RetrogeneDB ID: retro_mdom_799

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:4820218..4820626(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000005554
• Aliases: None
• Description: Proteasome subunit beta type [Source:UniProtKB/TrEMBL;Acc:F7FH35]

Sequence

>retro_mdom_799
CATAGCATTGAAGTGAGTGAACCTCTCCTGGTGCATGCAGCTGCTAAGCTCTTCAAGAAGATGTGTTACCATTACCAGGA
GGATCTCATGGCTGGGATCATCACTGCTGGCTGGGATTCCCATGAGAGGGGACAGGTCTACAAGGTCCCCATGGGAGGTA
TGATGGTTCGGCAGCCTTTCTCCACTGGGGGCTCAGGGAGCTCCTACATCTATGGCTCTGTTGATGCCTCCTATTGAGAA
AGTATAACTGAAAAGCAGTGTCTTCAGTCCACCACCAATGCTCTTGCTTTGGCCATGGATTGAGATGGTTCAGTAGTAAT
CCAGTTGGCAGCATTTACTGAAAAAGGAGTGGAATGGCAGATGCTTCTAGGAGACTAGCTTCCTCAGTTCCCTAGTTCTG
CCTATCCT

Alignment

ORF - retro_mdom_799 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.09 %
• Parental protein coverage: 68.32 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  HSIELNEPPLVHTAANLFKEMCYRYREDLMAGIIVAGWDPREGGQVYSVPMGGMMVRQPFSIGGSGSSYI
          HSIE..EP.LVH.AA.LFK.MCY.Y.EDLMAGII.AGWD..E.GQVY.VPMGGMMVRQPFS.GGSGSSYI
Retrocopy HSIEVSEPLLVHAAAKLFKKMCYHYQEDLMAGIITAGWDSHERGQVYKVPMGGMMVRQPFSTGGSGSSYI

Parental  YGYVDASYREGMNEKQCLQFTANALALAMDRDGSSGGVIRLAAITEKGVERQVLMGDQLPQFPSTTYP
          YG.VDASY.E...EKQCLQ.T.NALALAMD.DGS...VI.LAA.TEKGVE.Q.L.GD.LPQFPS..YP
Retrocopy YGSVDASY*ESITEKQCLQSTTNALALAMD*DGSV--VIQLAAFTEKGVEWQMLLGD*LPQFPSSAYP

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_799 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_799 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 20 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016075	1 retrocopy	retro_amel_1834,
Bos taurus	ENSBTAG00000013390	2 retrocopies	retro_btau_1734, retro_btau_534,
Canis familiaris	ENSCAFG00000015855	1 retrocopy	retro_cfam_2173,
Callithrix jacchus	ENSCJAG00000012010	1 retrocopy	retro_cjac_775,
Dipodomys ordii	ENSDORG00000005851	1 retrocopy	retro_dord_613,
Erinaceus europaeus	ENSEEUG00000002083	3 retrocopies	retro_eeur_203, retro_eeur_607, retro_eeur_71,
Felis catus	ENSFCAG00000008036	2 retrocopies	retro_fcat_1813, retro_fcat_1995,
Loxodonta africana	ENSLAFG00000012859	1 retrocopy	retro_lafr_874,
Macropus eugenii	ENSMEUG00000010676	1 retrocopy	retro_meug_621,
Microcebus murinus	ENSMICG00000014854	2 retrocopies	retro_mmur_140, retro_mmur_718,
Monodelphis domestica	ENSMODG00000005554	1 retrocopy	retro_mdom_799 ,
Mus musculus	ENSMUSG00000018286	2 retrocopies	retro_mmus_348, retro_mmus_3569,
Otolemur garnettii	ENSOGAG00000009653	1 retrocopy	retro_ogar_2114,
Pteropus vampyrus	ENSPVAG00000006048	1 retrocopy	retro_pvam_618,
Rattus norvegicus	ENSRNOG00000019551	1 retrocopy	retro_rnor_56,
Sorex araneus	ENSSARG00000006615	1 retrocopy	retro_sara_689,
Ictidomys tridecemlineatus	ENSSTOG00000014871	1 retrocopy	retro_itri_514,
Tarsius syrichta	ENSTSYG00000010674	1 retrocopy	retro_tsyr_1807,
Tursiops truncatus	ENSTTRG00000000566	1 retrocopy	retro_ttru_405,
Vicugna pacos	ENSVPAG00000000595	1 retrocopy	retro_vpac_400,