RetrogeneDB ID: retro_dnov_50

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_96978:3061..3763(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000018346
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: NKAP
• Ensembl ID: ENSDNOG00000000072
• Aliases: None
• Description: NFKB activating protein [Source:HGNC Symbol;Acc:29873]

Sequence

>retro_dnov_50
AAAAAAGGAAAAAAGAAGACCAGTCATTCAAAAAACAAGAAAAAAAGAAAGAAAAAGTCATCCAAAAGAAAACTTAGGAA
GTATTCGGGTAATAGTAACAGTAATTCAGACTCTGACACTAATTGTAGCTCTGGTGATGATAAAAAGAGAGTCAGAAAAG
CCAAGAAGAAAGAGAAGAAAAAGAAATACAAAACAAAAAAGCCCAAGAAAAAGAAGAAGAAGACTAGGAAAGAACCCAGT
GATTCAAGCTATAAGGATTCAGAAGGGGAGTTGACTGAATATATTTGGACTGAGCATACAAAGATTGCAGATACCATGGA
TTTAATAGGTCCAGAAGCACCTGTAATACACACCTCTCAAGATGAGAAACCTTTGAACTATGGCCATGCTCTGCTGCCAG
GTGAAGGTGCAGCAATGGCTGAGTATGTAAAAGCTGGAAAGCGCATCCCTCGAAGAGGTGAAATCGGGCTGACAAGTGAA
GAGATCGCTTCATTTGAAAGCTCAGGTTACGTCATGAGTGGCAGCAGGCATCGCAGGATGGAGGCTGTACGCCTGCGAAA
AGAGAACCAGATATACAGTGCCGATGAGAAGAGAGCCCTTGCATCCTTTAACCAAGAAGAGAGACGAAAGAGAGAGAATA
AGATTCTGGCCAGTTTCCGAGAGATGGTGTACAGAAAGACAAAAGGGAAAGATGACAAGTAA

Alignment

ORF - retro_dnov_50 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.97 %
• Parental protein coverage: 56.59 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KKKKKKSARSKERSKKRRKKKSSKRKHKKYSDDSDSDSDSETDSSDEDTKRRAKKAKKKEKKKKHRSKKY
          KK.KKK...SK...KK.RKKKSSKRK..KYS..S.S.SDS.T..S..D.K.R..KAKKKEKKKK...KK.
Retrocopy KKGKKKTSHSK--NKKKRKKKSSKRKLRKYSGNSNSNSDSDTNCSSGDDKKRVRKAKKKEKKKKYKTKKP

Parental  KKKKSKKSRKETSDSSSKDSQEEFLENPWKDRSKPEEPSDLIGPEAPKSLASQDDKPLNYGHALLPGEGA
          KKKK.KK.RKE.SDSS.KDS..E..E..W....K.....DLIGPEAP....SQD.KPLNYGHALLPGEGA
Retrocopy KKKK-KKTRKEPSDSSYKDSEGELTEYIWTEHTKIADTMDLIGPEAPVIHTSQDEKPLNYGHALLPGEGA

Parental  AMAEYVKAGKRIPRRGEIGLTSEEIASFECSGYVMSGSRHRRMEAVRLRKENQIYSADEKRALASFNQEE
          AMAEYVKAGKRIPRRGEIGLTSEEIASFE.SGYVMSGSRHRRMEAVRLRKENQIYSADEKRALASFNQEE
Retrocopy AMAEYVKAGKRIPRRGEIGLTSEEIASFESSGYVMSGSRHRRMEAVRLRKENQIYSADEKRALASFNQEE

Parental  RRKRENKILASFREMVYRKTKGKDDK
          RRKRENKILASFREMVYRKTKGKDDK
Retrocopy RRKRENKILASFREMVYRKTKGKDDK

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	15.75 RPM
SRP012922_cerebellum	0.00 RPM	12.51 RPM
SRP012922_heart	0.00 RPM	6.96 RPM
SRP012922_kidney	0.00 RPM	20.53 RPM
SRP012922_liver	0.00 RPM	8.20 RPM
SRP012922_lung	0.00 RPM	25.05 RPM
SRP012922_quadricep_muscle	0.00 RPM	10.21 RPM
SRP012922_spleen	0.00 RPM	24.95 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_50 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 15 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018433	1 retrocopy	retro_cfam_172,
Dasypus novemcinctus	ENSDNOG00000000072	1 retrocopy	retro_dnov_50 ,
Echinops telfairi	ENSETEG00000001007	1 retrocopy	retro_etel_1882,
Felis catus	ENSFCAG00000004392	1 retrocopy	retro_fcat_10,
Homo sapiens	ENSG00000101882	1 retrocopy	retro_hsap_15,
Loxodonta africana	ENSLAFG00000002962	1 retrocopy	retro_lafr_37,
Macaca mulatta	ENSMMUG00000012382	1 retrocopy	retro_mmul_121,
Mus musculus	ENSMUSG00000016409	1 retrocopy	retro_mmus_279,
Nomascus leucogenys	ENSNLEG00000014922	1 retrocopy	retro_nleu_88,
Otolemur garnettii	ENSOGAG00000001004	1 retrocopy	retro_ogar_239,
Pongo abelii	ENSPPYG00000020679	1 retrocopy	retro_pabe_198,
Pan troglodytes	ENSPTRG00000022233	1 retrocopy	retro_ptro_117,
Rattus norvegicus	ENSRNOG00000031169	1 retrocopy	retro_rnor_93,
Sus scrofa	ENSSSCG00000012613	1 retrocopy	retro_sscr_13,
Ictidomys tridecemlineatus	ENSSTOG00000001134	1 retrocopy	retro_itri_73,