RetrogeneDB ID: retro_mdom_1186

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:405698309..405699311(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000021479
• Aliases: None
• Description: None

Sequence

>retro_mdom_1186
ATGTCCACCATAGGTTCCATGCTTCAGAACCAGCTTGTCCCAGAACAGAGAGGCAAGCCCCAGAATGATGCAGCCTCAGC
CTCCTCTGCCTCTGTCTACCAGCCCAGAGAATGACCCCTGCCCCAACCCCAGTCCCCCCACTCTAGGTGCATGGGGAGAA
GCAGTATCTGCAGCAGATTGTGCTTGTCATCCAGTAAGGCTTCAAGAAGAAGGACTGCACATGCACTGGCACCCTGTCTG
TGTTGGGCATGCAAGCCTGCTACAACCTATGAGGTGAATTTCCTTTGCTGACAACCAAGCATATGTTCTGGAAGGGTGCC
CTTCGGAACTGCTGGGGTTTATTAGGGGTTGCACAAATGGTAAGGAGCTCTCTGCCAAAGGGGTGAAGATCTGGGATGCC
AATGGGTCACATTAATTTTTGGAAACCTGGGCTTCACTCACAGAGAAGAAGATTTGAGACCAGTGTATGACTTCCAGTGG
AGACATTTTGGGGCAGAATTCAAAGAGATTAACACAGATTATTCTGGACAAGGAGTGGATCAGCTTCAAAAAGTCATTGA
CAAAATCAAAACCAACCTTGATGACAGAAGGATCATTTTGTCATTATGTGCATTTGGAATTCAAAAGATCATGGCTTTGC
CACCATACCATGCTCTCTGTCAGTTCTATGTAGTGAATGATGAGCTTTCCTGGCAGCTATACCAGTGATCTGGAGATATG
GGTCTTGGGGTGCTGTTCAACATCACCAGTTACTCCCTGCTCACCTACAATATTCTCTCACATCACAGGCCTGAAGTTAA
GTGATTTTGCACACTCTCTGGGAGATGTTCATGTATATGTGAATCATATTGAGCCAATAACAATTCAGCTTCAGCAAGAA
CCAAAACCTTTCCCCAAGTTCAAAATTCTCTGGAAAGTGTAAAAAATGATGACTTCAAGGCTGAGGACTTCCTGATGGAA
GGCTACAACCCTCACTGGACCATTAAGATGGATATGGCAGTG

Alignment

ORF - retro_mdom_1186 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.9 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 6
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MPALGSAPQNQPVPEPRAEPQNDTASDASASV-SSPESDPSPNPSPP-LQMHGEKQYLQQIEHILQYGSK
          M...GS..QNQ.VPE.R..PQND.AS..SASV..SPE.DP.PNPSPP.L..HGEKQYLQQI....Q.G.K
Retrocopy MSTIGSMLQNQLVPEQRGKPQNDAASASSASV>TSPENDPCPNPSPP>L*VHGEKQYLQQIVLVIQ*GFK

Parental  KNDRTGTGTMSVFGMQARYNLRGEFPLLTTKRVFWKGVLE-ELLWFIRGCTNGKELSAKGVKIWDANGSR
          K.D.T.TGT.SV.GMQA.YNL.GEFPLLTTK..FWKG.L..ELL.FIRGCTNGKELSAKGVKIWDANGS.
Retrocopy KKDCTCTGTLSVLGMQACYNL*GEFPLLTTKHMFWKGALR<ELLGFIRGCTNGKELSAKGVKIWDANGSH

Parental  EFLD-NLGLTQREEGDLGPVYGFQWRHFGAEYKEMNTDYSGQGVDQLQKVIDKIKTNPDDRRLIMCAWNP
          .FL..NLG.T.REE.DL.PVY.FQWRHFGAE.KE.NTDYSGQGVDQLQKVIDKIKTN.DDRR.I......
Retrocopy *FLE<NLGFTHREE-DLRPVYDFQWRHFGAEFKEINTDYSGQGVDQLQKVIDKIKTNLDDRRIILSLCAF

Parental  KDLPLMALPPCHALCQFYVANGELSCQLYQRSGDMGLGVPFNIASYSLLTYMI-AHITGLKPGDFVHSLG
          .....MALPP.HALCQFYV.N.ELS.QLYQ.SGDMGLGV.FNI.SYSLLTY.I..HITGLK..DF.HSLG
Retrocopy GIQKIMALPPYHALCQFYVVNDELSWQLYQ*SGDMGLGVLFNITSYSLLTYNI>SHITGLKLSDFAHSLG

Parental  DAHVYMNHIEPLKIQLQREPRPFPKLKILRKVESI-DDFKAEDFLIEGYNPHPTIKMDMAV
          D.HVY.NHIEP..IQLQ.EP.PFPK.KIL.KV....DDFKAEDFL.EGYNPH.TIKMDMAV
Retrocopy DVHVYVNHIEPITIQLQQEPKPFPKFKILWKV*KM<DDFKAEDFLMEGYNPHWTIKMDMAV

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_1186 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1186 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 9 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000009230	2 retrocopies	retro_fcat_1107, retro_fcat_339,
Loxodonta africana	ENSLAFG00000014910	2 retrocopies	retro_lafr_1030, retro_lafr_635,
Macropus eugenii	ENSMEUG00000009507	1 retrocopy	retro_meug_175,
Monodelphis domestica	ENSMODG00000021479	2 retrocopies	retro_mdom_1084, retro_mdom_1186 ,
Mustela putorius furo	ENSMPUG00000005419	2 retrocopies	retro_mputfur_1155, retro_mputfur_860,
Mus musculus	ENSMUSG00000025747	1 retrocopy	retro_mmus_584,
Otolemur garnettii	ENSOGAG00000024349	2 retrocopies	retro_ogar_2956, retro_ogar_3211,
Sarcophilus harrisii	ENSSHAG00000003102	1 retrocopy	retro_shar_424,
Sus scrofa	ENSSSCG00000023869	2 retrocopies	retro_sscr_810, retro_sscr_841,