RetrogeneDB ID: retro_dnov_331

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_3705:199352..200154(+)
• Located in intron of: ENSDNOG00000015624

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACAT2
• Ensembl ID: ENSDNOG00000002502
• Aliases: None
• Description: acetyl-CoA acetyltransferase 2 [Source:HGNC Symbol;Acc:94]

Sequence

>retro_dnov_331
TCCTTCAATGGAACCCTGTCTACTGTTCCTGTACACTACCTGGATTCAATTGTCATCAAAGAAGTCCTGAAGAGGGTCAA
TGTGGACCCTGAAGAGGTGTCTGAGGTCATATTTGGACATGTGTAGGCAGCAGGATGTGGGAAGAATCCCACTCTGCAAG
CCAGTGTAGGTGCGGGAATCCCCTGTACTGTTCCAGTATGGAGTTGCCAGATGATCTGTGGGTCATGACTAAAAGCTGTG
TGACTTGCAGCCCAATCTGTGGGAACAGGAGACTTCAGCATTGTGTCTGCAGGAGGCATGGAAAATATGAGCCAGGCTCC
TCATTTGGTTCACTGGAGTACAGGAATCAAGATGGGTGAGAAGTCACTAACTTATAGTATCCTCTGTAATGGTCTTACGT
ATGCATTTTACAACTATCACAAGGGTGTTAAAGCTGAAAATGTAGCCAAAAAATGGCAAGTAAGTATAGAAGATCAAGAC
AAGGCTGCAGTTCTGTCCCAGGACAGGACCGGGAGTAAATAGAAAGCAGGCTTTTTGACAAAAATCATACCAGTTTTAGC
ACCTTCTAGAAAAGATCCCATTAAGGTTAAAAGACATGAGATTCCTCGCCATGGAAGCAACATAGAAGCTATGTTCAAGC
TAAAGCCTTACTTTCTTACAGATTGAACAGGAACAGTTACCCCAGCTAATGCTTCAGAAATAAACCAATGGTTCTGCAGT
TGTGGTTCTTATCAAGTCAGAAGATGATAAAATGCAGGGGCTTACACCTTTAGCACAGATCATTTCCTGGTCATAAGTAG
GT

Alignment

ORF - retro_dnov_331 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.81 %
• Parental protein coverage: 73.02 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SFNGALSTVPVHDLGSTVIKEVLKRANVAPEEVSEVIFGHVLTAGCGQNPTRQASVGAGIPYTVPAWSCQ
          SFNG.LSTVPVH.L.S.VIKEVLKR.NV.PEEVSEVIFGHV..AGCG.NPT.QASVGAGIP.TVP.WSCQ
Retrocopy SFNGTLSTVPVHYLDSIVIKEVLKRVNVDPEEVSEVIFGHV*AAGCGKNPTLQASVGAGIPCTVPVWSCQ

Parental  MICGSGLKAVCLAAQSVGMGDSRIVVAGGMENMSQAPHLVHLRTGIKMGEKSLTDSILCDGLTDAFYNYH
          MICGS.LKAV.LAAQSVG.GD..IV.AGGMENMSQAPHLVH..TGIKMGEKSLT.SILC.GLT.AFYNYH
Retrocopy MICGS*LKAV*LAAQSVGTGDFSIVSAGGMENMSQAPHLVHWSTGIKMGEKSLTYSILCNGLTYAFYNYH

Parental  MGVTAENVAKKWQVSREDQDKAAVLSQNRTESAQKAGYFDKEIVPVLVPSRKDPIEVKRDEFPRHGSNIE
          .GV.AENVAKKWQVS.EDQDKAAVLSQ.RT.S..KAG...K.I.PVL.PSRKDPI.VKR.E.PRHGSNIE
Retrocopy KGVKAENVAKKWQVSIEDQDKAAVLSQDRTGSK*KAGFLTK-IIPVLAPSRKDPIKVKRHEIPRHGSNIE

Parental  AMSKLKPYFLTDGTGTVTPANASGIN-DGAAAVVLMKKSEADSRGLTPLAQIVSWAQVG
          AM.KLKPYFLTD.TGTVTPANAS.IN..G.A.VVL.K.......GLTPLAQI.SW..VG
Retrocopy AMFKLKPYFLTD*TGTVTPANASEIN>NGSAVVVLIKSEDDKMQGLTPLAQIISWS*VG

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	0.19 RPM	49.20 RPM
SRP012922_cerebellum	0.00 RPM	26.53 RPM
SRP012922_heart	0.00 RPM	7.89 RPM
SRP012922_kidney	0.00 RPM	24.92 RPM
SRP012922_liver	0.00 RPM	14.55 RPM
SRP012922_lung	0.00 RPM	14.66 RPM
SRP012922_quadricep_muscle	0.00 RPM	6.23 RPM
SRP012922_spleen	0.00 RPM	21.29 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_331 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002827	1 retrocopy	retro_btau_560,
Callithrix jacchus	ENSCJAG00000011777	1 retrocopy	retro_cjac_1372,
Dasypus novemcinctus	ENSDNOG00000002502	1 retrocopy	retro_dnov_331 ,
Macaca mulatta	ENSMMUG00000012843	1 retrocopy	retro_mmul_277,
Monodelphis domestica	ENSMODG00000007156	1 retrocopy	retro_mdom_1493,
Rattus norvegicus	ENSRNOG00000019189	1 retrocopy	retro_rnor_1055,
Xenopus tropicalis	ENSXETG00000021174	1 retrocopy	retro_xtro_45,