:152860278..152860667(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMB4
• Ensembl ID: ENSMODG00000018871
• Aliases: None
• Description: proteasome (prosome, macropain) subunit, beta type, 4 [Source:HGNC Symbol;Acc:9541]

Sequence

>retro_mdom_1459
ATATCTCAAATCATGCCTGTCAACTATTACATGTTTGGTACTTCTGGGGATTATTCTGATTTTCAGTACATGAAGCAAGT
CATTGACCAGATGGTTACTAATGAAGAGCTGATGAGTGATGAATATAGCTGTAGCCCCAAAGCTATCTACTCTTGGTTGA
CCAGAGTTATATATATTTGTTTCTCCAAGATGAACTCCCTCTAAAACATGATAGTCATTGTTGGATTTTAGGATGTGAAG
AACTTCCTTGGTTATGTGGACATACTTAGTGTATCCTATGAAGTCACCATGCTGGTTCCTAGTTATGATGTCTATTGGCC
CAGTCCTTGATGAAAGAGCTTTTGAAAAAGCCAATTCTAATCCATACAAAATCATGTGAGTTAGTGGAG

Alignment

ORF - retro_mdom_1459 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.82 %
• Parental protein coverage: 58.22 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ISRIMRVNNNTMLGASGDYADFQYVKQVIDQMVIDEELLGDGHSYSPKAIHSWLTRAMYSRRSKMNPLWN
          IS.IM.VN...M.G.SGDY.DFQY.KQVIDQMV..EEL..D..S.SPKAI.SWLTR..Y...SKMN.L.N
Retrocopy ISQIMPVNYY-MFGTSGDYSDFQYMKQVIDQMVTNEELMSDEYSCSPKAIYSWLTRVIYICFSKMNSL*N

Parental  TMVIGGYADGESFLGYVDMLGVAYEAPTLATGYGAY-LAQPLMREVLEKKQFKQAEARELVE
          ..VI.G..D...FLGYVD.L.V.YE...L...Y..Y.LAQ.LM.E.L.K.........ELVE
Retrocopy MIVIVGF*DVKNFLGYVDILSVSYEVTMLVPSYDVY<LAQSLMKELLKKPILIHTKSCELVE

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_1459 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1459 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
Microcebus murinus	ENSMICG00000016746	1 retrocopy	retro_mmur_1545,
Monodelphis domestica	ENSMODG00000018871	1 retrocopy	retro_mdom_1459 ,