RetrogeneDB ID: retro_mdom_419

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:471746093..471746677(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TIMMDC1
• Ensembl ID: ENSMODG00000018197
• Aliases: None
• Description: translocase of inner mitochondrial membrane domain containing 1 [Source:HGNC Symbol;Acc:1321]

Sequence

>retro_mdom_419
GTCAGAGATGAATGTGAACCAATACCAGAGGAAAGTGACTATATTTACAAAGTAGCAACTTTAGGAGCAATCATTGGTTG
GATATATGGAGGCATAACCTGCTTTTTATCATGCCAAACAATATTATATTTCAGAACATGTAGAGATTTATTAAAACCAA
TTTGATGCTGTGCAATTTGCCCATCGAGATGCCATTCAAGGGTTCATCCGATATGGCTGTTGGTGGTGTTGGAAAACAAC
CTTGTTTGTCACTATATTTAACACAGCGAGCATTGGTCTGAATGTATACTAAAATAAAAATGCCTTAAGCCATTTTGTTG
TTGCAGGAGCTGCTATTTGAGGTCTTTTCAGAATGTACTTGGGTTTGAGTAGTATGCTGACTGGTGGTTTGTTTGGAGCT
TTTCTGGGGTGTTCCTCTGGGAGTCATGATCATAGCCATTCAGAAGTACCAGGGAGAGACTGTTTGGGACAGAAAACAGA
AAGCACAGAAAGAGCTCTAGCAGTCAAAGCTGGATGAGTAGAAGGCAAGGCTATGTGTTGCTGATGCCGTCACACGAGAG
TTTAAAAGTAACAGGGAAAAATCA

Alignment

ORF - retro_mdom_419 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.13 %
• Parental protein coverage: 61.13 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VRDEHQPVPQEIDYIFKAATTGAIVGWIYGGI-PAFYHAKQRYISQSHAEIYYSRFDAVQSAQRAAIRGF
          VRDE..P.P.E.DYI.K.AT.GAI.GWIYGGI.PAFYHAKQ.YIS..H.EIY...FDAVQ.A.R.AI.GF
Retrocopy VRDECEPIPEESDYIYKVATLGAIIGWIYGGI>PAFYHAKQYYISE-HVEIY*NQFDAVQFAHRDAIQGF

Parental  IRYGWRWSWRTALFVTIFNTVSTGLNVYRNKNALSHFVVAGAATGGLFRFYLGLSSMLAGGLFGAIL-GV
          IRYG..W.W.T.LFVTIFNT.S.GLNVY.NKNALSHFVVAGAA..GLFR.YLGLSSML.GGLFGA.L.GV
Retrocopy IRYGCWWCWKTTLFVTIFNTASIGLNVY*NKNALSHFVVAGAAI*GLFRMYLGLSSMLTGGLFGAFL>GV

Parental  PFGVMIMAIEKYQGETVWDRKQKARKELYELKLDEWKARLHVTDAVTEEFKSNLGKN
          P.GVMI.AI.KYQGETVWDRKQKA.KEL...KLDE.KARL.V.DAVT.EFKSN..K.
Retrocopy PLGVMIIAIQKYQGETVWDRKQKAQKEL*QSKLDE*KARLCVADAVTREFKSNREKS

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	0.20 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_419 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_419 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000002519	1 retrocopy	retro_etel_1905,
Macropus eugenii	ENSMEUG00000003777	1 retrocopy	retro_meug_1317,
Monodelphis domestica	ENSMODG00000018197	2 retrocopies	retro_mdom_1842, retro_mdom_419 ,
Oryctolagus cuniculus	ENSOCUG00000009500	1 retrocopy	retro_ocun_940,