RetrogeneDB ID: retro_mdom_331

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:164789539..164789962(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000001899
• Aliases: None
• Description: None

Sequence

>retro_mdom_331
ATCTTGCACTACATTGCCCAAAAATACAACTTGTGTAGTGAGATGGAGGAAGAACACATCCAAGTTGATGTGCTTGAGAA
CCACATCATGGACATCCAAATGCAGCTGGTTCATGTCTGCTACAATCCAAACTTTGAAATAATAAAAATTGAGTGCCTTC
ATCAGCTTCCAGGGCAATTGAAGCTCTTCTCCCTGTTCCTGGGGAAATGTACCTGGTTTGCAGGAAACAAGATCACATAC
GTGGACTTTCTTGTGTAAGATGTCCTTGACCAGAACTAAAAGTTTGAACCCACTTGCTTGTAGAAGTTCTTAAAACTCAA
GGAGTTTTTACATTGGTTTGAGAGTCTAAGTAGCATCTCCACCTACTTAGCATTTGAACACTGCCAACTGTACCCAATCT
TCACAAAAATGGCTTGTTGGGGG

Alignment

ORF - retro_mdom_331 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.72 %
• Parental protein coverage: 64.68 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ILRYIARQYNLCGETEEERIRVDMLENHVMDIRMQLARVCYNPNFEVMKIEYLQQLPGQLKLFSLFLGKC
          IL.YIA..YNLC.E.EEE.I.VD.LENH.MDI.MQL..VCYNPNFE..KIE.L.QLPGQLKLFSLFLGKC
Retrocopy ILHYIAQKYNLCSEMEEEHIQVDVLENHIMDIQMQLVHVCYNPNFEIIKIECLHQLPGQLKLFSLFLGKC

Parental  SWFAGNKITFVDFLVYDVLDQNRKFEPSCLEKFSNLKEFLHRFESLSSIATYLASERCQPYPIFAKMACW
          .WFAGNKIT.VDFLV.DVLDQN.KFEP.CL.KF..LKEFLH.FESLSSI.TYLA.E.CQ.YPIF.KMACW
Retrocopy TWFAGNKITYVDFLV*DVLDQN*KFEPTCL*KFLKLKEFLHWFESLSSISTYLAFEHCQLYPIFTKMACW

Parental  G
          G
Retrocopy G

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	0.33 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_331 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_331 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.

---

Parental genes homology:

Parental genes homology involve 15 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005380	2 retrocopies	retro_chof_1850, retro_chof_1989,
Callithrix jacchus	ENSCJAG00000003168	1 retrocopy	retro_cjac_4,
Erinaceus europaeus	ENSEEUG00000014211	1 retrocopy	retro_eeur_112,
Echinops telfairi	ENSETEG00000005817	2 retrocopies	retro_etel_1074, retro_etel_1910,
Homo sapiens	ENSG00000134202	1 retrocopy	retro_hsap_2419,
Microcebus murinus	ENSMICG00000005185	1 retrocopy	retro_mmur_1571,
Macaca mulatta	ENSMMUG00000008029	2 retrocopies	retro_mmul_610, retro_mmul_941,
Monodelphis domestica	ENSMODG00000001899	1 retrocopy	retro_mdom_331 ,
Mus musculus	ENSMUSG00000004032	2 retrocopies	retro_mmus_491, retro_mmus_547,
Nomascus leucogenys	ENSNLEG00000003302	1 retrocopy	retro_nleu_1895,
Pan troglodytes	ENSPTRG00000001063	2 retrocopies	retro_ptro_1393, retro_ptro_1709,
Rattus norvegicus	ENSRNOG00000047034	1 retrocopy	retro_rnor_963,
Sus scrofa	ENSSSCG00000006821	2 retrocopies	retro_sscr_10, retro_sscr_855,
Tarsius syrichta	ENSTSYG00000006736	1 retrocopy	retro_tsyr_145,
Tursiops truncatus	ENSTTRG00000009682	1 retrocopy	retro_ttru_1828,