RetrogeneDB ID: retro_dnov_1189

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_160298:3412..3904(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000005824
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NABP2
• Ensembl ID: ENSDNOG00000013517
• Aliases: None
• Description: nucleic acid binding protein 2 [Source:HGNC Symbol;Acc:28412]

Sequence

>retro_dnov_1189
AAGGACGGGCATGAGGTTCGGGACCTGCAAAGTGGCAGACGAAACAGGCAGCATCAATATCTCTGTCTGGGATGATGTGG
GCAACCTGATCCAGCCTGGGGACATTATCAGACCGACCAAAGGGTATGCATCTGTGTTCAAAGGTTGTCTAACAGTCTAC
ACTGGCCGTGGGGGAGATCTGCAGAAGACTGGAGAATTCTGTATGGTTTATTCTGAAGTTCCTAACTTCAGTGAGCCAGA
CCCGGAGCACAGCGCCCAACGGGCACCCAGCAAGGCGTGCAGCTCGACAGCAGCCCTGGAGCTCCCCAGCCTCCCTCTGG
ACCCCCTGCTGCTCCGCCAGCCTCTGAGAGCCAGGACGGGAATGGACTGAGCACCCTGCCAGGTCCTGGTGGTGGCCCGC
ACCCCGCTCACGCTACCCCCCAGCCCCCCAGCCCCCGCATCACTCGCAGCCAGCCCAGCCACACACCTGCCGGCCCCGCT
GGTGCCCCCAGT

Alignment

ORF - retro_dnov_1189 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.75 %
• Parental protein coverage: 97.04 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KDGHEVR-TCKVADKTGSINISVWDDVGNLIQPGDIIRLTKGYASVFKGCLTLYTGRGGDLQKIGEFCMV
          KDGHEVR.TCKVAD.TGSINISVWDDVGNLIQPGDIIR.TKGYASVFKGCLT.YTGRGGDLQK.GEFCMV
Retrocopy KDGHEVR>TCKVADETGSINISVWDDVGNLIQPGDIIRPTKGYASVFKGCLTVYTGRGGDLQKTGEFCMV

Parental  YSEVPNFSEPNPEYSAQQAPSKA-VQLDSSPGAPQPPSGPPAAPPASESQNGNGLSTPPGPGGGPHPPHA
          YSEVPNFSEP.PE.SAQ.APSKA.VQLDSSPGAPQPPSGPPAAPPASESQ.GNGLST.PGPGGGPHP.HA
Retrocopy YSEVPNFSEPDPEHSAQRAPSKA<VQLDSSPGAPQPPSGPPAAPPASESQDGNGLSTLPGPGGGPHPAHA

Parental  TPHPPSTRITRSQPNHTPAGPAGAPN
          ........ITRSQP.HTPAGPAGAP.
Retrocopy XXXXXXXXITRSQPSHTPAGPAGAPS

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	2.14 RPM	11.47 RPM
SRP012922_cerebellum	4.95 RPM	24.47 RPM
SRP012922_heart	2.78 RPM	8.35 RPM
SRP012922_kidney	1.64 RPM	11.23 RPM
SRP012922_liver	0.46 RPM	3.10 RPM
SRP012922_lung	3.36 RPM	14.66 RPM
SRP012922_quadricep_muscle	2.77 RPM	11.42 RPM
SRP012922_spleen	2.52 RPM	15.68 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_1189 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 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002798	1 retrocopy	retro_btau_545,
Callithrix jacchus	ENSCJAG00000011455	1 retrocopy	retro_cjac_1961,
Dasypus novemcinctus	ENSDNOG00000013517	1 retrocopy	retro_dnov_1189 ,
Erinaceus europaeus	ENSEEUG00000001325	1 retrocopy	retro_eeur_1,
Gorilla gorilla	ENSGGOG00000009050	1 retrocopy	retro_ggor_2094,
Macropus eugenii	ENSMEUG00000004485	4 retrocopies	retro_meug_1118, retro_meug_123, retro_meug_1835, retro_meug_540,
Mustela putorius furo	ENSMPUG00000001297	1 retrocopy	retro_mputfur_59,
Sarcophilus harrisii	ENSSHAG00000002240	1 retrocopy	retro_shar_493,