RetrogeneDB ID: retro_mdom_1327

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:14496359..14496686(-)
• Located in intron of: ENSMODG00000021068

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000001323
• Aliases: None
• Description: None

Sequence

>retro_mdom_1327
AAAGGGTTTGCACTAGTATATTCTATTACAGCTCAGTCCACGTTTAATGACTTTCAGGACTTGAGGGAACAGATTTTACG
GGTTAAAGATACCAGAGATGCTCCAATGATTTTGGTTGGCAATAAATGTGACCTGGAAGATGAACGAGTAATTGGCAAAG
AACAGGGTCAGAATTTAGCAAGACAGTGGTGTAACTGTGCCTTTTTAGAGTCTTCTGCAAAGTCAAAGATCAATGTTAAT
GAGATATTTTATGGCCTGGTCAGACAAATAAATAGAAAAACACCAGTGGAAAAGAAGAAACCTAAAAAGAAATCATGCCT
GCTGCTT

Alignment

ORF - retro_mdom_1327 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.5 %
• Parental protein coverage: 92.37 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QGFALVYSITAQSTFNDLQDLREQILRVKDTEDVPMILVGNKCDLEDERVVGKEQGQNLARQWCNCAFLE
          .GFALVYSITAQSTFND.QDLREQILRVKDT.D.PMILVGNKCDLEDERV.GKEQGQNLARQWCNCAFLE
Retrocopy KGFALVYSITAQSTFNDFQDLREQILRVKDTRDAPMILVGNKCDLEDERVIGKEQGQNLARQWCNCAFLE

Parental  SSAKSKINVNEIFYDLVRQINRKTPVEKKKPKKKSCLLL
          SSAKSKINVNEIFY.LVRQINRKTPVEKKKPKKKSCLLL
Retrocopy SSAKSKINVNEIFYGLVRQINRKTPVEKKKPKKKSCLLL

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_1327 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1327 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 22 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005384	1 retrocopy	retro_amel_1764,
Canis familiaris	ENSCAFG00000013686	1 retrocopy	retro_cfam_696,
Callithrix jacchus	ENSCJAG00000013392	7 retrocopies	retro_cjac_1671, retro_cjac_2218, retro_cjac_3376, retro_cjac_3707, retro_cjac_3843, retro_cjac_3844, retro_cjac_728,
Dasypus novemcinctus	ENSDNOG00000007809	5 retrocopies	retro_dnov_101, retro_dnov_1617, retro_dnov_1764, retro_dnov_628, retro_dnov_94,
Equus caballus	ENSECAG00000016434	1 retrocopy	retro_ecab_99,
Erinaceus europaeus	ENSEEUG00000010446	2 retrocopies	retro_eeur_306, retro_eeur_361,
Echinops telfairi	ENSETEG00000016893	2 retrocopies	retro_etel_1196, retro_etel_176,
Homo sapiens	ENSG00000116473	1 retrocopy	retro_hsap_1364,
Myotis lucifugus	ENSMLUG00000010571	3 retrocopies	retro_mluc_2311, retro_mluc_2312, retro_mluc_2313,
Monodelphis domestica	ENSMODG00000001323	3 retrocopies	retro_mdom_1327 , retro_mdom_139, retro_mdom_1777,
Monodelphis domestica	ENSMODG00000004590	1 retrocopy	retro_mdom_51,
Monodelphis domestica	ENSMODG00000007323	5 retrocopies	retro_mdom_11, retro_mdom_1570, retro_mdom_1756, retro_mdom_1897, retro_mdom_429,
Monodelphis domestica	ENSMODG00000017458	1 retrocopy	retro_mdom_153,
Mus musculus	ENSMUSG00000068798	2 retrocopies	retro_mmus_1963, retro_mmus_3027,
Nomascus leucogenys	ENSNLEG00000004018	1 retrocopy	retro_nleu_1069,
Ochotona princeps	ENSOPRG00000003999	3 retrocopies	retro_opri_321, retro_opri_460, retro_opri_875,
Pongo abelii	ENSPPYG00000001028	1 retrocopy	retro_pabe_1132,
Pan troglodytes	ENSPTRG00000001102	1 retrocopy	retro_ptro_937,
Rattus norvegicus	ENSRNOG00000032463	3 retrocopies	retro_rnor_1147, retro_rnor_1494, retro_rnor_1639,
Ictidomys tridecemlineatus	ENSSTOG00000027847	1 retrocopy	retro_itri_81,
Tarsius syrichta	ENSTSYG00000004521	3 retrocopies	retro_tsyr_1546, retro_tsyr_1829, retro_tsyr_2140,
Vicugna pacos	ENSVPAG00000010033	1 retrocopy	retro_vpac_491,