RetrogeneDB ID: retro_mdom_1800

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 7:156605097..156605435(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GMNN
• Ensembl ID: ENSMODG00000011682
• Aliases: None
• Description: geminin, DNA replication inhibitor [Source:HGNC Symbol;Acc:17493]

Sequence

>retro_mdom_1800
TCTGAAGAAGCTTTTGATCTCATGATTAAAGAAAACCCTTCTTCTCAATACTAGAAAGAAGTGGCAGAAAAACAGAGGAA
GATTCTTTATGAAGTACTACAAAAAATGAGAAACTACATAAATAAATTGAACAGAAGAACAATGAAATTACCCAACTAAA
AGAATAAAATAAGGAACTGGAAGAACTAGCAGGATCTGTACAATATATGACAGATATAATAGAACGGCTAACTGGGCAGT
CTGTAGAAAGCTTTGAATTACAGGACAAGCTAGCATCTGAAGATTCAGATTCTGGAAGGGAAGAAGTAGACAAAGATTCT
GAAGAAAATAGCCAGATG

Alignment

ORF - retro_mdom_1800 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.58 %
• Parental protein coverage: 54.59 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SQEAFDLMIKENPPSQYWKEVAEKRRKVLYEVLQE-NEKLHKEIEQKDNEIAHLKEENKELVELAGHVQY
          S.EAFDLMIKENP.SQY.KEVAEK.RK.LYEVLQ..NEKLHK.IEQK.NEI..LKE.NKEL.ELAG.VQY
Retrocopy SEEAFDLMIKENPSSQY*KEVAEKQRKILYEVLQK<NEKLHK*IEQKNNEITQLKE*NKELEELAGSVQY

Parental  MADIIERLTGQSVENFELRDNLAFEDSDSGREEVDKDSEENSEI
          M.DIIERLTGQSVE.FEL.D.LA.EDSDSGREEVDKDSEENS..
Retrocopy MTDIIERLTGQSVESFELQDKLASEDSDSGREEVDKDSEENSQM

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_1800 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1800 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 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006161	1 retrocopy	retro_cjac_1012,
Microcebus murinus	ENSMICG00000014010	1 retrocopy	retro_mmur_594,
Myotis lucifugus	ENSMLUG00000014849	2 retrocopies	retro_mluc_1589, retro_mluc_743,
Monodelphis domestica	ENSMODG00000011682	1 retrocopy	retro_mdom_1800 ,
Mus musculus	ENSMUSG00000006715	2 retrocopies	retro_mmus_1525, retro_mmus_2213,
Oryctolagus cuniculus	ENSOCUG00000000728	1 retrocopy	retro_ocun_613,
Otolemur garnettii	ENSOGAG00000004982	1 retrocopy	retro_ogar_1726,
Ochotona princeps	ENSOPRG00000007969	1 retrocopy	retro_opri_439,
Rattus norvegicus	ENSRNOG00000018782	1 retrocopy	retro_rnor_820,
Sarcophilus harrisii	ENSSHAG00000004058	2 retrocopies	retro_shar_581, retro_shar_769,
Tupaia belangeri	ENSTBEG00000010502	2 retrocopies	retro_tbel_1028, retro_tbel_353,