RetrogeneDB ID: retro_mdom_1839

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 8:58264784..58265495(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: REXO4
• Ensembl ID: ENSMODG00000012817
• Aliases: None
• Description: REX4, RNA exonuclease 4 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:12820]

Sequence

>retro_mdom_1839
GGCAGCCTTTACCAGAAAATATAGGACATCAAGCATGAGAAGAGGAAAGAAGTATTAGTTCTTCCTCCACCAACAGAAGA
AGACATCAGGCTTGATGATGTAGATCCTAAGGATACCAAAGCTGCCATTGGTCCAGAAGCTGCTGAAATAACCTCCAAAA
AACTGGGTCTGAAGGAAACAAATCTGTCACTGGCAAAAGAAAGGGCATTTGAAGGCATGACCGAAGATGTAGCCATGACT
GTGAGATGGAACGAGCAGGATCAAATGGGGAATAAAACATCCTTGCCTGAGTGTCCATTATAAACCAATTTGGAAAGTGT
GTTTTTGACAAGTGTGTCAAGCCAACAGAGAAAGAGACTGATTACCAGACAGATGTAAGTGGAATTCCACCAGAAGACAT
CAAACACAGAGAAAAGTTTCAGGTTGTTCAAAAGGAAGTGGCAGCTCTACTTAAGGGCAGGATTCTAGCTGGACATACTC
TACATAATGACTTAAAAATTCTCCTTCTTGATCATCCCAAAAAGAAGATCTCGGATACACAAAAATATAAAAACTTTCAG
AACACAAGTAAAGACTATAAGACCATCTCTGAAACAGTTTAGGCAGAAAATTCTTGGTATCAGAATAGAGCAGTCAGAAC
ACTGTTTGTTTCAAGGTGCTCAGGCAGCAATGAGACTTTACATAATGATTAAAAAACACTGGGAAGACACT

Alignment

ORF - retro_mdom_1839 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.5 %
• Parental protein coverage: 55.76 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GSLHQKIVDIKREKRKAELVPPPPTEADIWFDDVDPKDIEAAIGPEAAEIARKKLGLKETNLSLVKERAF
          GSL.QKI.DIK.EKRK..LV.PPPTE.DI..DDVDPKD..AAIGPEAAEI..KKLGLKETNLSL.KERAF
Retrocopy GSLYQKI*DIKHEKRKEVLVLPPPTEEDIRLDDVDPKDTKAAIGPEAAEITSKKLGLKETNLSLAKERAF

Parental  EGMTKAVAM-DCEMVGAGPNGEENILARVSIVNQFGKCVYDKYVKPTEKVTDYRTDVSGIRPEDIKHGEK
          EGMT..VAM.DCEM..AG.NGE.NILA.VSI.NQFGKCV.DK.VKPTEK.TDY.TDVSGI.PEDIKH.EK
Retrocopy EGMTEDVAM<DCEMERAGSNGE*NILA*VSIINQFGKCVFDKCVKPTEKETDYQTDVSGIPPEDIKHREK

Parental  FKVVQKEVADLLKDRILVGHALHNDLKILLLDHPKKKIRDTQKY-KPFRTQVKTGRPSLKLLSQKILGIR
          F.VVQKEVA.LLK.RIL.GH.LHNDLKILLLDHPKKKI.DTQKY.K.FRTQVKT.RPSLK...QKILGIR
Retrocopy FQVVQKEVAALLKGRILAGHTLHNDLKILLLDHPKKKISDTQKY>KTFRTQVKTIRPSLKQFRQKILGIR

Parental  IQQSEHCSIQDAQAAMRLYVMVKKQWEGT
          I.QSEHC..Q.AQAAMRLY.M.KK.WE.T
Retrocopy IEQSEHCLFQGAQAAMRLYIMIKKHWEDT

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	49.94 RPM
SRP007412_cerebellum	0.00 RPM	60.07 RPM
SRP007412_heart	0.00 RPM	27.51 RPM
SRP007412_kidney	0.00 RPM	56.62 RPM
SRP007412_liver	0.00 RPM	48.33 RPM
SRP007412_testis	0.00 RPM	62.66 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1839 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1839 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
Monodelphis domestica	ENSMODG00000012817	1 retrocopy	retro_mdom_1839 ,
Mus musculus	ENSMUSG00000052406	2 retrocopies	retro_mmus_1006, retro_mmus_2104,
Nomascus leucogenys	ENSNLEG00000013130	1 retrocopy	retro_nleu_2930,
Pongo abelii	ENSPPYG00000019735	1 retrocopy	retro_pabe_1278,