RetrogeneDB ID: retro_mdom_1855

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 8:114821769..114822259(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GPATCH11
• Ensembl ID: ENSMODG00000015289
• Aliases: None
• Description: G patch domain containing 11 [Source:HGNC Symbol;Acc:26768]

Sequence

>retro_mdom_1855
GATAGTATTTTAAAGAATGCTTTGGTGGAGAAAACAAGGAATTTGCTTTGCTTCAAAAGATGAGCTATCAAAGTGACCTG
GCTCTTGGCAAGGGTGCTGATGGCATTGTTGAAACCATTTCTCTGAACAGCAAAACAGGAAGAAGTGGCATTTGTCATGA
GACACTCATCAAAAGGAAAGTTGAGGAAGAACTGGGGAATTACAGAAGAAAGATTCATTTGAGAAAGCAAAATGAAGACA
AAGCTCTAGATCAGTTTCATTGGTGACTCAAAAGTAGACAAGAAGAATGAAAGCTAGAATATGATCTCATAAGAAGCCAG
GAAGTCTGACACTACATCGACCCTCAGAAAGATGTTCCAAAATACATCAAGCCATGGTTCTGACTCATGCCCGAAAAGAG
CGAAGAAAGGATGACAACAGATAAGGGAGAGGGAAGCAGATGGAATATAGTGGTGAAGATTTAAGTATAATGGAAAGATG
ACAAATACTG

Alignment

ORF - retro_mdom_1855 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.64 %
• Parental protein coverage: 62.93 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ENVLKNAL-GSENKGFALLQKMGYKSGQALGKTGSGIVEPIPLNIKTGRSGIGHETLIKRKAEEELENNR
          ...LKNAL.G.ENK.FALLQKM.Y.S..ALGK...GIVE.I.LN.KTGRSGI.HETLIKRK.EEEL.N.R
Retrocopy DSILKNAL<GGENKEFALLQKMSYQSDLALGKGADGIVETISLNSKTGRSGICHETLIKRKVEEELGNYR

Parental  RKIHLRNQYEEKATDQFRLRLKSKKEELKLEGDLKRSQKACHQLDTQKDIQVPKEPWYWFMSEEEEQEDE
          RKIHLR.Q.E.KA.DQF...LKS..EE.KLE.DL.RSQ...H..D.QKD......PW...M.E..E....
Retrocopy RKIHLRKQNEDKALDQFHW*LKSRQEE*KLEYDLIRSQEV*HYIDPQKDVPKYIKPWF*LMPEKSEERMT

Parental  KEK-ELEED-EYGDEELSVLEKLQIL
          ..K.E.E.D.EY..E.LS..E..QIL
Retrocopy TDK>EREAD>EYSGEDLSIMER*QIL

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	62.58 RPM
SRP007412_cerebellum	0.00 RPM	28.73 RPM
SRP007412_heart	0.00 RPM	22.13 RPM
SRP007412_kidney	0.00 RPM	38.19 RPM
SRP007412_liver	0.00 RPM	21.65 RPM
SRP007412_testis	0.00 RPM	104.50 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1855 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1855 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 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000006041	1 retrocopy	retro_cfam_708,
Choloepus hoffmanni	ENSCHOG00000004377	3 retrocopies	retro_chof_1420, retro_chof_2292, retro_chof_398,
Homo sapiens	ENSG00000152133	1 retrocopy	retro_hsap_2802,
Monodelphis domestica	ENSMODG00000015289	1 retrocopy	retro_mdom_1855 ,
Nomascus leucogenys	ENSNLEG00000027017	1 retrocopy	retro_nleu_1542,
Pan troglodytes	ENSPTRG00000011832	1 retrocopy	retro_ptro_1899,