RetrogeneDB ID: retro_dnov_533

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_5853:295487..296117(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MED20
• Ensembl ID: ENSDNOG00000016666
• Aliases: None
• Description: mediator complex subunit 20 [Source:HGNC Symbol;Acc:16840]

Sequence

>retro_dnov_533
TTGGGAGGGACTTGTGTGTCCCAGATGCCTGTGGCTGAGGGCAAGAGTGTCCAGCAGACTGTGGAGCACCTTATCCGGAA
GTTGGAGATGCTTGGAACAGAGGAACAAGGAACATTTTGTGTGGACTGTGAGACCTGCTATACAGCTGGTTCCACCCTTG
GCAGCCAAGGTCAGGCCAGGAAGCTGATGTATGTGATGCACTCAGGGTACTCTTTGAGCTGCTTTGCCCTCTTTGAGAAT
GGACATTGCCTTATTGCTGATACCAACTTTGATGTGCTTATGGTGAAGCTCAAGGGTTTTGTCCAGAGTGCCAAGGCCAG
CAAGATGGAGACCCGGGGTACCCGTCACCAGTGCTGTGACTTCCTAGTGAAGGTGGGCACAGTCACAATGGGACCCAGCA
CCCGGGGCATCTCTGTGGAGGTGGAGTATGGCCCGTGTGTGGTACCCAGTGGCTGCTGGAGCCTGCTACTTGAGTTCCTA
CAGAGTTTTTTGGGTACCCACACACCAGGGCCTCCTGCAGTGTTTGGGAATAGACATGATGCAATATATGGCCCAGCAGA
TACCATGATCCAGTACATGGAATTGTTCAACAAGATCCGCAACCAGCAGCAGGTGCTGGTGGCTGGGATT

Alignment

ORF - retro_dnov_533 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.04 %
• Parental protein coverage: 99.53 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGVTCVSQMPVAEGKSVQQTVELLTRKLEMLGAEKQGTFCVDCETFHTAASTLGSQGQAGKLMYVMHNSE
          .G.TCVSQMPVAEGKSVQQTVE.L.RKLEMLG.E.QGTFCVDCET..TA.STLGSQGQA.KLMYVMH.S.
Retrocopy LGGTCVSQMPVAEGKSVQQTVEHLIRKLEMLGTEEQGTFCVDCETCYTAGSTLGSQGQARKLMYVMH-SG

Parental  YPLSCFALFENGPCLIADTNFDVLMVKLKGFFQSAKASKIETRGTRYQYCDFLVKVGTVTMGPSARGISV
          Y.LSCFALFENG.CLIADTNFDVLMVKLKGF.QSAKASK.ETRGTR.Q.CDFLVKVGTVTMGPS.RGISV
Retrocopy YSLSCFALFENGHCLIADTNFDVLMVKLKGFVQSAKASKMETRGTRHQCCDFLVKVGTVTMGPSTRGISV

Parental  EVEYGPCVVASDCWSLLLEFLQSFLGTXXXXXXXXXXSRHDAVYGPADTMVQYMEC-HKIRKQQQVPVAE
          EVEYGPCVV.S.CWSLLLEFLQSFLGT...........RHDA.YGPADTM.QYME...KIR.QQQV.VA.
Retrocopy EVEYGPCVVPSGCWSLLLEFLQSFLGTHTPGPPAVFGNRHDAIYGPADTMIQYMELFNKIRNQQQVLVAG

Parental  I
          I
Retrocopy I

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
SRP012922_ascending_colon	0.78 RPM	19.84 RPM
SRP012922_cerebellum	0.27 RPM	10.72 RPM
SRP012922_heart	0.93 RPM	5.80 RPM
SRP012922_kidney	0.27 RPM	13.14 RPM
SRP012922_liver	0.15 RPM	8.82 RPM
SRP012922_lung	0.46 RPM	14.20 RPM
SRP012922_quadricep_muscle	0.17 RPM	6.06 RPM
SRP012922_spleen	0.80 RPM	18.89 RPM

ChIP-Seq

Dasypus novemcinctus was not studied using ChIP-Seq data.

EST

Dasypus novemcinctus was not studied using EST data.

TSS

Dasypus novemcinctus was not studied using FANTOM5 data.

Lab

retro_dnov_533 was not experimentally validated.

Homology

Retrocopy orthology:

Dasypus novemcinctus 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001613	1 retrocopy	retro_cfam_1492,
Dasypus novemcinctus	ENSDNOG00000016666	1 retrocopy	retro_dnov_533 ,
Microcebus murinus	ENSMICG00000011326	1 retrocopy	retro_mmur_972,
Myotis lucifugus	ENSMLUG00000014024	1 retrocopy	retro_mluc_2117,