RetrogeneDB ID: retro_mdom_384

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:343728923..343729887(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TUFM
• Ensembl ID: ENSMODG00000015564
• Aliases: None
• Description: Tu translation elongation factor, mitochondrial [Source:HGNC Symbol;Acc:12420]

Sequence

>retro_mdom_384
CATGCTGACTATGTCAAGAACATGATTACTGGCACAGCCCCACTGGATGAATGGCTGCATCCTAGTGGTGGCAACCAATG
ATGGTCCCATGCCCCAGACAAGGGAGTACCTGCTGCTTGCTAAACAGATTGGTGTGGAGCACTTGGTAGTGTTTGTGAAC
AAGGCAGATGCTATCTAGGACAATGAGATGGTGGAACTAGTAGAGCTAGAAATAAGGGAGCTGCTTATTGAGTTTGGCTA
TGATGGGGAGAAGACTCCTGTCATTGTTGGTTCTGCCCTATGTGCCCTGGGGCAACGGCAGCCAGAGATGGGGTGAATGC
TGTAAGGAAACTGTTGGACACTCATGATCCTGTGCCTACTCGGGATCTAGAGAAGCCCTTACTGCTGCTGGTGGAGTCTG
TTTACTCCATCCCTTGCTGAGGCACAGTGATGGCAGGGACTCTGGAAAGAGGAACTGTGAAGATGGGAGATGAATGTGAA
TTCCTGTGTCACAGCAAGACTTTTCACTTTCTGGTCAAAGGAATTGAAATGTTTTCACCAGAGTCTGGAATGAATTGAGG
CTGGAGATAATCTTGGTGCGTTAATTCGGAGGCTGACAAGGAAGGATGTTCGATGGGGCATATGGTGATGCTTAAAAGGC
TCCATTCAGACCCATCAGAAGGTTGAGACTCAGGTTTGCATTCTCAGCAAGGAGTAAGGTGGCTACCACAAGCCATTTGT
GACCCACTTCATATCTGTCATGTTCTATCTTATGTGAAATTTGGCCTCTCGGGTCCTTCTACCACCAGAGAAGGAGATGG
CCATGCCTGGAGAAGACCTGAAACTAAACTTAATCTTAAAACAACCCATGATCTTGAAGAAAGTTCAGCATTTTACCCTG
AGGGATGGTGGTAAAACCATTGGTACTGGCCTGGTCACTAATATATCAGCTATGACTGAAGAGGATAAGGACATTAAGTG
GAGC

Alignment

ORF - retro_mdom_384 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.43 %
• Parental protein coverage: 71.3 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  HADYVKNMITGTAPLDGCI-LVVAA-NDGPMPQTREHLLLAKQIGVEHMVVFVNKADAVQDNEMVELVEL
          HADYVKNMITGTAPLD......V.A.NDGPMPQTRE.LLLAKQIGVEH.VVFVNKADA..DNEMVELVEL
Retrocopy HADYVKNMITGTAPLDEWL>ILVVATNDGPMPQTREYLLLAKQIGVEHLVVFVNKADAI*DNEMVELVEL

Parental  EIRELLTEFGYDGEKTPVIVGSALCALEQRQPEL-GVNAVMKLLDAVDTHIPVPTRDLEKPFLLPVESVY
          EIRELL.EFGYDGEKTPVIVGSALCAL.QRQPE..GVNAV.KLLD...TH.PVPTRDLEKP.LL.VESVY
Retrocopy EIRELLIEFGYDGEKTPVIVGSALCALGQRQPEM<GVNAVRKLLD---THDPVPTRDLEKPLLLLVESVY

Parental  SIPGRGTVVTGTLERGTVKKGDECEFLGHSKNFRSVVTGIEM-FHQSLERAEAGDNLGALIRGLKREDVR
          SIP..GTV..GTLERGTVK.GDECEFL.HSK.F...V.GIEM.FHQSLE..EAGDNLGALIR.L.R.DVR
Retrocopy SIPC*GTVMAGTLERGTVKMGDECEFLCHSKTFHFLVKGIEM>FHQSLE*IEAGDNLGALIRRLTRKDVR

Parental  RGMVMVKPGSIQTHQKVEAQVYILSKEEGGRHKPFVSHFMPVMFSLTWDMACRVLLPPEKEMAMPGEDLK
          .G......GSIQTHQKVE.QV.ILSKE.GG.HKPFV.HF..VMF.L....A.RVLLPPEKEMAMPGEDLK
Retrocopy WGIW*CLKGSIQTHQKVETQVCILSKE*GGYHKPFVTHFISVMFYLM*NLASRVLLPPEKEMAMPGEDLK

Parental  LNLILRQPMILEKGQRFTLRDGGKTIGTGLVTNISAMTEEDKDIKWS
          LNLIL.QPMIL.K.Q.FTLRDGGKTIGTGLVTNISAMTEEDKDIKWS
Retrocopy LNLILKQPMILKKVQHFTLRDGGKTIGTGLVTNISAMTEEDKDIKWS

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	9.30 RPM	0.00 RPM
SRP007412_cerebellum	15.67 RPM	0.00 RPM
SRP007412_heart	2.99 RPM	0.00 RPM
SRP007412_kidney	1.32 RPM	0.00 RPM
SRP007412_liver	0.50 RPM	0.00 RPM
SRP007412_testis	5.11 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_384 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_384 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 11 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000016474	1 retrocopy	retro_dord_278,
Homo sapiens	ENSG00000178952	1 retrocopy	retro_hsap_1816,
Macropus eugenii	ENSMEUG00000011131	1 retrocopy	retro_meug_1783,
Monodelphis domestica	ENSMODG00000015564	1 retrocopy	retro_mdom_384 ,
Mus musculus	ENSMUSG00000073838	1 retrocopy	retro_mmus_10,
Ornithorhynchus anatinus	ENSOANG00000013114	1 retrocopy	retro_oana_36,
Oryctolagus cuniculus	ENSOCUG00000002683	1 retrocopy	retro_ocun_333,
Pan troglodytes	ENSPTRG00000007939	1 retrocopy	retro_ptro_1174,
Rattus norvegicus	ENSRNOG00000018604	1 retrocopy	retro_rnor_1134,
Vicugna pacos	ENSVPAG00000009541	1 retrocopy	retro_vpac_346,
Drosophila melanogaster	FBgn0033184	1 retrocopy	retro_dmel_52,