RetrogeneDB ID: retro_mdom_614

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:533091789..533092451(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDHB
• Ensembl ID: ENSMODG00000002398
• Aliases: None
• Description: pyruvate dehydrogenase (lipoamide) beta [Source:HGNC Symbol;Acc:8808]

Sequence

>retro_mdom_614
CTATGGAAGAAGCATGGAGGCAAGAGAATCACTGACAAGTCCATATCTGAGATGGGCTTTACTGAGGTTGCTATAGGGCA
CCTATGGTTGGATGGAGGCCCATCTATGAATTTGTGACCTTCAATTTTTCTATGCTAGCAATTGACCTGGTTAAAACTCA
GATGAAATGTCTTACTATATGTCAAGTCAGTTTTATCCTGTTCCTATAGCCTTCAGGGGACTTAATCATGCTTCAATTGC
TGTGGCTGCCCAGCATCCAGAGTGTTTTGCAGCTTGGTCTGGACCCTGTGGTGGATTTAAAGTGGTCAGTCCTTAGTATT
TAGAGGCAATGCAAAAGGGCTTATCAAATTAGCAATTCAGAATGACAATCCAGTTTTAGTGCTGGAAAACTAGCTGATAT
ATGGAGTTCTTTTTGAATTTCCAGAAAAAGCTCAGTCAAAAAATTTCCTGATTCCTATTGGAAAATCTAAATTAAAAAGG
CAAAGAATGCATGTTATATTGGTTCCCCATTCATGACCTGTTGGCCATTATATGGAAGCAGCTGCTCTACTAGCTAACAA
GGAAGTGAAATGTGAGTTGATCAACCTGTGAACCATTAGACCAATGGATGGAGAACCATTGAGGCCAGTGTGATGAAAAT
CAATTATCTCATAACCATTGAA

Alignment

ORF - retro_mdom_614 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.6 %
• Parental protein coverage: 61.22 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LWKKYGDKRIIDTPISEMGFAGIAVG-AAMAGLRPICEFMTFNFSMQAIDQVI-NSAAKTYYMSGGLQPV
          LWKK.G.KRI.D..ISEMGF...A.G.A.M.G.RPI.EF.TFNFSM.AID.V..NS....YYMS....PV
Retrocopy LWKKHGGKRITDKSISEMGFTEVAIG<APMVGWRPIYEFVTFNFSMLAIDLVK<NSDEMSYYMSSQFYPV

Parental  PIVFRGPNGASAGVAAQHSQCFAAWYGHCPGLKVVSP-WSSEDAKGL-IKSAIRDDNPVVVLENELMYGV
          PI.FRG.N.AS..VAAQH..CFAAW.G.C.G.KVVSP.......KGL.IK.AI..DNPV.VLEN.L.YGV
Retrocopy PIAFRGLNHASIAVAAQHPECFAAWSGPCGGFKVVSP*YLEAMQKGL<IKLAIQNDNPVLVLEN*LIYGV

Parental  PFEFPDEAQSKDFLIPIGKAKIERQGTHVTLVSHSRPVGHCMEAAAILSKEGVECEVINMRTIRPMDTQ-
          .FEFP..AQSK.FLIPIGK.K..RQ..HV.LV.HS.PVGH.MEAAA.L....V.CE.IN..TIRPMD...
Retrocopy LFEFPEKAQSKNFLIPIGKSKLKRQRMHVILVPHS*PVGHYMEAAALLANKEVKCELINL*TIRPMDGE<

Parental  TIEASVMKTNHLITVE
          TIEASVMK.N.LIT.E
Retrocopy TIEASVMKINYLITIE

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_614 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_614 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
Bos taurus	ENSBTAG00000021724	1 retrocopy	retro_btau_596,
Canis familiaris	ENSCAFG00000007340	2 retrocopies	retro_cfam_1215, retro_cfam_2031,
Callithrix jacchus	ENSCJAG00000019739	1 retrocopy	retro_cjac_3875,
Dasypus novemcinctus	ENSDNOG00000006937	1 retrocopy	retro_dnov_1090,
Monodelphis domestica	ENSMODG00000002398	1 retrocopy	retro_mdom_614 ,
Mus musculus	ENSMUSG00000021748	1 retrocopy	retro_mmus_290,
Oryctolagus cuniculus	ENSOCUG00000015632	1 retrocopy	retro_ocun_342,
Procavia capensis	ENSPCAG00000016595	1 retrocopy	retro_pcap_261,
Sarcophilus harrisii	ENSSHAG00000008480	1 retrocopy	retro_shar_5,
Ictidomys tridecemlineatus	ENSSTOG00000019553	2 retrocopies	retro_itri_1349, retro_itri_249,
Tupaia belangeri	ENSTBEG00000016148	2 retrocopies	retro_tbel_1651, retro_tbel_3170,