RetrogeneDB ID: retro_mdom_810

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:60932273..60932737(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS7
• Ensembl ID: ENSMODG00000014495
• Aliases: None
• Description: ribosomal protein S7 [Source:HGNC Symbol;Acc:10440]

Sequence

>retro_mdom_810
ATATTCTGTTCCAGCACCGAGATTGCGAAGCCCAATGGCAGGAAGCCAGATGAATTTGAGCCTGGTATTCACAGGCTCTC
CTGGAGTTGGAGATAAACTCTTACTTAAAAGCTCAATTAAAAGCACCACATATCACAGTTGCTTAATGAAATTGAAGTTG
TTGGTGGCAGAAAAGCTATGAACGATGTCATTTCAATTCTTAACTGAAATCTATTTAGAAGATCCAAGAATGGCTAGTTC
ATGAATTGGGGAAATCATCCAGTGGCAAGCATGTATGTTTTTTGTTTTTCAGAGGAGACTTCATATTAAGTCAAACAAGA
AAAAGTTATACAAAATATTTGCAAAAACATCTCAGAAGCCATATTTCCACTGCTGTATATGATCCAATCTTTAAAGATTT
TGTTTTTCCAAGTAAAATTATTGGTAATTTTAACTAAATAACAGCAGACTCATAAAGGTATATT

Alignment

ORF - retro_mdom_810 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.43 %
• Parental protein coverage: 79.38 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MFSSSAKIVKPNGEKPDEFESGI-SQALLELEMNSDLKAQLRELNITAA-KEIEVGGGRKAIIIFVPVPQ
          .F.SS..I.KPNG.KPDEFE.GI.SQALLELE.NS.LKAQL....IT.A..EIEV.GGRKA.........
Retrocopy IFCSSTEIAKPNGRKPDEFEPGI<SQALLELEINSYLKAQLKAPHITVA>NEIEVVGGRKAMNDVISILN

Parental  -LKSFQKIQVRLVRELEKKFSGKHVVFIAQR-RILPKPTRKSRTKNKQKRPRSRTLTAVHDAILEDLVFP
          .LKS..KIQ..LV.EL.K..SGKHV.F...R.......TRKS.TK..QK..RS...TAV.D.I..D.VFP
Retrocopy <LKSI*KIQEWLVHELGKSSSGKHVCFLFFRGDFILSQTRKSYTKYLQKHLRSHISTAVYDPIFKDFVFP

Parental  SEIVGKRIRVKLDGSRLI
          S.I.G.......D..R.I
Retrocopy SKIIGNFN*ITADS*RYI

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	458.31 RPM
SRP007412_cerebellum	0.00 RPM	217.75 RPM
SRP007412_heart	0.00 RPM	577.52 RPM
SRP007412_kidney	0.00 RPM	1131.16 RPM
SRP007412_liver	0.00 RPM	1676.62 RPM
SRP007412_testis	0.00 RPM	336.49 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_810 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_810 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 16 parental genes, and 84 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016462	2 retrocopies	retro_cjac_16, retro_cjac_2287,
Felis catus	ENSFCAG00000023243	2 retrocopies	retro_fcat_1534, retro_fcat_41,
Homo sapiens	ENSG00000171863	14 retrocopies	retro_hsap_111, retro_hsap_112, retro_hsap_1242, retro_hsap_1737, retro_hsap_1837, retro_hsap_2907, retro_hsap_2925, retro_hsap_329, retro_hsap_3635, retro_hsap_404, retro_hsap_4711, retro_hsap_4760, retro_hsap_528, retro_hsap_703,
Gorilla gorilla	ENSGGOG00000023095	13 retrocopies	retro_ggor_2028, retro_ggor_2090, retro_ggor_2161, retro_ggor_218, retro_ggor_2452, retro_ggor_2927, retro_ggor_294, retro_ggor_2965, retro_ggor_3047, retro_ggor_346, retro_ggor_400, retro_ggor_484, retro_ggor_597,
Loxodonta africana	ENSLAFG00000015087	11 retrocopies	retro_lafr_1223, retro_lafr_160, retro_lafr_217, retro_lafr_318, retro_lafr_319, retro_lafr_413, retro_lafr_514, retro_lafr_720, retro_lafr_786, retro_lafr_964, retro_lafr_970,
Myotis lucifugus	ENSMLUG00000006121	1 retrocopy	retro_mluc_1118,
Macaca mulatta	ENSMMUG00000011870	7 retrocopies	retro_mmul_1831, retro_mmul_1846, retro_mmul_1929, retro_mmul_23, retro_mmul_2403, retro_mmul_2540, retro_mmul_357,
Monodelphis domestica	ENSMODG00000014495	2 retrocopies	retro_mdom_662, retro_mdom_810 ,
Mus musculus	ENSMUSG00000061477	2 retrocopies	retro_mmus_271, retro_mmus_53,
Oryctolagus cuniculus	ENSOCUG00000008507	2 retrocopies	retro_ocun_203, retro_ocun_230,
Otolemur garnettii	ENSOGAG00000028165	1 retrocopy	retro_ogar_133,
Ochotona princeps	ENSOPRG00000005085	3 retrocopies	retro_opri_1036, retro_opri_415, retro_opri_500,
Pongo abelii	ENSPPYG00000025872	12 retrocopies	retro_pabe_1033, retro_pabe_1555, retro_pabe_2506, retro_pabe_2982, retro_pabe_2983, retro_pabe_31, retro_pabe_313, retro_pabe_360, retro_pabe_3659, retro_pabe_3803, retro_pabe_499, retro_pabe_524,
Pan troglodytes	ENSPTRG00000011615	3 retrocopies	retro_ptro_202, retro_ptro_3132, retro_ptro_58,
Pteropus vampyrus	ENSPVAG00000002071	7 retrocopies	retro_pvam_1051, retro_pvam_1183, retro_pvam_1330, retro_pvam_1437, retro_pvam_207, retro_pvam_543, retro_pvam_887,
Rattus norvegicus	ENSRNOG00000008551	2 retrocopies	retro_rnor_39, retro_rnor_391,