RetrogeneDB ID: retro_mdom_1543

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:174252291..174252822(-)
• Located in intron of: ENSMODG00000020640

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000019356
• Aliases: None
• Description: None

Sequence

>retro_mdom_1543
GGAATCCGGTGGCTGGGGGCAGCGGCCCAGCAGGTTATCCCTCTGGGGGCCCGGGCAGCCTCAGGCCTCAGCAAGGACAT
GCCCCCGGGACCGTACCCCCGCACACCAGAGGAGCGCACTGATGCCGCCAAGAAGTACAACATGCGAGTGGAGGACTATG
AGCCCTATCCAGATGACGGTTTCAGGTTTGGTGACTCTCCCAAGCTTCCCGAACGATCTCAGCATGAACGAGACCCATGG
TATGACTGGGACCATTCAGAACTGAGACTGAACTGGGGTGAACCGATGCACTTTGACCTTGATATGTATACTCGGAATCA
TGTGGATACATCCCCCACACCTGTCTCCTGGAACACTATGTGTAAGCATTTATTGAGCTTTGTCGGCTTCATGCTGTTCA
TGTTCTATTTAGGAGAGATGTACCCATCCTATCAGCCTGTGGCTCCAAAGCAATATCCTTATAACAACCTGTACCTAGAA
CACGGAGGTGATCCTTCAGCAAATCCAGAGTCTGTGAAACACTATGAAATC

Alignment

ORF - retro_mdom_1543 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.53 %
• Parental protein coverage: 95.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GIRWLGAAAQRVTPLGTRAASGLSKDMLPGPYPRTPEERAAAAKKYNMRVEDYEPYPDDGFGFGDYPKLP
          GIRWLGAAAQ.V.PLG.RAASGLSKDM.PGPYPRTPEER..AAKKYNMRVEDYEPYPDDGF.FGD.PKLP
Retrocopy GIRWLGAAAQQVIPLGARAASGLSKDMPPGPYPRTPEERTDAAKKYNMRVEDYEPYPDDGFRFGDSPKLP

Parental  ERSQHERDPWYDWDHSELRLNWGEPMHFDLDMYTRNRVDTSPTPVSWNTMCKHLFGFVGFMLFMFYLGEV
          ERSQHERDPWYDWDHSELRLNWGEPMHFDLDMYTRN.VDTSPTPVSWNTMCKHL..FVGFMLFMFYLGE.
Retrocopy ERSQHERDPWYDWDHSELRLNWGEPMHFDLDMYTRNHVDTSPTPVSWNTMCKHLLSFVGFMLFMFYLGEM

Parental  YPSYQPVAPKQYPYNNLYLERGGDPSVNPEPVKHYEI
          YPSYQPVAPKQYPYNNLYLE.GGDPS.NPE.VKHYEI
Retrocopy YPSYQPVAPKQYPYNNLYLEHGGDPSANPESVKHYEI

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	275.94 RPM
SRP007412_cerebellum	0.00 RPM	350.29 RPM
SRP007412_heart	0.00 RPM	1337.45 RPM
SRP007412_kidney	0.00 RPM	641.30 RPM
SRP007412_liver	0.00 RPM	734.09 RPM
SRP007412_testis	0.00 RPM	176.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1543 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1543 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 20 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006651	3 retrocopies	retro_amel_1460, retro_amel_1467, retro_amel_931,
Bos taurus	ENSBTAG00000000091	1 retrocopy	retro_btau_1844,
Canis familiaris	ENSCAFG00000009698	2 retrocopies	retro_cfam_1405, retro_cfam_1947,
Callithrix jacchus	ENSCJAG00000037906	1 retrocopy	retro_cjac_870,
Dasypus novemcinctus	ENSDNOG00000003661	1 retrocopy	retro_dnov_65,
Felis catus	ENSFCAG00000006453	2 retrocopies	retro_fcat_501, retro_fcat_856,
Homo sapiens	ENSG00000166136	3 retrocopies	retro_hsap_1363, retro_hsap_1772, retro_hsap_770,
Gorilla gorilla	ENSGGOG00000027239	3 retrocopies	retro_ggor_1062, retro_ggor_2240, retro_ggor_639,
Microcebus murinus	ENSMICG00000001341	1 retrocopy	retro_mmur_859,
Myotis lucifugus	ENSMLUG00000015094	1 retrocopy	retro_mluc_1830,
Macaca mulatta	ENSMMUG00000006636	5 retrocopies	retro_mmul_1098, retro_mmul_1232, retro_mmul_1620, retro_mmul_415, retro_mmul_753,
Monodelphis domestica	ENSMODG00000019356	1 retrocopy	retro_mdom_1543 ,
Mustela putorius furo	ENSMPUG00000016959	1 retrocopy	retro_mputfur_1259,
Mus musculus	ENSMUSG00000025204	2 retrocopies	retro_mmus_1995, retro_mmus_2909,
Nomascus leucogenys	ENSNLEG00000014774	3 retrocopies	retro_nleu_1068, retro_nleu_2810, retro_nleu_398,
Otolemur garnettii	ENSOGAG00000030711	3 retrocopies	retro_ogar_1237, retro_ogar_152, retro_ogar_2593,
Pongo abelii	ENSPPYG00000002570	3 retrocopies	retro_pabe_1131, retro_pabe_1541, retro_pabe_756,
Pan troglodytes	ENSPTRG00000002851	3 retrocopies	retro_ptro_1186, retro_ptro_539, retro_ptro_936,
Sus scrofa	ENSSSCG00000006166	2 retrocopies	retro_sscr_1092, retro_sscr_444,
Tupaia belangeri	ENSTBEG00000000209	8 retrocopies	retro_tbel_1872, retro_tbel_2950, retro_tbel_3122, retro_tbel_322, retro_tbel_3696, retro_tbel_4042, retro_tbel_4718, retro_tbel_540,