RetrogeneDB ID: retro_dnov_866

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_115851:4142..4703(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJB12
• Ensembl ID: ENSDNOG00000009977
• Aliases: None
• Description: DnaJ (Hsp40) homolog, subfamily B, member 12 [Source:HGNC Symbol;Acc:14891]

Sequence

>retro_dnov_866
ATTGGAAATGCTTATGCTGTTTCAAGCAATCCAGAAAAATGAAAACAGTATGACCTTATGGGCAATGAAGAACAAGCTGT
AATCACCAAAACAATGGCAGATTTAATTTCCATAGAGGTTGTGAAGCTGGTATAACTCCAGAAGACTTATTTAATATATT
CTTTGGTGGTGGATTTCCTTCAGGTAGTGTACATTCATTTTCAAAATGGATGAACTAGTTATAGCCATCAACATCAACAT
TGGCATAGTGGACATGAAAGAGAAGAAGAAAGAGGAGAAGGAGGTTTTTCTGTGTTTCTCCAGCTGATGCCCATTATTTT
CTTGATCCCTGTGTCATTGTTAAGCCAGGTGATGGTCTCTAATCTTCCTTACTCCTTATATCCCAGACTGGGATCAGGGC
AGACCATTAAAATGCAGACAGAAAACTTGGGTGTCATTTATTATGTCAACAAGGACTTTAAAAATGAATATAAAGGAATG
TTATTACAAAAGGTAGAAAAGAGTGTGGAAGAAGATTATGTGACTAATATTTGAGATAATTGCTAGAAAGAAAGACACCA
A

Alignment

ORF - retro_dnov_866 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.79 %
• Parental protein coverage: 62.54 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IGTAYAVLSNPEKRKQYDQFGDD-KSQAARHGHGHGDFHRGFEADISPEDLFNMFFGGGFPSSNVHVYS-
          IG.AYAV.SNPEK.KQYD..G............G...FHRG.EA.I.PEDLFN.FFGGGFPS..VH..S.
Retrocopy IGNAYAVSSNPEK*KQYDLMGNE<RTSCNHQNNGRFNFHRGCEAGITPEDLFNIFFGGGFPSGSVHSFS>

Parental  NGRMRYTYQQRQ----DRRENQGDGG-LGVFVQLMPILILILVSALSQLMVSSPPYSLSPRPSVGHVHKR
          NG...Y..Q.........RE.....G...VF.QLMPI..LI.VS.LSQ.MVS..PYSL.PR...G...K.
Retrocopy NG*TSYSHQHQHWHSGHEREEERGEGGFSVFLQLMPIIFLIPVSLLSQVMVSNLPYSLYPRLGSGQTIKM

Parental  VTDHLSVVYYVADSFSEEYTGSSLKTVERNVEDDYIANLRNNCWKEKQQ
          .T..L.V.YYV...F..EY.G..L..VE..VE.DY..N...NC.KE..Q
Retrocopy QTENLGVIYYVNKDFKNEYKGMLLQKVEKSVEEDYVTNI*DNC*KERHQ

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	1.17 RPM	12.06 RPM
SRP012922_cerebellum	0.55 RPM	11.13 RPM
SRP012922_heart	0.70 RPM	5.34 RPM
SRP012922_kidney	1.10 RPM	13.96 RPM
SRP012922_liver	0.15 RPM	8.20 RPM
SRP012922_lung	1.22 RPM	11.61 RPM
SRP012922_quadricep_muscle	0.87 RPM	6.23 RPM
SRP012922_spleen	1.72 RPM	15.22 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_866 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 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007303	1 retrocopy	retro_cjac_1200,
Dasypus novemcinctus	ENSDNOG00000009977	1 retrocopy	retro_dnov_866 ,
Homo sapiens	ENSG00000148719	1 retrocopy	retro_hsap_2273,
Gorilla gorilla	ENSGGOG00000000683	1 retrocopy	retro_ggor_1691,
Macropus eugenii	ENSMEUG00000002024	2 retrocopies	retro_meug_1115, retro_meug_1511,
Pongo abelii	ENSPPYG00000002353	1 retrocopy	retro_pabe_1945,
Pan troglodytes	ENSPTRG00000002613	1 retrocopy	retro_ptro_1608,