RetrogeneDB ID: retro_dnov_1798

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_30941:12038..12347(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000024666
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ZNRD1
• Ensembl ID: ENSDNOG00000015720
• Aliases: None
• Description: zinc ribbon domain containing 1 [Source:HGNC Symbol;Acc:13182]

Sequence

>retro_dnov_1798
TGCCCAGACTGCGGCAGGTCCTGCCTGCCCGGGCTCGGGATTCAGTCACCTGCACTCGCTGCGCCCTCTCCGTCAACGTG
GGGACTTTGAAAGGAGTATGGTGAAGACCTCTTTCGCGTTCCACAAATTGAGAGCAGCCGTGCCTGTGGCGGTGGAGCCA
GAGCCCGAGTTACAGGGGCCTGCGATGGACAGGCGCTGCCTGCGACGTGGTCCTGCAGGAATGGCACAGCACAGCAGACA
GATGGCTCAGCGGATGAAGGGCAGACCGTCCTCTACACCTGTACCGACTGCAGGCTCCAGAAGAAGGAC

Alignment

ORF - retro_dnov_1798 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 83.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  CPDCGSVLPLPG-AQDSVICTRCGLSINVR-DFEGKVVKTSFVFHKLGTAVPAAVEQGPEFQGPVVDRRC
          CPDCG....LPG.A.DSV.CTRC.LS.NV..DFE...VKTSF.FHKL..AVP.AVE..PE.QGP..DRRC
Retrocopy CPDCGRSC-LPG<ARDSVTCTRCALSVNVG<DFERSMVKTSFAFHKLRAAVPVAVEPEPELQGPAMDRRC

Parental  PRCGHEGMAYHTRQMR-SADEGQTVFYTCTNCRFQEKE
          .R.G..GMA.H.RQM..SADEGQTV.YTCT.CR.Q.K.
Retrocopy LRRGPAGMAQHSRQMA<SADEGQTVLYTCTDCRLQKKD

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	0.00 RPM	35.00 RPM
SRP012922_cerebellum	0.00 RPM	23.64 RPM
SRP012922_heart	0.00 RPM	18.79 RPM
SRP012922_kidney	0.00 RPM	38.33 RPM
SRP012922_liver	0.00 RPM	21.83 RPM
SRP012922_lung	0.00 RPM	34.36 RPM
SRP012922_quadricep_muscle	0.00 RPM	23.71 RPM
SRP012922_spleen	0.00 RPM	42.81 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_1798 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 8 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007328	2 retrocopies	retro_chof_1997, retro_chof_2061,
Dasypus novemcinctus	ENSDNOG00000015720	9 retrocopies	retro_dnov_1020, retro_dnov_1103, retro_dnov_1472, retro_dnov_1726, retro_dnov_1798 , retro_dnov_1881, retro_dnov_2400, retro_dnov_2420, retro_dnov_933,
Myotis lucifugus	ENSMLUG00000007272	1 retrocopy	retro_mluc_126,
Monodelphis domestica	ENSMODG00000016023	1 retrocopy	retro_mdom_1799,
Mustela putorius furo	ENSMPUG00000007474	1 retrocopy	retro_mputfur_968,
Rattus norvegicus	ENSRNOG00000000779	1 retrocopy	retro_rnor_978,
Sorex araneus	ENSSARG00000009716	2 retrocopies	retro_sara_431, retro_sara_745,
Sarcophilus harrisii	ENSSHAG00000001554	1 retrocopy	retro_shar_796,