RetrogeneDB ID: retro_mdom_1478

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:227443078..227443492(+)
• Located in intron of: ENSMODG00000003150

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000018083
• Aliases: None
• Description: None

Sequence

>retro_mdom_1478
GTGCTTCTTCCTACAAAGACTAAGTCTAATACAAGTGCCTCAATACTTCAGAAATATCAGAATGATGAAGTTCCACCTAT
GCCCACCCCTCTGCCTCCTCTGCATACAGTCTCCCAAAATAATCTGCAGATCTGGTGTCAGAGACTCAATATCAGCAAAA
ATGGTTGAAAGCGCATTCTATACAAGAGACTTATGGACCATGTATCACCTTCTAAGCAAGACATCCCTCCAATAGAAGAA
AAGGCCTGATGGATAAAAATAAAAACAGAAGCTTTGCTTGAAGAGTATTCTCCAGGTGAAAGTCAGACAATGGTTAGAGC
AGCAGAGCCTTTCACAAATAAGAAAAAGAAAAGAGAGGCAACAAAGACTTCTCTAGTTCAGAAAGCCAGCATGGCAGCAT
GGAGCAGGCTCATG

Alignment

ORF - retro_mdom_1478 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.78 %
• Parental protein coverage: 60.27 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VVLPTKTKSNTTP---QKSQNDEVPPMPTPLPPLHTVSRNNLQTWCQRLNISKNGRKHILYKRLMDHVSP
          V.LPTKTKSNT.....QK.QNDEVPPMPTPLPPLHTVS.NNLQ.WCQRLNISKNG.K.ILYKRLMDHVSP
Retrocopy VLLPTKTKSNTSASILQKYQNDEVPPMPTPLPPLHTVSQNNLQIWCQRLNISKNG*KRILYKRLMDHVSP

Parental  SEQDIPTVEEKDQWIKVKTEALLEEDSPGESQAMVRAAEPFTNKKKKREATKTSLVQTASMAAWGRLM
          S.QDIP..EEK..WIK.KTEALLEE.SPGESQ.MVRAAEPFTNKKKKREATKTSLVQ.ASMAAW.RLM
Retrocopy SKQDIPPIEEKA*WIKIKTEALLEEYSPGESQTMVRAAEPFTNKKKKREATKTSLVQKASMAAWSRLM

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_1478 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1478 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 37 parental genes, and 96 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020460	2 retrocopies	retro_btau_435, retro_btau_529,
Canis familiaris	ENSCAFG00000010335	5 retrocopies	retro_cfam_1332, retro_cfam_1540, retro_cfam_1905, retro_cfam_1934, retro_cfam_996,
Callithrix jacchus	ENSCJAG00000020168	4 retrocopies	retro_cjac_1378, retro_cjac_1991, retro_cjac_3832, retro_cjac_944,
Callithrix jacchus	ENSCJAG00000020171	2 retrocopies	retro_cjac_1334, retro_cjac_1491,
Dasypus novemcinctus	ENSDNOG00000010745	6 retrocopies	retro_dnov_1248, retro_dnov_1626, retro_dnov_1714, retro_dnov_2462, retro_dnov_2583, retro_dnov_2656,
Erinaceus europaeus	ENSEEUG00000008944	4 retrocopies	retro_eeur_205, retro_eeur_415, retro_eeur_426, retro_eeur_616,
Echinops telfairi	ENSETEG00000002722	1 retrocopy	retro_etel_312,
Echinops telfairi	ENSETEG00000007985	4 retrocopies	retro_etel_2051, retro_etel_2058, retro_etel_506, retro_etel_918,
Homo sapiens	ENSG00000121570	1 retrocopy	retro_hsap_893,
Homo sapiens	ENSG00000163530	3 retrocopies	retro_hsap_1642, retro_hsap_2903, retro_hsap_357,
Gorilla gorilla	ENSGGOG00000015121	2 retrocopies	retro_ggor_1970, retro_ggor_723,
Loxodonta africana	ENSLAFG00000016804	1 retrocopy	retro_lafr_456,
Microcebus murinus	ENSMICG00000013744	6 retrocopies	retro_mmur_1171, retro_mmur_156, retro_mmur_1634, retro_mmur_213, retro_mmur_598, retro_mmur_955,
Myotis lucifugus	ENSMLUG00000007444	1 retrocopy	retro_mluc_1706,
Myotis lucifugus	ENSMLUG00000016423	1 retrocopy	retro_mluc_973,
Macaca mulatta	ENSMMUG00000016901	1 retrocopy	retro_mmul_1515,
Macaca mulatta	ENSMMUG00000022112	3 retrocopies	retro_mmul_1550, retro_mmul_342, retro_mmul_475,
Monodelphis domestica	ENSMODG00000018083	3 retrocopies	retro_mdom_1057, retro_mdom_1478 , retro_mdom_999,
Mustela putorius furo	ENSMPUG00000010206	1 retrocopy	retro_mputfur_800,
Mus musculus	ENSMUSG00000058550	3 retrocopies	retro_mmus_1907, retro_mmus_2085, retro_mmus_3656,
Mus musculus	ENSMUSG00000072419	7 retrocopies	retro_mmus_1303, retro_mmus_1832, retro_mmus_1847, retro_mmus_2391, retro_mmus_2935, retro_mmus_3699, retro_mmus_394,
Nomascus leucogenys	ENSNLEG00000004020	2 retrocopies	retro_nleu_1329, retro_nleu_633,
Nomascus leucogenys	ENSNLEG00000004030	3 retrocopies	retro_nleu_2888, retro_nleu_3018, retro_nleu_388,
Oryctolagus cuniculus	ENSOCUG00000003175	1 retrocopy	retro_ocun_61,
Oryctolagus cuniculus	ENSOCUG00000016435	1 retrocopy	retro_ocun_114,
Otolemur garnettii	ENSOGAG00000031228	7 retrocopies	retro_ogar_1678, retro_ogar_1722, retro_ogar_1953, retro_ogar_2404, retro_ogar_2567, retro_ogar_2900, retro_ogar_586,
Ochotona princeps	ENSOPRG00000005059	1 retrocopy	retro_opri_433,
Pongo abelii	ENSPPYG00000013565	3 retrocopies	retro_pabe_2316, retro_pabe_2349, retro_pabe_770,
Pongo abelii	ENSPPYG00000013566	3 retrocopies	retro_pabe_1360, retro_pabe_2401, retro_pabe_346,
Pan troglodytes	ENSPTRG00000015199	3 retrocopies	retro_ptro_1113, retro_ptro_1962, retro_ptro_281,
Pan troglodytes	ENSPTRG00000015200	2 retrocopies	retro_ptro_1923, retro_ptro_616,
Pteropus vampyrus	ENSPVAG00000010677	1 retrocopy	retro_pvam_1237,
Rattus norvegicus	ENSRNOG00000025404	4 retrocopies	retro_rnor_2750, retro_rnor_2996, retro_rnor_861, retro_rnor_862,
Sarcophilus harrisii	ENSSHAG00000017398	1 retrocopy	retro_shar_542,
Tupaia belangeri	ENSTBEG00000006212	1 retrocopy	retro_tbel_3864,
Tursiops truncatus	ENSTTRG00000009500	1 retrocopy	retro_ttru_1524,
Tursiops truncatus	ENSTTRG00000009508	1 retrocopy	retro_ttru_1772,