RetrogeneDB ID: retro_mdom_1573

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 6:24482644..24483320(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000002006
• Aliases: None
• Description: None

Sequence

>retro_mdom_1573
GATGAATCAATGTTATCTGATCCAGTTATGAGCAATGTCTTGAAAGTCAGGGGTTCAGAGTTAATCCTCTTCAACAGTCC
AGAGTATCAGAGACTCAGGATCAATTCTATGAATGAAAGATCATTTACATGCAATTATAAAGAGCATTTGGTTTACAGTT
CAAAAATTAGGAAAACAGTGGTTTCACCTGAACTCTCTTTGACAGGTCTAGAATTAATATCACATACTTACTTTGAGCTT
TTCCTGGCTCAGTTACTAAAGAAAGCTTATTCCACATTCGTTCTTAAGGGTGAACTACCAGACTGTGAAGCTAACCAGCT
CCTGAAGATCATTCAGGTACAACAAATGGATAGACCAAAACTCATTGGAGAAAAGTTAGCTCTTCTAAAAGATTCAAGAA
TGCAGAAAATAGACATAGAGTGGTCTTTAGAAGCAAGTTATCTGTATGATGGAACAGGAATGTTAGATGAAGATGAAGAG
AATCTACAAAGAGCTCTAGCACTAAGTTGACAGGAAATTGATATGGAAGACAATGAAGCAGATGTGCTAAAGAGCAATTT
GACTTAGTATGCAATGCACTTCCAGAAATAGTATTTCAGAAGATATCCCACAGACATCAGGTACAAATTCACCAACATCT
CTTTCTTCAAAAGATCTACAAAAGAGAAAAGAAGCC

Alignment

ORF - retro_mdom_1573 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.56 %
• Parental protein coverage: 64.84 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DSGFFSIQVISNALKVWGLELILFNSPEYQRLGIDPINERSFICNYKEH-WFTVRKLGKQWFNLNSL-LT
          D....S..V.SN.LKV.G.ELILFNSPEYQRL.I...NERSF.CNYKEH.WFTV.KLGKQWF.LNSL.LT
Retrocopy DESMLSDPVMSNVLKVRGSELILFNSPEYQRLRINSMNERSFTCNYKEH>WFTVQKLGKQWFHLNSL<LT

Parental  GPELISDTYLALFLAQLQQEGYSIFVVKGDLPDCEADQLLQMIRVQQMHRPKLIGEELAHLKDQRMQKID
          G.ELIS.TY..LFLAQL....YS.FV.KG.LPDCEA.QLL..I.VQQM.RPKLIGE.LA.LKD.RMQKID
Retrocopy GLELISHTYFELFLAQLLKKAYSTFVLKGELPDCEANQLLKIIQVQQMDRPKLIGEKLALLKDSRMQKID

Parental  LDQSLEASHPYDGTGMLDEDEENLQRALALSRQEIDMEDEEADLR-RAIRLSMQGSSRSSISEDIPQTSG
          ...SLEAS..YDGTGMLDEDEENLQRALALS.QEIDMED.EAD...RAI.LSMQ..SR.SISEDIPQTSG
Retrocopy IEWSLEASYLYDGTGMLDEDEENLQRALALS*QEIDMEDNEADVL>RAI*LSMQCTSRNSISEDIPQTSG

Parental  TNSSASLSSEELRKRREA
          TNS..SLSS..L.KR.EA
Retrocopy TNSPTSLSSKDLQKRKEA

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	78.55 RPM
SRP007412_cerebellum	0.00 RPM	50.60 RPM
SRP007412_heart	0.00 RPM	34.49 RPM
SRP007412_kidney	0.00 RPM	86.91 RPM
SRP007412_liver	0.00 RPM	74.01 RPM
SRP007412_testis	0.00 RPM	231.60 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1573 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1573 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 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005786	2 retrocopies	retro_btau_1652, retro_btau_330,
Choloepus hoffmanni	ENSCHOG00000005302	1 retrocopy	retro_chof_2238,
Callithrix jacchus	ENSCJAG00000018025	2 retrocopies	retro_cjac_1724, retro_cjac_375,
Cavia porcellus	ENSCPOG00000010887	1 retrocopy	retro_cpor_1460,
Homo sapiens	ENSG00000066427	1 retrocopy	retro_hsap_89,
Macaca mulatta	ENSMMUG00000020751	1 retrocopy	retro_mmul_298,
Monodelphis domestica	ENSMODG00000002006	2 retrocopies	retro_mdom_1498, retro_mdom_1573 ,
Nomascus leucogenys	ENSNLEG00000017126	1 retrocopy	retro_nleu_66,
Pongo abelii	ENSPPYG00000006075	1 retrocopy	retro_pabe_9,
Pteropus vampyrus	ENSPVAG00000015316	2 retrocopies	retro_pvam_1201, retro_pvam_587,
Tupaia belangeri	ENSTBEG00000008099	3 retrocopies	retro_tbel_102, retro_tbel_2635, retro_tbel_3925,