RetrogeneDB ID: retro_mdom_1749

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 7:188698227..188698972(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMADHC
• Ensembl ID: ENSMODG00000003566
• Aliases: None
• Description: methylmalonic aciduria (cobalamin deficiency) cblD type, with homocystinuria [Source:HGNC Symbol;Acc:25221]

Sequence

>retro_mdom_1749
CCCCCAGATATATGTTCAAGGAGTATGTGGCCAGATGAAACAAGGGGACCATTTGGGCCCCAGGATCAAAGATTTATGCT
CCATAGGAATTTAGGTTATGATTGTCACTTCAATGGAGAAGTTTTGCAAAGTAAAATTCAGTTCAGAGACCTTTGCCTGA
TGTCATAGCATATCCTTTATCAAGTGAAAGTTGAAAATTTGTGATGGTACAATATGTAAAAATGAATTTAAGGGCAATGT
TGCACCTGTTAAAACAACAGGAAATCAATAGGGCAGAAATTTATTTTGAAAGAGCCAAAGTAGAATGTCTACTACAAACA
TCTGCAGAGTTACTTCAAAGAGATTTTGAATCAATGTTTCCATAAGTAAATTCTGAAAAAATAATGGTACTGACTTTAAC
ATAGAAAACTAAAAATGATATGACTACACTGAGGGAGAAAGTTGAACGTATAAGAGAAATGCTGTTCGAAATGTTTATAG
ATGGAACTAAAGAAATTTGCTATGCTTTGTGTGTCAAAAGCTATTGGGTTGATCATATTGATCTATCATCTGAATTGGTA
TTTTTTTGGACTATATACAAGTGACTCTTTTTGAAGCAGATAAGTATTATCGAACCTTAAGATTCTCTCTTGATGATCTT
GGCTACTGGAAAGTGATTTATCATAGTCATTGGGGTATCCATGTGGTTGTTGGAAGTGTCTTCATGAATGTCACAGCTAA
TAGTCAAATTATGAAGAAATTAAGC

Alignment

ORF - retro_mdom_1749 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.35 %
• Parental protein coverage: 83.5 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PPDICSRTVWPDETMGPFGPQDQRFQLPGNIGFDCHLNGTALQKK-NPVHRTLPDVLAEPLSSERHEFVM
          PPDICSR..WPDET.GPFGPQDQRF.L..N.G.DCH.NG..LQ.K.N.V.R.LPDV.A.PLSSE...FVM
Retrocopy PPDICSRSMWPDETRGPFGPQDQRFMLHRNLGYDCHFNGEVLQSK<NSVQRPLPDVIAYPLSSES*KFVM

Parental  AQYVNEFEGSDVPVEQQE-VNKAETYFENAKVECVLQTCPELLRKDFESIFPEVNSGKLMVLTVTQKTKN
          .QYV............Q...N.AE.YFE.AKVEC.LQT..ELL..DFES.FP.VNS.K.MVLT.T.KTKN
Retrocopy VQYVKMNLRAMLHLLKQQEINRAEIYFERAKVECLLQTSAELLQRDFESMFP*VNSEKIMVLTLT*KTKN

Parental  DMTTWSEEVENEREMLLEKFITGAKEICYALRTEGYWADFIDPSSGLAFFG-PYTSNTLFETDERYRHLG
          DMTT..E.VE..REML.E.FI.G.KEICYAL....YW.D.ID.SS.L.FF...Y...TLFE.D..YR.L.
Retrocopy DMTTLREKVERIREMLFEMFIDGTKEICYALCVKSYWVDHIDLSSELVFFW<DYIQVTLFEADKYYRTLR

Parental  FSVDDLGCCKVIRHSIWGTHVVVGSIFTNATPDSRIMKKLS
          FS.DDLG..KVI.HS.WG.HVVVGS.F.N.T..S.IMKKLS
Retrocopy FSLDDLGYWKVIYHSHWGIHVVVGSVFMNVTANSQIMKKLS

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_1749 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1749 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 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003086	2 retrocopies	retro_cjac_4082, retro_cjac_4101,
Cavia porcellus	ENSCPOG00000007690	1 retrocopy	retro_cpor_30,
Homo sapiens	ENSG00000168288	2 retrocopies	retro_hsap_4716, retro_hsap_865,
Gorilla gorilla	ENSGGOG00000027348	1 retrocopy	retro_ggor_704,
Macaca mulatta	ENSMMUG00000005633	1 retrocopy	retro_mmul_1058,
Monodelphis domestica	ENSMODG00000003566	2 retrocopies	retro_mdom_1749 , retro_mdom_620,
Mustela putorius furo	ENSMPUG00000000323	1 retrocopy	retro_mputfur_1253,
Nomascus leucogenys	ENSNLEG00000010795	2 retrocopies	retro_nleu_1988, retro_nleu_426,
Otolemur garnettii	ENSOGAG00000034385	4 retrocopies	retro_ogar_3266, retro_ogar_356, retro_ogar_688, retro_ogar_813,
Pan troglodytes	ENSPTRG00000012525	1 retrocopy	retro_ptro_599,
Ictidomys tridecemlineatus	ENSSTOG00000021576	1 retrocopy	retro_itri_1809,
Tarsius syrichta	ENSTSYG00000009075	1 retrocopy	retro_tsyr_1690,