RetrogeneDB ID: retro_mdom_299

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:31410312..31411104(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C16orf72
• Ensembl ID: ENSMODG00000005378
• Aliases: None
• Description: chromosome 16 open reading frame 72 [Source:HGNC Symbol;Acc:30103]

Sequence

>retro_mdom_299
GAGATCCAGGAGCATGGGCCAGAGCATTGGTTCACCAAGTGGGAGAGGCAGTGCCTGGATGAGTTTGAGCAGGAGGAGCA
GATGCCCCCAAAACTCCATGAAGAAGTGGCTGCTGCACATCCTGAGCACAGGCAGCAGAAGCTGTGTCACTTGCTCCAGA
ACTCAGCCATTGAGGTGGCCCAGCTTTACAAAGATCGAGTATGTCAACAGCAAGGACTCTCCCTCTGGGTTCCCTTCCAA
AATGCAGCCACTACTGTTACCAACCTCTACAAAGAAAGTGTGTATGCCCATCAACAAAGTTTTGATCTAGGAATTCAAAT
TGGCTATCAGCGCTGCAATAAGGATGTGTTAACATGGGTTAAAAAACATAGAAGAACTATTCGTAGAGAAGACTTGATCA
GCTTCCTCTGTGGAAAAGTTCCTCCTCCACAAAACTATACAGCTTCCCCAAGACTAACTGTAGTATCCTCTAACTGAGCT
ATTTCAACAGAAACTAGCTCATCTGTAGAGACTGATTTGCAACCCTTTCATGAAGCCATAGTTCTGCATAGTCTCAGTGG
TGCAATGGCTAATATAAGCATTTGTTCAAGTACTCCAGGCTCTCCTACTCATGTAAGCAGTGGATCGAATACTAGTCAAA
GAAAAAATGGATTCCGTGATGTGGATTTGGACACTTTCATATCAGAAGAAATGGCACTCTACTTGGGCAATGGTGGAACT
AGAAAGCGTACCTCAGCCCAATGTGGCGATGTCATTACAGACTCACCAACTCATAAATGCAACAGAATGATC

Alignment

ORF - retro_mdom_299 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.85 %
• Parental protein coverage: 96.35 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EIQEHGPEHWFTKWERQCLAEAEQEEQLPPELQEEAAAAQPEHKQQKLWHLFQNSATAVAQLYKDRVCQQ
          EIQEHGPEHWFTKWERQCL.E.EQEEQ.PP.L.EE.AAA.PEH.QQKL.HL.QNSA..VAQLYKDRVCQQ
Retrocopy EIQEHGPEHWFTKWERQCLDEFEQEEQMPPKLHEEVAAAHPEHRQQKLCHLLQNSAIEVAQLYKDRVCQQ

Parental  QGLSLWVPFQNAATAVTNLYKESVDAHQRSFDLGIQIGYQRRNKDVLAWVKKRRRTIRREDLISFLCGKV
          QGLSLWVPFQNAAT.VTNLYKESV.AHQ.SFDLGIQIGYQR.NKDVL.WVKK.RRTIRREDLISFLCGKV
Retrocopy QGLSLWVPFQNAATTVTNLYKESVYAHQQSFDLGIQIGYQRCNKDVLTWVKKHRRTIRREDLISFLCGKV

Parental  PPPRNSRAPPRLTVVSPNRATSTETSSSVETDLQPFREAIALHGLSGAMASISVRSSTPGSPTHVSSGSN
          PPP.N..A.PRLTVVS.N.A.STETSSSVETDLQPF.EAI.LH.LSGAMA.IS..SSTPGSPTHVSSGSN
Retrocopy PPPQNYTASPRLTVVSSN*AISTETSSSVETDLQPFHEAIVLHSLSGAMANISICSSTPGSPTHVSSGSN

Parental  ASRRRNGLHDVDLNTFISEEMALHLDNGGTRKRTSAQCGDVITDSPTHKRNRMI
          .S.R.NG..DVDL.TFISEEMAL.L.NGGTRKRTSAQCGDVITDSPTHK.NRMI
Retrocopy TSQRKNGFRDVDLDTFISEEMALYLGNGGTRKRTSAQCGDVITDSPTHKCNRMI

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	0.20 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_299 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_299 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 17 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010719	2 retrocopies	retro_amel_1715, retro_amel_88,
Canis familiaris	ENSCAFG00000018981	1 retrocopy	retro_cfam_147,
Cavia porcellus	ENSCPOG00000010925	1 retrocopy	retro_cpor_101,
Dasypus novemcinctus	ENSDNOG00000015893	3 retrocopies	retro_dnov_1575, retro_dnov_2266, retro_dnov_827,
Equus caballus	ENSECAG00000009430	1 retrocopy	retro_ecab_1091,
Homo sapiens	ENSG00000182831	1 retrocopy	retro_hsap_4765,
Gorilla gorilla	ENSGGOG00000010744	1 retrocopy	retro_ggor_2968,
Monodelphis domestica	ENSMODG00000005378	2 retrocopies	retro_mdom_1716, retro_mdom_299 ,
Mustela putorius furo	ENSMPUG00000014707	1 retrocopy	retro_mputfur_44,
Mus musculus	ENSMUSG00000022507	1 retrocopy	retro_mmus_3460,
Nomascus leucogenys	ENSNLEG00000010106	1 retrocopy	retro_nleu_2348,
Otolemur garnettii	ENSOGAG00000003909	1 retrocopy	retro_ogar_74,
Pongo abelii	ENSPPYG00000007088	1 retrocopy	retro_pabe_163,
Pan troglodytes	ENSPTRG00000007751	1 retrocopy	retro_ptro_3172,
Rattus norvegicus	ENSRNOG00000002545	2 retrocopies	retro_rnor_156, retro_rnor_1928,
Sus scrofa	ENSSSCG00000028454	1 retrocopy	retro_sscr_1177,
Ictidomys tridecemlineatus	ENSSTOG00000009324	1 retrocopy	retro_itri_137,