RetrogeneDB ID: retro_mdom_50

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:584501175..584501526(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000023165
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000009218
• Aliases: None
• Description: None

Sequence

>retro_mdom_50
GAAATGGCAGTCTCCGAGCTCGCTTGCATCTACTCCGCTCTCATCCTTCACGATGATGAGGTTACAGTTATGGAGGATAA
AATTAATGCTCTCATTAAAGCAGCAGGTATAAATGTTGAACCATTCTGGCCTGGATTATTTGCAAAGGCCTTAAACAATG
TAAACATTGGTAGTCTCATCTACAATGTAGGAGTTGGTGGCCCTGCCCCAGCAGCTGGTGGTGCTGCCCCTGCTGGAGGT
GCTGCTCCTGCTAGCATAGCTGCCCCTGCTGAGGAGAAGAAGAAAGAGGAAGCAAAAAAAGAAGAATCCGAGGAATCTGA
TGATGACATGGGTTTTGGTCTGTTTGACTAA

Alignment

ORF - retro_mdom_50 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.55 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EMAVSELACIYSALILHDDEVTVTEDKINALIKAAGVNVEPFWPGLFAKALNNVNIGSLICNVGVGGPAP
          EMAVSELACIYSALILHDDEVTV.EDKINALIKAAG.NVEPFWPGLFAKALNNVNIGSLI.NVGVGGPAP
Retrocopy EMAVSELACIYSALILHDDEVTVMEDKINALIKAAGINVEPFWPGLFAKALNNVNIGSLIYNVGVGGPAP

Parental  AAGGAAPAGGAAPASTAAPAEEKKKEEAKKEESEESDDDMGFGLFD
          AAGGAAPAGGAAPAS.AAPAEEKKKEEAKKEESEESDDDMGFGLFD
Retrocopy AAGGAAPAGGAAPASIAAPAEEKKKEEAKKEESEESDDDMGFGLFD

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	0.83 RPM	676.80 RPM
SRP007412_cerebellum	2.61 RPM	470.09 RPM
SRP007412_heart	1.59 RPM	1522.45 RPM
SRP007412_kidney	1.32 RPM	1632.87 RPM
SRP007412_liver	4.03 RPM	1362.94 RPM
SRP007412_testis	0.39 RPM	214.11 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_50 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_50 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 162 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014251	20 retrocopies	retro_amel_1030, retro_amel_1076, retro_amel_110, retro_amel_1152, retro_amel_1191, retro_amel_128, retro_amel_1343, retro_amel_1345, retro_amel_1354, retro_amel_1428, retro_amel_161, retro_amel_1694, retro_amel_1696, retro_amel_1705, retro_amel_1852, retro_amel_205, retro_amel_316, retro_amel_395, retro_amel_404, retro_amel_769,
Choloepus hoffmanni	ENSCHOG00000005944	10 retrocopies	retro_chof_1312, retro_chof_1527, retro_chof_1753, retro_chof_1944, retro_chof_2325, retro_chof_2461, retro_chof_2714, retro_chof_337, retro_chof_666, retro_chof_928,
Cavia porcellus	ENSCPOG00000004321	6 retrocopies	retro_cpor_1011, retro_cpor_1058, retro_cpor_260, retro_cpor_305, retro_cpor_667, retro_cpor_75,
Dasypus novemcinctus	ENSDNOG00000014224	26 retrocopies	retro_dnov_1130, retro_dnov_1325, retro_dnov_1410, retro_dnov_1439, retro_dnov_146, retro_dnov_1467, retro_dnov_1580, retro_dnov_1660, retro_dnov_1667, retro_dnov_17, retro_dnov_1748, retro_dnov_179, retro_dnov_1878, retro_dnov_1911, retro_dnov_1967, retro_dnov_20, retro_dnov_2075, retro_dnov_2234, retro_dnov_240, retro_dnov_2421, retro_dnov_2618, retro_dnov_2640, retro_dnov_405, retro_dnov_561, retro_dnov_601, retro_dnov_746,
Felis catus	ENSFCAG00000032037	23 retrocopies	retro_fcat_1034, retro_fcat_1047, retro_fcat_1089, retro_fcat_1207, retro_fcat_1244, retro_fcat_1436, retro_fcat_1466, retro_fcat_1550, retro_fcat_1580, retro_fcat_1594, retro_fcat_1617, retro_fcat_1797, retro_fcat_1972, retro_fcat_552, retro_fcat_56, retro_fcat_571, retro_fcat_597, retro_fcat_825, retro_fcat_849, retro_fcat_908, retro_fcat_92, retro_fcat_928, retro_fcat_947,
Latimeria chalumnae	ENSLACG00000012630	1 retrocopy	retro_lcha_7,
Macropus eugenii	ENSMEUG00000015277	6 retrocopies	retro_meug_1096, retro_meug_1283, retro_meug_1312, retro_meug_1401, retro_meug_1515, retro_meug_793,
Macropus eugenii	ENSMEUG00000015282	2 retrocopies	retro_meug_207, retro_meug_45,
Monodelphis domestica	ENSMODG00000009209	1 retrocopy	retro_mdom_1022,
Monodelphis domestica	ENSMODG00000009218	4 retrocopies	retro_mdom_1168, retro_mdom_2001, retro_mdom_385, retro_mdom_50 ,
Mustela putorius furo	ENSMPUG00000017096	2 retrocopies	retro_mputfur_1016, retro_mputfur_266,
Oryctolagus cuniculus	ENSOCUG00000015087	8 retrocopies	retro_ocun_1009, retro_ocun_1464, retro_ocun_1655, retro_ocun_1735, retro_ocun_48, retro_ocun_551, retro_ocun_647, retro_ocun_884,
Ochotona princeps	ENSOPRG00000001163	11 retrocopies	retro_opri_1010, retro_opri_130, retro_opri_214, retro_opri_245, retro_opri_38, retro_opri_530, retro_opri_645, retro_opri_768, retro_opri_784, retro_opri_96, retro_opri_972,
Sarcophilus harrisii	ENSSHAG00000014818	6 retrocopies	retro_shar_182, retro_shar_234, retro_shar_449, retro_shar_550, retro_shar_614, retro_shar_742,
Sus scrofa	ENSSSCG00000004970	16 retrocopies	retro_sscr_1105, retro_sscr_1165, retro_sscr_1184, retro_sscr_1185, retro_sscr_16, retro_sscr_176, retro_sscr_18, retro_sscr_259, retro_sscr_307, retro_sscr_323, retro_sscr_4, retro_sscr_47, retro_sscr_583, retro_sscr_776, retro_sscr_904, retro_sscr_923,
Tursiops truncatus	ENSTTRG00000013656	20 retrocopies	retro_ttru_1388, retro_ttru_1502, retro_ttru_1645, retro_ttru_1730, retro_ttru_182, retro_ttru_1820, retro_ttru_1826, retro_ttru_227, retro_ttru_266, retro_ttru_28, retro_ttru_389, retro_ttru_553, retro_ttru_626, retro_ttru_666, retro_ttru_679, retro_ttru_687, retro_ttru_711, retro_ttru_755, retro_ttru_768, retro_ttru_803,