RetrogeneDB ID: retro_mdom_1842

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 8:66289183..66289918(+)
• 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_1842
TCTCCCTGGAGGAAACTGCCTCATCACATTAAGGGTCCAGTTTACCCAGAGACAGGATGGGAAAGCCTCAAGGAGCTCCT
TGTCAGAGATGAACGCCAACCAATACCACAGGAAATTGACTATATTTTCAAAGCAGCAACTTCAGGGGCAATTGTTGGGT
GGATATATGGGGGCGTACCTGCTTTTTATCAAGCCAAACAGCTTTACATTTCACAGAGCCATTCAGAGATTTATTACAAC
CGATTTGATGCTGTGCAATCTGCCCAGTGAGCTGCCATTGGAGGGTTCATCCAGTATGGCTGGTGGTGGAGTTAGAGAAC
AGCCTTGTTCGTAACTATATTTAACACAGTGAGCACTGGTCTGAATGTATATGGAAATAAAAATACCTTAAGCCATTTTG
TTGTTGCAGGAACTGCTAAGGGAGGTCTTTTCAGATTGTACTTGGGTCTGAGTAGTGTGCTGGCTGGTGTTTTGTTTGGA
GCCATTCTGGGGGTTCCTTTTCGGGTCATGATCATGGCCATTGAGAAGTATCAAGGAGAGACTGTTTGGGACAGAAAACA
GAAGGAGCTCTATGAGTTAAAGCTGGATGAATGGAAGGCCAGGCTACATGTTACTGATGCTGTCACTGAAGAGTTTAAAA
ATAACTTAGGGGAAAACCAATCAGAAAGAGATATAAAGAGAATTGAAGAGCTGTTAAATCTTCCTAGAAACTCTTCAATA
ACTGATAGTAAAGAT

Alignment

ORF - retro_mdom_1842 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.14 %
• Parental protein coverage: 78.06 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SPEETLPHHIKGPVYPETGWERLKELLVRDEHQPVPQEIDYIFKAATTGAIVGWIYGGIPAFYHAKQRYI
          SP...LPHHIKGPVYPETGWE.LKELLVRDE.QP.PQEIDYIFKAAT.GAIVGWIYGG.PAFY.AKQ.YI
Retrocopy SPWRKLPHHIKGPVYPETGWESLKELLVRDERQPIPQEIDYIFKAATSGAIVGWIYGGVPAFYQAKQLYI

Parental  SQSHAEIYYSRFDAVQSAQRAAIRGFIRYGWRWSWRTALFVTIFNTVSTGLNVYRNKNALSHFVVAGAAT
          SQSH.EIYY.RFDAVQSAQ.AAI.GFI.YGW.WS.RTALFVTIFNTVSTGLNVY.NKN.LSHFVVAG.A.
Retrocopy SQSHSEIYYNRFDAVQSAQ*AAIGGFIQYGWWWS*RTALFVTIFNTVSTGLNVYGNKNTLSHFVVAGTAK

Parental  GGLFRFYLGLSSMLAGGLFGAILGVPFGVMIMAIEKYQGETVWDRKQKARKELYELKLDEWKARLHVTDA
          GGLFR.YLGLSS.LAG.LFGAILGVPF.VMIMAIEKYQGETVWDRKQK...ELYELKLDEWKARLHVTDA
Retrocopy GGLFRLYLGLSSVLAGVLFGAILGVPFRVMIMAIEKYQGETVWDRKQK---ELYELKLDEWKARLHVTDA

Parental  VTEEFKSNLGKNQTEKDVKRIEELLNLPRNPSLTTDSED
          VTEEFK.NLG.NQ.E.D.KRIEELLNLPRN.S..TDS.D
Retrocopy VTEEFKNNLGENQSERDIKRIEELLNLPRNSSI-TDSKD

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_1842 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1842 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,