RetrogeneDB ID: retro_dnov_990

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_131286:3200..3753(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000025597
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CXADR
• Ensembl ID: ENSDNOG00000012975
• Aliases: None
• Description: coxsackie virus and adenovirus receptor [Source:HGNC Symbol;Acc:2559]

Sequence

>retro_dnov_990
TCACAGAAAATGCCCAGCTCATGGTTATCAGAGATGACTTCACCTATTGTATCTATGGAAAATGCCACTGCTGAATATTC
TGGGACATACCGTTATACAGTCAGGAACAATGTGAGTTCTGACAGTGCCTGCTATGCCTGGATGTTGTTCCTCCTTCAAG
TGGACCTGCAACAATTGTGGAGGCTATTAGAGGAACTCTGCTTGCTCTTTTGCTCATTGGTCTCATCCCCCTTTGCTGTC
GTAAAAAGCGCAGAGAAGAAAAATGTGAAAAAGAAGTACATCGTGAAATCAGGGAAGATGTGCCTCTGCCAAGGAGCCGC
CTGTCCTCAGCCAGGAGCTACATCGGCCGCAGTCACTCATCCCTGAGAGCCACATCTCCTTCCAACATGGAAGAATATTC
CAAGACTCAATATAACCAAGCCCGGAGTGAAGATTTTGAACACCCTTCTCAGAGCCCAACTCTCGAGCCTGCCAGGGTAG
CTGTCCCTAATCTGAGTAGAATGGGAGAGTTGCCTGTGATATTCCAACACTGAGTGAGGATGGGTCTCTAGTA

Alignment

ORF - retro_dnov_990 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.81 %
• Parental protein coverage: 52.99 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SQKMSTPWLSEMTSSPIISIKNATAEYSGTYSCTVKNRVGSD-QCLLLLNVVPPSNRAATIAGAIIGTLL
          SQKM...WLSEMTS.PI.S..NATAEYSGTY..TV.N.V.SD.QCLL.L.VVPPS...ATI..AI.GTLL
Retrocopy SQKMPSSWLSEMTS-PIVSMENATAEYSGTYRYTVRNNVSSD<QCLLCLDVVPPSSGPATIVEAIRGTLL

Parental  ALLLIGLIIFCCRKKRREEKYEKEVHHDIREDVPPPKSRTSTARSYMGSNHSSLGSMSPSNMEGYSKAQY
          ALLLIGLI..CCRKKRREEK.EKEVH..IREDVP.P.SR.S.ARSY.G..HSSL...SPSNME.YSK.QY
Retrocopy ALLLIGLIPLCCRKKRREEKCEKEVHREIREDVPLPRSRLSSARSYIGRSHSSLRATSPSNMEEYSKTQY

Parental  NQVPSEDFERASQSPTLAPAKVAAPNLSRMGAVPVM-IPAQSKDGSIV
          NQ..SEDFE..SQSPTL.PA.VA.PNLSRMG..PV..IP..S.DGS.V
Retrocopy NQARSEDFEHPSQSPTLEPARVAVPNLSRMGELPVI<IPTLSEDGSLV

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	55.23 RPM
SRP012922_cerebellum	0.41 RPM	2.20 RPM
SRP012922_heart	0.00 RPM	12.76 RPM
SRP012922_kidney	0.00 RPM	4.38 RPM
SRP012922_liver	0.00 RPM	19.82 RPM
SRP012922_lung	0.15 RPM	20.62 RPM
SRP012922_quadricep_muscle	0.00 RPM	0.69 RPM
SRP012922_spleen	0.11 RPM	0.80 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_990 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 6 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000012975	1 retrocopy	retro_dnov_990 ,
Homo sapiens	ENSG00000154639	6 retrocopies	retro_hsap_1533, retro_hsap_1535, retro_hsap_1918, retro_hsap_2492, retro_hsap_4322, retro_hsap_4323,
Nomascus leucogenys	ENSNLEG00000002063	2 retrocopies	retro_nleu_138, retro_nleu_58,
Pongo abelii	ENSPPYG00000011295	2 retrocopies	retro_pabe_1273, retro_pabe_2776,
Pan troglodytes	ENSPTRG00000013795	4 retrocopies	retro_ptro_1244, retro_ptro_1444, retro_ptro_801, retro_ptro_995,
Sarcophilus harrisii	ENSSHAG00000005309	1 retrocopy	retro_shar_252,