RetrogeneDB ID: retro_mdom_588

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:422741504..422741903(-)
• Located in intron of: ENSMODG00000019794

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000008032
• Aliases: None
• Description: None

Sequence

>retro_mdom_588
TGCTGCACAGTAAACATCAGCCTTGCAGCCCATGAGGACACCTCCCATTTGTATAATTTCAAATATAATCACTTTGGAAT
GATGTCTCCAACCTGTAAGCACCACTTTATCCAGGACACACGTGTCTATGAGTGATCCTCCAACCTAGGGCCCAGCTTCC
AACAGAAAGACTTATGCAGGTGGAAGGAATAAATGCTGATTATGCCTTCATGCAGAGAGAACTATAACCACTGGTAGGAG
GACTACAGATACTACACTTCAAGAGAACTGGCACAAAGGTTGGAATTTGACTCTGGGGATTAACTAGTACCCATGTAAGG
CTGTCTAACATCCTTTCACTTTTTACTCCCCAACACCAGCCTCCTTGGTGAGAACATTTGGAATCACTCCTACAAGGCC

Alignment

ORF - retro_mdom_588 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.09 %
• Parental protein coverage: 53.78 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  CCTASTSIAAHEDASHSYGFNFNHCGTMTPACKRHFVQDTCLYECSPNLGPWIQPVNSSWRKERVMNIPL
          CCT...S.AAHED.SH.Y.F..NH.G.M.P.CK.HF.QDT..YE.S.NLGP..Q.......KE.....P.
Retrocopy CCTVNISLAAHEDTSHLYNFKYNHFGMMSPTCKHHFIQDTRVYE*SSNLGPSFQQKDLCRWKE*MLIMPS

Parental  CKEDCNMWWEDCKTSYTCKENWQKGWNWSSG-INECPVKAACHPFSFYFPTPTSLC-ENIWSRSYNA
          C.E..N.W.ED....YT..E..Q......SG.IN..P.KA..HPF.FY.PTP.SL..ENIW..SY.A
Retrocopy CRENYNHW*EDYR-YYTSRELAQR-LEFDSG>IN*YPCKAV*HPFTFYSPTPASLV<ENIWNHSYKA

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	0.33 RPM	0.00 RPM
SRP007412_heart	0.20 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_588 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_588 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 12 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005777	1 retrocopy	retro_cfam_1723,
Callithrix jacchus	ENSCJAG00000015224	1 retrocopy	retro_cjac_3330,
Dasypus novemcinctus	ENSDNOG00000000856	1 retrocopy	retro_dnov_1751,
Echinops telfairi	ENSETEG00000015365	2 retrocopies	retro_etel_1160, retro_etel_128,
Myotis lucifugus	ENSMLUG00000014126	2 retrocopies	retro_mluc_1199, retro_mluc_567,
Monodelphis domestica	ENSMODG00000008017	1 retrocopy	retro_mdom_990,
Monodelphis domestica	ENSMODG00000008032	1 retrocopy	retro_mdom_588 ,
Monodelphis domestica	ENSMODG00000008042	1 retrocopy	retro_mdom_648,
Mus musculus	ENSMUSG00000001827	1 retrocopy	retro_mmus_1438,
Oryctolagus cuniculus	ENSOCUG00000000165	1 retrocopy	retro_ocun_472,
Otolemur garnettii	ENSOGAG00000000641	5 retrocopies	retro_ogar_2539, retro_ogar_2666, retro_ogar_2758, retro_ogar_2908, retro_ogar_532,
Tarsius syrichta	ENSTSYG00000003503	3 retrocopies	retro_tsyr_1057, retro_tsyr_111, retro_tsyr_1651,