RetrogeneDB ID: retro_mdom_1020

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:235463575..235464439(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BTBD10
• Ensembl ID: ENSMODG00000008728
• Aliases: None
• Description: BTB (POZ) domain containing 10 [Source:HGNC Symbol;Acc:21445]

Sequence

>retro_mdom_1020
GAATGAGAAAAAGATAGTAGTTCTTCCTGCCCAAGTAGTTCTTGTCCTCAAAAAGCTTCCCTCGATGGTTCCAGGAGCAG
TGTTGGGAACAACAGCCGAAACAGTAGTCAGTCAAGTTCAGATGGTGGTTGTAAGACATCTGTGGAAATGATATTTGTCT
ATGAGAATGCAAAAGAGGGAGCCTGGAGTATAAGAACATCTGAAAGTGTAACAGTAATCATGGATAACCCTAGATTTGTT
GTAGATCCATCTATTTTTATTGCCCAGCCAAATACAATGTTGGACAGGATGTTTGGATCTGGCAGAGAACATAACTTCAC
ACATCCTAATGAGAAAGGAGAGTATGAAGTAACAGAGGGAATTGGTTCTACTGTATTTCAAGCTATCTTGGATTACTACA
AGACTGGAATAATTCATTGTCCTGATGGCATCTCTATTCCTGAGCTAAGAGAAGTGTTTGACTATCTTTGTATGTCTTTT
GAATATAGTATTATAAAATGTAGAGATCTCAGTGCCCTCATGCATGAGTTATCAAATGATGGTGCTCCTAGACAATTTGA
GTTTTATTTAGAGGAAATGATCCTCCCTCTTATGGTGGGTGCCCAGAGTGGTAAAAGAGTGTCATATTGTAGTACTCACA
GATGATGTTGTGGTTGATTGGGATGAAGAATACCCAACACAGGTAGAAAAAGAATATTCACAGATTGTTTATAGCACAAA
GTTGTATAGATTTTTCAAGTACATTGAAAATAGAGATGTGGTCAAATCTGTTTTGAAGGAGCGAGGTCTTAAGAAAATTC
AATTGGGTATAGAAGGGTATCCCACTTACAAATAAAAAGGCAAGAAAAACCTGGTGGGTGCCCA

Alignment

ORF - retro_mdom_1020 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.88 %
• Parental protein coverage: 61.05 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EREKDHSSSRPSSPRPQKASPNGSSSSVGNNSRNSSQSSSDGGCKTSGEMIFVYENAKEGARSIRTSERV
          E.EKD.SSS.PSS..PQKAS..GS.SSVGNNSRNSSQSSSDGGCKTS.EMIFVYENAKEGA.SIRTSE.V
Retrocopy E*EKDSSSSCPSSSCPQKASLDGSRSSVGNNSRNSSQSSSDGGCKTSVEMIFVYENAKEGAWSIRTSESV

Parental  TLIVDNTRFVVDPSIFTAQPNTMLGRMFGSGREHNFTRPNEKGEYEVAEGIGSTVFRAILDYYKTGIIRC
          T.I.DN.RFVVDPSIF.AQPNTML.RMFGSGREHNFT.PNEKGEYEV.EGIGSTVF.AILDYYKTGII.C
Retrocopy TVIMDNPRFVVDPSIFIAQPNTMLDRMFGSGREHNFTHPNEKGEYEVTEGIGSTVFQAILDYYKTGIIHC

Parental  PDGISIPELREACDYLCISFEYSTIKCRDLSALMHELSNDGARRQFEFYLEEMILPLMVASAQSGERECH
          PDGISIPELRE..DYLC.SFEYS.IKCRDLSALMHELSNDGA.RQFEFYLEEMILPLMV..AQSG.R...
Retrocopy PDGISIPELREVFDYLCMSFEYSIIKCRDLSALMHELSNDGAPRQFEFYLEEMILPLMV-GAQSGKRVSY

Parental  -IVVLTDDDVVDWDEEYPPQMGEEYSQIIYSTKLYRFFKYIENRDVAKSVLKERGLKKIRLGIEGYPTYK
          ..V...D..VVDWDEEYP.Q...EYSQI.YSTKLYRFFKYIENRDV.KSVLKERGLKKI.LGIEGYPTYK
Retrocopy >VVLTDD-VVVDWDEEYPTQVEKEYSQIVYSTKLYRFFKYIENRDVVKSVLKERGLKKIQLGIEGYPTYK

Parental  EKVKK-RPGGRP
          .K.KK..PGG.P
Retrocopy *KGKK<KPGGCP

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_1020 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1020 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 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000024984	1 retrocopy	retro_cpor_137,
Monodelphis domestica	ENSMODG00000008728	1 retrocopy	retro_mdom_1020 ,
Mus musculus	ENSMUSG00000038187	1 retrocopy	retro_mmus_3560,
Nomascus leucogenys	ENSNLEG00000017691	1 retrocopy	retro_nleu_232,
Otolemur garnettii	ENSOGAG00000000739	1 retrocopy	retro_ogar_3201,
Pan troglodytes	ENSPTRG00000003377	1 retrocopy	retro_ptro_753,
Rattus norvegicus	ENSRNOG00000014341	2 retrocopies	retro_rnor_2220, retro_rnor_2872,
Sorex araneus	ENSSARG00000000266	1 retrocopy	retro_sara_405,
Sus scrofa	ENSSSCG00000013395	2 retrocopies	retro_sscr_639, retro_sscr_640,
Tarsius syrichta	ENSTSYG00000000445	2 retrocopies	retro_tsyr_196, retro_tsyr_367,
Tursiops truncatus	ENSTTRG00000013943	1 retrocopy	retro_ttru_897,