RetrogeneDB ID: retro_mdom_1794

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 7:135700815..135702126(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000009521
• Aliases: None
• Description: None

Sequence

>retro_mdom_1794
CAGAATCTCAAGATGTCTATTCTAAATACGCATGCAAGAGAGATCTTCAACTCTTGGGGAAACCCACCCCCACCCCCATT
AACATTAATCTCTACACTTCAAAAGCTCTCTTCCAAGTTGCTCTACCCAGTGGTGCATCTACTGGTGTCCATGAAGCTCT
GGAGCTACAAGACAATGCTAAAACCCACTACATGGGGAAAGTTATCTCAAAAGCAATTGAGCACATCAATAAATCTATTG
CCCCATGCCTGATTAGCAAGAAACTGAATGTTGTAGAGCAGGAGAAAATTGACAAATTGATGCTAGAAATGGATGCCACT
ACTTAATTTGGTGCCAAGGCCATCCTGGGAGTACCTCTGGCTGTTTGTAAGGCTGGAGCTGCAGAGAAATGTGTCTCCCT
GTACCGCCACATTGCTGACCTTGTAGGCAATGAAGAAGTTGTCCTTCCAGTTCCTGTCTTCAATGTGATCAACAGTGGCC
CCCATGCTGGTAACAAGCTGGCCATGCAGAGTTTCATGATTCTCCCAGTTGGGGCAGCAAGCTTCAAGGAGGCCATGAGC
ATTTGGAACTGAGATATACCACAACCTGAAGAATGTGATTAAGCAGAAATATGGACAGGATGCTACCAATGAAGGGGATG
AGGGTGACTTTGCACCTAACATCCTAGAGAATTAAGAAGCTCTGCAGCTTCTGAAGACTGCTATTAGTAAAGTTGACTAT
TCTGATAAGGTTTGATTGGCATGGATGCTGCTACTTCAGAATTCTACCGATCTGGGAAATATGACTTGGACTTTAAGTCC
CTTGATTACTCCAGCAGACACATCTCCTCTAAGGCTGTTGGGGACCTATAAGGGCTTCATCAAGGATTATCCAGCGGTGT
CCATTGAAGATACCTTTGGCCAGAATGATTGGGAAGCTTGGACAAAATTCACTGCTGCTGCAGGCATCCAGGTGGTAGAG
GATGACCTCACTGTGGCCAATCCCAAGTTCATTAAAAAGGCCATGGATATCAAAGCCTGCAACTGCCTCCTGCTCAAAGT
GAACCAGATTGGCACCATGACTGAATCTCTCCAGGCATGCAAGCTGGTCCAGTCCAATGGGTGGGGCTTAATGGTTTCCC
ATCATTCTGGGGAAACTGAGGATACCTTCATTGTAGACCTAGTGTTGGATCTGTGCACTGGACAGAACAAAATAGGTGTC
CCCTGCCAATCTGAGCTTCTGGCCAAGTATAATCAGATTCTCAGAATTATGGAAGAGCTGGGGAGTGAGGCTAAGTTTGC
TGGAAGAAACTTCAGATACCCTAAAGCCCAG

Alignment

ORF - retro_mdom_1794 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.78 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  QNLKMSILKLHAREIFDSRGN-PT---VEVDLCTSKGLFRAAVPSGASTGVHEALELRDNDKTRYMGKGV
          QNLKMSIL..HAREIF.S.GN.PT.......L.TSK.LF..A.PSGASTGVHEALEL.DN.KT.YMGK..
Retrocopy QNLKMSILNTHAREIFNSWGN<PTPTPININLYTSKALFQVALPSGASTGVHEALELQDNAKTHYMGKVI

Parental  SKAVEHINKTIAPCLVSKKLNVVEQEKIDKLMLEMDGTDNKSKFGANAILGVSLAVCKAGAAEKCVSLYR
          SKA.EHINK.IAPCL.SKKLNVVEQEKIDKLMLEMD.T.....FGA.AILGV.LAVCKAGAAEKCVSLYR
Retrocopy SKAIEHINKSIAPCLISKKLNVVEQEKIDKLMLEMDAT---T*FGAKAILGVPLAVCKAGAAEKCVSLYR

Parental  HIADLAGNEEVVLPVPAFNVINGGSHAGNKLAMQEFMILPVGAANFKEAMRI-GAEVYHNLKNVIKQKYG
          HIADL.GNEEVVLPVP.FNVIN.G.HAGNKLAMQ.FMILPVGAA.FKEAM.I.G.E.YHNLKNVIKQKYG
Retrocopy HIADLVGNEEVVLPVPVFNVINSGPHAGNKLAMQSFMILPVGAASFKEAMSI>GTEIYHNLKNVIKQKYG

Parental  QDATNVGDEGGFAPNILENKEALELLTTAISKAGYTDKV-VIGMDVAASEFYRSGKYDLDFKSPDDPSRH
          QDATN.GDEG.FAPNILEN.EAL.LL.TAISK..Y.DKV..IGMD.A.SEFYRSGKYDLDFKS.D..SRH
Retrocopy QDATNEGDEGDFAPNILEN*EALQLLKTAISKVDYSDKV<LIGMDAATSEFYRSGKYDLDFKSLDYSSRH

Parental  ISSEA-LGDLYKGFIKDYPVVSIEDPFDQDDWEAWTNFTATAGIQVVGDDLTVTNPKRIEKAVDVKACNC
          ISS.A.LG..YKGFIKDYP.VSIED.F.Q.DWEAWT.FTA.AGIQVV.DDLTV.NPK.I.KA.D.KACNC
Retrocopy ISSKA>LGT-YKGFIKDYPAVSIEDTFGQNDWEAWTKFTAAAGIQVVEDDLTVANPKFIKKAMDIKACNC

Parental  LLLKVNQIGTVTESLQACKLAQSNGWGVMVSHRSGETEDTFIADLVVGLCTGQIKTGAPCRSERLAKYNQ
          LLLKVNQIGT.TESLQACKL.QSNGWG.MVSH.SGETEDTFI.DLV..LCTGQ.K.G.PC.SE.LAKYNQ
Retrocopy LLLKVNQIGTMTESLQACKLVQSNGWGLMVSHHSGETEDTFIVDLVLDLCTGQNKIGVPCQSELLAKYNQ

Parental  ILRIEEELGGKAKFAGRNFRNPKAQ
          ILRI.EELG..AKFAGRNFR.PKAQ
Retrocopy ILRIMEELGSEAKFAGRNFRYPKAQ

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	0.00 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1794 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1794 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 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003483	2 retrocopies	retro_chof_1289, retro_chof_1811,
Callithrix jacchus	ENSCJAG00000000359	4 retrocopies	retro_cjac_1963, retro_cjac_2238, retro_cjac_3891, retro_cjac_438,
Erinaceus europaeus	ENSEEUG00000008602	2 retrocopies	retro_eeur_23, retro_eeur_243,
Homo sapiens	ENSG00000074800	1 retrocopy	retro_hsap_325,
Macropus eugenii	ENSMEUG00000005942	11 retrocopies	retro_meug_1445, retro_meug_1521, retro_meug_353, retro_meug_472, retro_meug_494, retro_meug_652, retro_meug_664, retro_meug_765, retro_meug_794, retro_meug_874, retro_meug_888,
Macropus eugenii	ENSMEUG00000007840	1 retrocopy	retro_meug_96,
Monodelphis domestica	ENSMODG00000009521	1 retrocopy	retro_mdom_1794 ,
Mustela putorius furo	ENSMPUG00000006382	2 retrocopies	retro_mputfur_1162, retro_mputfur_547,
Mus musculus	ENSMUSG00000063524	1 retrocopy	retro_mmus_109,
Oryctolagus cuniculus	ENSOCUG00000010086	1 retrocopy	retro_ocun_933,
Otolemur garnettii	ENSOGAG00000004001	1 retrocopy	retro_ogar_1059,
Ochotona princeps	ENSOPRG00000009492	1 retrocopy	retro_opri_969,
Pan troglodytes	ENSPTRG00000000109	1 retrocopy	retro_ptro_261,
Pteropus vampyrus	ENSPVAG00000005030	1 retrocopy	retro_pvam_317,
Rattus norvegicus	ENSRNOG00000017895	1 retrocopy	retro_rnor_112,
Sarcophilus harrisii	ENSSHAG00000005522	1 retrocopy	retro_shar_304,
Tarsius syrichta	ENSTSYG00000002509	1 retrocopy	retro_tsyr_2011,