RetrogeneDB ID: retro_mdom_1178

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:377371510..377371926(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TAGLN2
• Ensembl ID: ENSMODG00000010032
• Aliases: None
• Description: transgelin 2 [Source:HGNC Symbol;Acc:11554]

Sequence

>retro_mdom_1178
GGCATGGTACTGTGTGAGCTCATCAATGGGCTGTATGCTGATGGCCAGGGCCCAGTAACGAAGATCCAGGCTTCGAACAT
AGCCTTCAAACAGATGGAATGGATTTCTCATTCCTAAAGGCAGCAGAGTGCTATGGCATCAATGCCACTGATAACTTCCA
AACTGTGGATCTCTGGGAAGGAATGAACATGGCCTGTGTGCAGTGGACACTGATGAACTTTGGTGGTCTGGCAATGGCCA
GGGGTGATGGGTTCTTCTCATGAGATCCTAACTGGTTCCCTAAGAAATCCAAGGAGAACACGAGAAACTTCACAGATAAC
CAGCTGCAGGAAGGCAAGAATGTCATCAGGCTGCAAATGGGCACCAACAATGGGGCATCTCAGGGGGGCATTACTGGTTA
TGGGATGCCATGCCAA

Alignment

ORF - retro_mdom_1178 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.71 %
• Parental protein coverage: 69.85 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GTVLCELINGLYAEGQGPVKKIQASNMAFKQMEQISQ-FLKAAENYGINATDIFQTVDLWEGKNMACVQR
          G.VLCELINGLYA.GQGPV.KIQASN.AFKQME.IS..FLKAAE.YGINATD.FQTVDLWEG.NMACVQ.
Retrocopy GMVLCELINGLYADGQGPVTKIQASNIAFKQMEWISH<FLKAAECYGINATDNFQTVDLWEGMNMACVQW

Parental  TLMNLGGLAVARGDGFFSGDPNWFPKKSKENPRNFTDNQLQEGKNVIGLQMGTNRGASQAGMTGYGMPRQ
          TLMN.GGLA.ARGDGFFS.DPNWFPKKSKEN.RNFTDNQLQEGKNVI.LQMGTN.GASQ.G.TGYGMP.Q
Retrocopy TLMNFGGLAMARGDGFFS*DPNWFPKKSKENTRNFTDNQLQEGKNVIRLQMGTNNGASQGGITGYGMPCQ

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_1178 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1178 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 14 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002068	1 retrocopy	retro_btau_1701,
Callithrix jacchus	ENSCJAG00000006156	2 retrocopies	retro_cjac_2035, retro_cjac_2444,
Homo sapiens	ENSG00000158710	1 retrocopy	retro_hsap_4108,
Macropus eugenii	ENSMEUG00000006573	9 retrocopies	retro_meug_1092, retro_meug_1242, retro_meug_128, retro_meug_1442, retro_meug_1998, retro_meug_309, retro_meug_483, retro_meug_690, retro_meug_880,
Myotis lucifugus	ENSMLUG00000026228	1 retrocopy	retro_mluc_274,
Macaca mulatta	ENSMMUG00000004705	1 retrocopy	retro_mmul_2328,
Monodelphis domestica	ENSMODG00000004326	1 retrocopy	retro_mdom_442,
Monodelphis domestica	ENSMODG00000010032	1 retrocopy	retro_mdom_1178 ,
Nomascus leucogenys	ENSNLEG00000013350	1 retrocopy	retro_nleu_575,
Pongo abelii	ENSPPYG00000000648	2 retrocopies	retro_pabe_3310, retro_pabe_3364,
Pan troglodytes	ENSPTRG00000001533	1 retrocopy	retro_ptro_2788,
Sus scrofa	ENSSSCG00000006395	2 retrocopies	retro_sscr_312, retro_sscr_313,
Tarsius syrichta	ENSTSYG00000001645	2 retrocopies	retro_tsyr_1911, retro_tsyr_950,
Tursiops truncatus	ENSTTRG00000001814	1 retrocopy	retro_ttru_1614,