RetrogeneDB ID: retro_mdom_733

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:256133100..256133395(+)
• Located in intron of: ENSMODG00000005473

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000019554
• Aliases: None
• Description: Peptidyl-prolyl cis-trans isomerase [Source:UniProtKB/TrEMBL;Acc:F6UTH0]

Sequence

>retro_mdom_733
CAAGCCATCTCCCCCAAAGACAGGCACACCTTTCCCGAGAGGTCAAATTTGTATGTTGTAATACATGTGGATGTTCAAAG
ATAGAAAAAAGTTTGATTCTTTCTGTGACAGTAATAAACTCTTAAAGTTTGTAGTGGGAAAACAGGAGGTGATCCAAGGC
TGGGGAGGAGTTCCCTAGGTGAATATGGGGAAGAGTAAAAATGACATCTCTCCAGGCTATGATTTATGGTTCCATCCAGG
CATCATTCCACTAAATGTTACTCTCATCTTTGATGTAGAACTTATAAAATTGGAA

Alignment

ORF - retro_mdom_733 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.77 %
• Parental protein coverage: 95.37 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ETISPGD-GRTFPKRGQTCVVHYTGMLEDGKKFDSSRDRNKPFKFVMGKQEVIRGWEEGVAQMSVGQRAK
          ..ISP.D.G..FP.RGQ.C...Y..M..D.KKFDS..D.NK..KFV.GKQEVI.GW..GV.....G...K
Retrocopy QAISPKD>GTPFP-RGQICML*YMWMFKDRKKFDSFCDSNKLLKFVVGKQEVIQGWG-GVP*VNMG-KSK

Parental  MTISPDYAYGPTGHPGIIPPNATLIFDVELLKME
          ..ISP...Y....HPGIIP.N.TLIFDVEL.K.E
Retrocopy NDISP--GYDLWFHPGIIPLNVTLIFDVELIKLE

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	4548.20 RPM
SRP007412_cerebellum	0.00 RPM	1523.56 RPM
SRP007412_heart	0.00 RPM	2570.24 RPM
SRP007412_kidney	0.00 RPM	1476.17 RPM
SRP007412_liver	0.00 RPM	976.27 RPM
SRP007412_testis	0.00 RPM	439.23 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_733 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_733 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 23 parental genes, and 60 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000008303	4 retrocopies	retro_btau_1220, retro_btau_1265, retro_btau_128, retro_btau_1760,
Callithrix jacchus	ENSCJAG00000020908	4 retrocopies	retro_cjac_1544, retro_cjac_3889, retro_cjac_4157, retro_cjac_537,
Ciona savignyi	ENSCSAVG00000006859	1 retrocopy	retro_csav_11,
Dasypus novemcinctus	ENSDNOG00000005868	16 retrocopies	retro_dnov_1289, retro_dnov_1577, retro_dnov_1666, retro_dnov_2236, retro_dnov_228, retro_dnov_2404, retro_dnov_2418, retro_dnov_2544, retro_dnov_2589, retro_dnov_263, retro_dnov_584, retro_dnov_621, retro_dnov_670, retro_dnov_684, retro_dnov_707, retro_dnov_937,
Echinops telfairi	ENSETEG00000007454	1 retrocopy	retro_etel_2059,
Felis catus	ENSFCAG00000026097	2 retrocopies	retro_fcat_168, retro_fcat_751,
Homo sapiens	ENSG00000088832	1 retrocopy	retro_hsap_1198,
Gorilla gorilla	ENSGGOG00000001729	3 retrocopies	retro_ggor_1494, retro_ggor_2344, retro_ggor_933,
Macaca mulatta	ENSMMUG00000015996	1 retrocopy	retro_mmul_10,
Monodelphis domestica	ENSMODG00000007352	1 retrocopy	retro_mdom_1554,
Monodelphis domestica	ENSMODG00000019554	2 retrocopies	retro_mdom_151, retro_mdom_733 ,
Mustela putorius furo	ENSMPUG00000017946	1 retrocopy	retro_mputfur_1649,
Mus musculus	ENSMUSG00000032966	1 retrocopy	retro_mmus_1293,
Nomascus leucogenys	ENSNLEG00000009356	5 retrocopies	retro_nleu_2009, retro_nleu_2628, retro_nleu_2728, retro_nleu_2730, retro_nleu_604,
Otolemur garnettii	ENSOGAG00000002629	1 retrocopy	retro_ogar_673,
Procavia capensis	ENSPCAG00000008816	2 retrocopies	retro_pcap_289, retro_pcap_37,
Pongo abelii	ENSPPYG00000010852	5 retrocopies	retro_pabe_1654, retro_pabe_1686, retro_pabe_2364, retro_pabe_2365, retro_pabe_998,
Pan troglodytes	ENSPTRG00000013163	2 retrocopies	retro_ptro_2983, retro_ptro_818,
Pteropus vampyrus	ENSPVAG00000013840	1 retrocopy	retro_pvam_1367,
Rattus norvegicus	ENSRNOG00000008822	1 retrocopy	retro_rnor_453,
Sus scrofa	ENSSSCG00000007188	1 retrocopy	retro_sscr_98,
Tursiops truncatus	ENSTTRG00000003547	3 retrocopies	retro_ttru_1227, retro_ttru_802, retro_ttru_904,
Vicugna pacos	ENSVPAG00000011511	1 retrocopy	retro_vpac_171,