RetrogeneDB ID: retro_mdom_1286

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:293716467..293716746(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000008433
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPS18
• Ensembl ID: ENSMODG00000014210
• Aliases: None
• Description: ribosomal protein S18 [Source:HGNC Symbol;Acc:10401]

Sequence

>retro_mdom_1286
TCTCTTGTGATCCCTGAGAAGTTCCAGCATATTTTGCTAGTGCTCAACACCAACATTGATGTATGGCAGAAAAAAGCTTT
TGCCATCAGCACCCTCAAAGGTGTGGGTCAAAGATATGCTCACGTAATACTGAGGAAAGCAGACATTGACCTCACCAAGA
GGGCTGTTGAGCTCACTGATGATGAAGTGGAGCACATGATCACTATCATGCAGAATCCTCAGCAATACAAGATCCCAGAC
TGGTTCCTTAATAGACAGAAAGATGTAAGTAACGGAAAG

Alignment

ORF - retro_mdom_1286 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.72 %
• Parental protein coverage: 62. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SLVIPEKFQHILRVLNTNIDGRRKIAFAITAIKGVGRRYAHVVLRKADIDLTKRAGELTEDEVERVITIM
          SLVIPEKFQHIL.VLNTNID...K.AFAI...KGVG.RYAHV.LRKADIDLTKRA.ELT.DEVE..ITIM
Retrocopy SLVIPEKFQHILLVLNTNIDVWQKKAFAISTLKGVGQRYAHVILRKADIDLTKRAVELTDDEVEHMITIM

Parental  QNPRQYKIPDWFLNRQKDVKDGK
          QNP.QYKIPDWFLNRQKDV..GK
Retrocopy QNPQQYKIPDWFLNRQKDVSNGK

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_1286 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1286 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 17 parental genes, and 99 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010356	1 retrocopy	retro_cjac_3061,
Callithrix jacchus	ENSCJAG00000021650	5 retrocopies	retro_cjac_22, retro_cjac_245, retro_cjac_2529, retro_cjac_2893, retro_cjac_2955,
Gorilla gorilla	ENSGGOG00000006571	5 retrocopies	retro_ggor_1496, retro_ggor_2310, retro_ggor_344, retro_ggor_77, retro_ggor_93,
Loxodonta africana	ENSLAFG00000032173	1 retrocopy	retro_lafr_1171,
Myotis lucifugus	ENSMLUG00000007360	2 retrocopies	retro_mluc_181, retro_mluc_932,
Macaca mulatta	ENSMMUG00000003867	1 retrocopy	retro_mmul_2198,
Monodelphis domestica	ENSMODG00000014210	4 retrocopies	retro_mdom_1041, retro_mdom_1286 , retro_mdom_1514, retro_mdom_642,
Mus musculus	ENSMUSG00000008668	2 retrocopies	retro_mmus_57, retro_mmus_66,
Nomascus leucogenys	ENSNLEG00000006840	10 retrocopies	retro_nleu_1074, retro_nleu_1161, retro_nleu_1176, retro_nleu_1466, retro_nleu_219, retro_nleu_2572, retro_nleu_2616, retro_nleu_525, retro_nleu_60, retro_nleu_737,
Oryctolagus cuniculus	ENSOCUG00000010546	1 retrocopy	retro_ocun_31,
Pongo abelii	ENSPPYG00000025953	14 retrocopies	retro_pabe_1138, retro_pabe_128, retro_pabe_1481, retro_pabe_1482, retro_pabe_1813, retro_pabe_1881, retro_pabe_2303, retro_pabe_2407, retro_pabe_2663, retro_pabe_2833, retro_pabe_2967, retro_pabe_3013, retro_pabe_3070, retro_pabe_368,
Pan troglodytes	ENSPTRG00000018039	1 retrocopy	retro_ptro_121,
Rattus norvegicus	ENSRNOG00000028505	4 retrocopies	retro_rnor_102, retro_rnor_234, retro_rnor_29, retro_rnor_70,
Sarcophilus harrisii	ENSSHAG00000006857	2 retrocopies	retro_shar_265, retro_shar_563,
Sarcophilus harrisii	ENSSHAG00000008658	1 retrocopy	retro_shar_618,
Sus scrofa	ENSSSCG00000001502	5 retrocopies	retro_sscr_112, retro_sscr_156, retro_sscr_157, retro_sscr_2, retro_sscr_831,
Tupaia belangeri	ENSTBEG00000012708	40 retrocopies	retro_tbel_1070, retro_tbel_1739, retro_tbel_1745, retro_tbel_1806, retro_tbel_1818, retro_tbel_1827, retro_tbel_1855, retro_tbel_205, retro_tbel_2087, retro_tbel_211, retro_tbel_2299, retro_tbel_2309, retro_tbel_2312, retro_tbel_234, retro_tbel_2364, retro_tbel_2424, retro_tbel_2473, retro_tbel_250, retro_tbel_2682, retro_tbel_2768, retro_tbel_295, retro_tbel_3189, retro_tbel_3317, retro_tbel_3383, retro_tbel_3625, retro_tbel_363, retro_tbel_3686, retro_tbel_3731, retro_tbel_3870, retro_tbel_4100, retro_tbel_4215, retro_tbel_4365, retro_tbel_45, retro_tbel_4562, retro_tbel_4578, retro_tbel_462, retro_tbel_57, retro_tbel_578, retro_tbel_856, retro_tbel_941,