RetrogeneDB ID: retro_mdom_1006

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:193507705..193507967(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: OCIAD2
• Ensembl ID: ENSMODG00000025531
• Aliases: None
• Description: OCIA domain containing 2 [Source:HGNC Symbol;Acc:28685]

Sequence

>retro_mdom_1006
ATGGCTTGAGAGCCTCCTCATGAAAAACAACCTAAAACTCCACACTTACCCCCAAACAAATAGAGCCTTTAATTTTGTCC
CAAATCAAAGGTCCATTTCCATAGAGGAGAGATCTCAAAGATCATCCATTAATATAAAGAAAAGAGTTCCTGGGAGAGAG
CTCTCCTTTTATCCTTGGTAAATATGCTTGAGTAATCAAAGATTTGTTTGCAAAGATTTCTTGGGATCAAACCCAAGATT
TGGATCATTGCCAAAGGTGGCA

Alignment

ORF - retro_mdom_1006 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.79 %
• Parental protein coverage: 88.89 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MASEPPHEEKQPKMPHLPPDKQSLLFCPKSKVHIHRGEISKIIRECKEESFWKRALPSALVGM-LITQGL
          MA.EPPHE.KQPK.PHLPP.K.SL.FCPKSKVH.HRGEISKII...KE.S.W.RAL...LV.M.L..Q..
Retrocopy MA*EPPHE-KQPKTPHLPPNK*SL*FCPKSKVHFHRGEISKIIH*YKEKSSWERALLLSLVNM>LSNQRF

Parental  VHKGYLASNPRFGSLPKVA
          V.K..L.SNPRFGSLPKVA
Retrocopy VCKDFLGSNPRFGSLPKVA

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_1006 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1006 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 14 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018637	1 retrocopy	retro_cjac_1505,
Erinaceus europaeus	ENSEEUG00000006759	1 retrocopy	retro_eeur_504,
Homo sapiens	ENSG00000145247	1 retrocopy	retro_hsap_4082,
Gorilla gorilla	ENSGGOG00000013778	1 retrocopy	retro_ggor_2738,
Microcebus murinus	ENSMICG00000006147	1 retrocopy	retro_mmur_1402,
Macaca mulatta	ENSMMUG00000014869	1 retrocopy	retro_mmul_2353,
Monodelphis domestica	ENSMODG00000020640	1 retrocopy	retro_mdom_1103,
Monodelphis domestica	ENSMODG00000025531	1 retrocopy	retro_mdom_1006 ,
Nomascus leucogenys	ENSNLEG00000017430	1 retrocopy	retro_nleu_2048,
Oryctolagus cuniculus	ENSOCUG00000007907	2 retrocopies	retro_ocun_1734, retro_ocun_1780,
Otolemur garnettii	ENSOGAG00000011039	1 retrocopy	retro_ogar_561,
Pongo abelii	ENSPPYG00000014722	1 retrocopy	retro_pabe_3350,
Pan troglodytes	ENSPTRG00000016048	1 retrocopy	retro_ptro_2768,
Vicugna pacos	ENSVPAG00000011765	1 retrocopy	retro_vpac_331,