RetrogeneDB ID: retro_mdom_186

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:371625749..371627018(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000006398
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000009574
• Aliases: None
• Description: None

Sequence

>retro_mdom_186
ATGGCAATGTCTCTGGGCTCCAACACCTACAATAGGCAGAACTGGGAGGACTCAGACTTCCCTATTCTATGTCAGACATG
CCTTGGAGAAAATCCTTACGTTCGGATGACCAAAGACATATATGGAAAAGCATGCAAAATTTGTGCCAAGCCGTTCACAG
TGTTCCGCTGGTGCCCCGGGGTTCGCATGCGTTTTAAGAAGACTGAAGTGTGCCAAACCTGCAGCAAGCTAAAAAATGTG
TGTCAGACCTGCCTTTTGGACCTAGAATATGGCTTACCTATTCAGGTTCGTGATGTGGGACTGTCCCTTAAAGATGACAT
GCCCAAGTCTGATGTGAACCAAGAATACTACACACAGAATGTTGAGCGAGAGATTTCTAACTCTGATGGAACCCGGCCAG
TTGGCCTTCTTGGGAAGGCTACAGCTACCAGTGACATGCTGCTCAAATTGGCTCGCACCACCCCTTACTACAAACGGAAC
CATCCTCACATTTGTTCCTTCTGGGTGAAAGGAGAATGTAAGAGAGGAGAGGAGTGTCCATATAGACATGAGAAGCCTAC
AAATCCTGAGGATCCTCTTGCTGATCAGAATATCAAAGACCGATATTATGCCATTAATGACCCTGTGGCAGACAAGCTTC
TGAAAAGGGCTTCCACAATGCCTCATCTGGACCCCCCAGATGATAAGACTATCACCACACTCTATGTTGGAGGCCTTGGA
GATACAATCAGTGAGGCAGATCTCAGAAATCATTTTTACCAGTTTGGTGAGATACGAACGATAACCGTGGTGCAGAGGCA
GCACTGTGCTTTCATACAGTTTGCCACAAGGCAAGCTGCAGAGATGGCTGCTGAGAAGTCCTTTAACAAACTGATCCTCA
ATGGAAGAAGGCTTAATGTGAAATGGGGAAGATCACAGGCAGCCAGAGGAAAAGAAAAGGAAAAAGAAGGAACCACAGAC
TCTGGACTTAAGCTGGAGCCTGTTCCTGGACTTCCTGGAGCTCTTCCTCCTCCTCCTCCTCCTCCAACAGCTGAAGAAGC
CTCTGCCAATTATTTTAATCTCCCTCCCAGTGGTCTCCCAGCAGTGGTTAATATTGCCCTGCCCCCACCTTCTAGAATTG
CACCTCCATCCCCACCAGGTTTTGGACCACAAGTGTTCCACCCAATGGGACCACCTCCTCCCTTCATGCCAGCTCCAGGC
CCCATCCACTATCCTTCCCAGGATCCCCAGAGGATGGGGGCTCATGCAGGAAAACACAGCAGTTCCTAA

Alignment

ORF - retro_mdom_186 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.4 %
• Parental protein coverage: 99.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MATSLGSNTYNRQNWEDADFPILCQTCLGENPYIRMTKEKYGKECKICARPFTVFRWCPGVRMRFKKTEV
          MA.SLGSNTYNRQNWED.DFPILCQTCLGENPY.RMTK..YGK.CKICA.PFTVFRWCPGVRMRFKKTEV
Retrocopy MAMSLGSNTYNRQNWEDSDFPILCQTCLGENPYVRMTKDIYGKACKICAKPFTVFRWCPGVRMRFKKTEV

Parental  CQTCSKLKNVCQTCLLDLEYGLPIQVRDAGLSFKDDMPKSDVNKEYYTQNVEREISNSDGTRPVGVLGKA
          CQTCSKLKNVCQTCLLDLEYGLPIQVRD.GLS.KDDMPKSDVN.EYYTQNVEREISNSDGTRPVG.LGKA
Retrocopy CQTCSKLKNVCQTCLLDLEYGLPIQVRDVGLSLKDDMPKSDVNQEYYTQNVEREISNSDGTRPVGLLGKA

Parental  TATSDMLLKLARTTPYYKRNRPHICSFWVKGECKRGEECPYRHEKPTDPDDPLADQNIKDRYYGINDPVA
          TATSDMLLKLARTTPYYKRN.PHICSFWVKGECKRGEECPYRHEKPT.P.DPLADQNIKDRYY.INDPVA
Retrocopy TATSDMLLKLARTTPYYKRNHPHICSFWVKGECKRGEECPYRHEKPTNPEDPLADQNIKDRYYAINDPVA

Parental  DKLLKRASTMPRLDPPDDKTITTLYVGGLGDTISETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAA
          DKLLKRASTMP.LDPPDDKTITTLYVGGLGDTISE.DLRNHFYQFGEIRTITVVQRQ.CAFIQFATRQAA
Retrocopy DKLLKRASTMPHLDPPDDKTITTLYVGGLGDTISEADLRNHFYQFGEIRTITVVQRQHCAFIQFATRQAA

Parental  EMAAEKSFNKLIVNGRRLNVKWGRSQAARGKEKEKEGTTDSGIKLEPVPGLPGAL--PPPPAAEEEASAN
          EMAAEKSFNKLI.NGRRLNVKWGRSQAARGKEKEKEGTTDSG.KLEPVPGLPGAL..PPPP...EEASAN
Retrocopy EMAAEKSFNKLILNGRRLNVKWGRSQAARGKEKEKEGTTDSGLKLEPVPGLPGALPPPPPPPTAEEASAN

Parental  YFNLPPSGPPAVVNIALPPPPGIAPPPPPGFGPHMFHPMGPPPPFMRAPGPIHYPSQDPQRMGAHAGKHS
          YFNLPPSG.PAVVNIALPPP..IAPP.PPGFGP..FHPMGPPPPFM.APGPIHYPSQDPQRMGAHAGKHS
Retrocopy YFNLPPSGLPAVVNIALPPPSRIAPPSPPGFGPQVFHPMGPPPPFMPAPGPIHYPSQDPQRMGAHAGKHS

Parental  S
          S
Retrocopy S

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	1.19 RPM	200.01 RPM
SRP007412_cerebellum	2.94 RPM	153.11 RPM
SRP007412_heart	1.20 RPM	69.37 RPM
SRP007412_kidney	1.32 RPM	146.17 RPM
SRP007412_liver	0.50 RPM	127.38 RPM
SRP007412_testis	0.20 RPM	155.38 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_186 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_186 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 15 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018082	1 retrocopy	retro_cfam_1480,
Callithrix jacchus	ENSCJAG00000020963	6 retrocopies	retro_cjac_1338, retro_cjac_2471, retro_cjac_3342, retro_cjac_3390, retro_cjac_3934, retro_cjac_990,
Cavia porcellus	ENSCPOG00000001946	2 retrocopies	retro_cpor_280, retro_cpor_283,
Dasypus novemcinctus	ENSDNOG00000011166	1 retrocopy	retro_dnov_2298,
Homo sapiens	ENSG00000086589	2 retrocopies	retro_hsap_3465, retro_hsap_4273,
Gorilla gorilla	ENSGGOG00000012947	2 retrocopies	retro_ggor_2337, retro_ggor_2859,
Myotis lucifugus	ENSMLUG00000009040	2 retrocopies	retro_mluc_1453, retro_mluc_153,
Macaca mulatta	ENSMMUG00000020683	4 retrocopies	retro_mmul_1199, retro_mmul_1348, retro_mmul_1553, retro_mmul_1762,
Monodelphis domestica	ENSMODG00000009574	1 retrocopy	retro_mdom_186 ,
Nomascus leucogenys	ENSNLEG00000010397	2 retrocopies	retro_nleu_1691, retro_nleu_1800,
Otolemur garnettii	ENSOGAG00000011086	1 retrocopy	retro_ogar_2206,
Pongo abelii	ENSPPYG00000015955	4 retrocopies	retro_pabe_1412, retro_pabe_1594, retro_pabe_2861, retro_pabe_3486,
Pan troglodytes	ENSPTRG00000017423	2 retrocopies	retro_ptro_2348, retro_ptro_2898,
Ictidomys tridecemlineatus	ENSSTOG00000027197	1 retrocopy	retro_itri_1188,
Tarsius syrichta	ENSTSYG00000003939	3 retrocopies	retro_tsyr_1090, retro_tsyr_1187, retro_tsyr_1231,