RetrogeneDB ID: retro_mdom_524

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:152643404..152644049(-)
• Located in intron of: ENSMODG00000009715

Retrocopy information

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

Parental gene information

• Parental gene symbol: MED6
• Ensembl ID: ENSMODG00000007174
• Aliases: None
• Description: mediator complex subunit 6 [Source:HGNC Symbol;Acc:19970]

Sequence

>retro_mdom_524
AGTGTAGGCATTGGAGATAACCTGCTGGGAATGTCATGGGTTGACAGTTCCTAGATCCCTATACTGAACAGTGGTAGTGT
CTTAGACTACTTCTCTGAAGGAACTGACTATTTTAATGATTAGACATGTAATAATGAAGTGGTCAAAATGCAGAGACTCA
CAATGAAGTATTTAAATCAAATGGTTGGAGTAGAGTACATCTTTCTGCATGCCCAACAGCCAATTCTTTTTATCATTCAG
AAATAATAGCAGCAATCCTCTACACACAAGTCACCCTATTAGCTGATTATCCTATCATTGCTGGAGCAATTATCTGGCAC
CTGACTTGGGATCTGTCATAAAGTCTAGAGTGTGCTACATGGGAATTTAGTCAGCTTTTGATGAAGCTATGTCATATTGT
CATTACCACCTTTCCAAAGGGTACTGGTGGTATTTAAAAAACAAGGAAGAACAAAATAAAGCCAAACCTAAAGTCAAGAG
AAATGAAGAACCAAATTCTATTTTTCAGAGACTGTGTGTGAATGTTTTACTCCTAGATCTTCAACAGAAATTTCCACCCA
AATTCGTTCAGCATACCCTGGAGAAAAGTATGTCCCAGTGGATCCAACCCAGAAGGAGTCAAAGCCTATACCTGAAGCTA
TAAAA

Alignment

ORF - retro_mdom_524 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.59 %
• Parental protein coverage: 88.21 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AVDIRDNLLGISWVDSSWIPILNSGSVLDYFSERSNPFYDRTCNNEVVKMQRLTLEHLNQMVGVEYILLH
          .V.I.DNLLG.SWVDSS.IPILNSGSVLDYFSE....F.D.TCNNEVVKMQRLT...LNQMVGVEYI.LH
Retrocopy SVGIGDNLLGMSWVDSS*IPILNSGSVLDYFSEGTDYFND*TCNNEVVKMQRLTMKYLNQMVGVEYIFLH

Parental  AQEP-ILFIIRKQQRQSS-TQVIPLADYYIIAGVI-YQAPDLGSVINSRVLTAVHGIQSAFDEAMSYCRY
          AQ.P....I....Q..S..TQV..LADY.IIAG.I.Y.APDLGSVI.SRV.....GI.SAFDEAMSYC.Y
Retrocopy AQQPILFIIQK**QQSST<TQVTLLADYPIIAGAI<YLAPDLGSVIKSRV--CYMGI*SAFDEAMSYCHY

Parental  HPSKGYWWHFKDQEEQDKAKPKAKRKEEPSSIFQRQRVDALLLDLRQKFPPKFVQQK-PGEKPVPVDQTK
          H.SKGYWW..K..EEQ.KAKPK.KR.EEP.SIFQR..V..LLLDL.QKFPPKFVQ...PGEK.VPVD.T.
Retrocopy HLSKGYWWYLKNKEEQNKAKPKVKRNEEPNSIFQRLCVNVLLLDLQQKFPPKFVQHT<PGEKYVPVDPTQ

Parental  KEPEPTPEAIK
          KE..P.PEAIK
Retrocopy KESKPIPEAIK

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	48.04 RPM
SRP007412_cerebellum	0.00 RPM	43.09 RPM
SRP007412_heart	0.00 RPM	21.93 RPM
SRP007412_kidney	0.00 RPM	31.60 RPM
SRP007412_liver	0.00 RPM	20.64 RPM
SRP007412_testis	0.00 RPM	38.11 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_524 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_524 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 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000013091	1 retrocopy	retro_fcat_1612,
Myotis lucifugus	ENSMLUG00000017357	1 retrocopy	retro_mluc_265,
Monodelphis domestica	ENSMODG00000007174	3 retrocopies	retro_mdom_1190, retro_mdom_524 , retro_mdom_625,
Otolemur garnettii	ENSOGAG00000001311	1 retrocopy	retro_ogar_2597,
Ochotona princeps	ENSOPRG00000008957	1 retrocopy	retro_opri_820,
Sorex araneus	ENSSARG00000002553	1 retrocopy	retro_sara_495,
Tupaia belangeri	ENSTBEG00000002302	1 retrocopy	retro_tbel_2272,