RetrogeneDB ID: retro_mdom_1758

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 7:3259377..3259809(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PIGX
• Ensembl ID: ENSMODG00000018455
• Aliases: None
• Description: phosphatidylinositol glycan anchor biosynthesis, class X [Source:HGNC Symbol;Acc:26046]

Sequence

>retro_mdom_1758
TTCTTTCCTTCTCCTTTGGGTTCCTCTGGCTTTTGCATCTTGGCTCCTCCAGTGGGGACTGGCTCCTGGTATGGAGGGCC
ACCTTGCTTCTTGGCTTGCATTGCAGCCAACCACTTGGACAGAAATACCAACTGTTCTGAGATTATCCTGTTAGAAGAAA
TTGTGAAAGATGGCTTTCACAGGGACTTGCTAATAAAAGTGAAACTTGGCATAAGCACTGAAAATTCACTGACTTGAAAT
GTTTAGATTAAACATTAACTCCCAACTGGATTACATGTGGATCCATATGAACTGGCTTCATTACAAGAACAGAATGTGAC
AGAGGCAATGATTATTCAAAATACTGTTGACTTAGAAGTTCCTGAGTATTTGTCCAAAGAATTTGATGTCTTTGTTTATG
CCAAGTCAGATTCTCAGTGTACGGAGTGTTTC

Alignment

ORF - retro_mdom_1758 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.51 %
• Parental protein coverage: 58.37 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FFPSS-GFSGFGILAPPVGA-WLLLWGATVLL-RCAAVNHSGRNTNCSEIILLQEIVKDGFHRDLLIKVK
          FFPS..G.SGF.ILAPPVG..WLL.W.AT.LL..C.A.NH..RNTNCSEIILL.EIVKDGFHRDLLIKVK
Retrocopy FFPSPLGSSGFCILAPPVGT<WLLVWRATLLL>ACIAANHLDRNTNCSEIILLEEIVKDGFHRDLLIKVK

Parental  LGTSIENSPTCSVLIKHHLPTGLYVDPYELASLQEHNVTEAMIIQNTVDLEAPEYLSKEFDVFVYAKSDS
          LG.S.ENS.T..V.IKH.LPTGL.VDPYELASLQE.NVTEAMIIQNTVDLE.PEYLSKEFDVFVYAKSDS
Retrocopy LGISTENSLT*NV*IKH*LPTGLHVDPYELASLQEQNVTEAMIIQNTVDLEVPEYLSKEFDVFVYAKSDS

Parental  QCSECF
          QC.ECF
Retrocopy QCTECF

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_1758 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1758 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 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003759	1 retrocopy	retro_amel_386,
Callithrix jacchus	ENSCJAG00000013676	1 retrocopy	retro_cjac_2794,
Monodelphis domestica	ENSMODG00000018455	1 retrocopy	retro_mdom_1758 ,
Mustela putorius furo	ENSMPUG00000003841	1 retrocopy	retro_mputfur_1090,
Mus musculus	ENSMUSG00000023791	1 retrocopy	retro_mmus_943,
Oryctolagus cuniculus	ENSOCUG00000012329	1 retrocopy	retro_ocun_977,
Rattus norvegicus	ENSRNOG00000033623	2 retrocopies	retro_rnor_1998, retro_rnor_2555,