RetrogeneDB ID: retro_mdom_1498

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:24706961..24707534(-)
• 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_1498
AAATCATTTATATGCAATTTTAAAGAACACTGGTTTACAGTTCAAGAATTAGGAAAACAGCAGTTTAACCTGAACTCTCT
CTTGATGGGTCCATAATTAATATCAGATGTTTATCTTGCACTTTTCTTGGCTCAGTTACAACAGGAAGGTTATTCCATAT
TTGTTTTTAAGAGTGGCCTACCAGACTGTGAAGCTGATCAGCTTCTGCAGATGATTTGAGTACAACAAATGCATAGACTA
AAACTCATTGGAGAAGAGTTATCTCATCTAAAAGATCAAAGAATGCAGAAAATAGACCTAGATCAGTCGTTAGAAGCAAG
TCATCCATATAACGGAACAGGAATGTTAGATGAAGATGAAAAGAATCTACAAAGAGCTCCAGCATTAAGTCAACAGGAAA
TTGATATGGAAGATGAAGAAGCAGATCTGCAAAGAGCAATTCAACTTAGTATGGAAGGTAGTTCCAGAAGTAGTATTTCA
GAAGATATTCCACAGACATCAGGTACAAATTCACCAGCATCTCTTTCTTCAGAAGAGCTACGAAAGAGAAGAGGAGCCTG
CTTTGAAAAACAA

Alignment

ORF - retro_mdom_1498 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.43 %
• Parental protein coverage: 55.04 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RSFICNYKEHWFTVRKLGKQWFNLNSLLTGPELISDTYLALFLAQLQQEGYSIFVVKGDLPDCEADQLLQ
          .SFICN.KEHWFTV..LGKQ.FNLNSLL.GP.LISD.YLALFLAQLQQEGYSIFV.K..LPDCEADQLLQ
Retrocopy KSFICNFKEHWFTVQELGKQQFNLNSLLMGP*LISDVYLALFLAQLQQEGYSIFVFKSGLPDCEADQLLQ

Parental  MIRVQQMHRPKLIGEELAHLKDQRMQKIDLDQSLEASHPYDGTGMLDEDEENLQRALALSRQEIDMEDEE
          MI.VQQMHR.KLIGEEL.HLKDQRMQKIDLDQSLEASHPY.GTGMLDEDE.NLQRA.ALS.QEIDMEDEE
Retrocopy MI*VQQMHRLKLIGEELSHLKDQRMQKIDLDQSLEASHPYNGTGMLDEDEKNLQRAPALSQQEIDMEDEE

Parental  ADLRRAIRLSMQGSSRSSISEDIPQTSGTNSSASLSSEELRKRREAYFEKQ
          ADL.RAI.LSM.GSSRSSISEDIPQTSGTNS.ASLSSEELRKRR.A.FEKQ
Retrocopy ADLQRAIQLSMEGSSRSSISEDIPQTSGTNSPASLSSEELRKRRGACFEKQ

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_1498 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1498 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,