RetrogeneDB ID: retro_dnov_534

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_5858:125567..126300(-)
• Located in intron of: ENSDNOG00000015859

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF149
• Ensembl ID: ENSDNOG00000011956
• Aliases: None
• Description: ring finger protein 149 [Source:HGNC Symbol;Acc:23137]

Sequence

>retro_dnov_534
ACAGGAAATATAGTGGTTATTATGATTAGCTACCCAAAAGGAAGAGAAATTTTGGATCTGGTGCAAAAAGGAATTCCAGT
AAAAATGTCCATTGGACTTGGCACCCGCCATGTGCAGGAGTTCGTCAGTGGTCAGTCTGTAGTGTTTGTGGCCATTGCCT
TCATCACCATGATGATCATCTCACTAGCCTGGCTGACACTTAACTCTATACAGTTTCCTATATATTGGCTCAGGGTTTGG
GAATCAGAGCCATAGATAAGAAACTAAGAAAGTTATTGGCCAGCTTCCACTTCATATTGGAAAGCATGGAGAAAAGGGAA
TCAATATTGATGCTGAAAATTGTGCAGTGTATATTGAAAATTTTAAAGTAAAGGATATTATCAGAATTCTGCCATGCAAG
CATATTTTTCATAGAACATGCATTGACCCACGGCTTCTGGATCACCAAACTTGTCCAGTGTGTAAGCTTGATGTCATCAA
AGCCCTGGGATATTGGGGAGAGCCTGAAGATGTGCAGGAAATGCCCACTCCAGAATCAACTTGTGGAAGTGTTTCTGCTG
CAAATTTGAGTAGTATTTTACAAGATGTCAGAAGTGACAAAAACAACTTGCCATCATCTTCCACTAATGAATCTGTGCCA
CAGGTTAATGCCAGTTTTAAAGAAGATGCAGGTGAAAACACAGCATTATTAGAAATGGGCACAAGTGACCCTCAGCATGA
TGGACCAGTCTCC

Alignment

ORF - retro_dnov_534 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.24 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TGNI-VIMISYPKGREILDLVQKGIPVKMSIGLGTRHVQEFVSGQSVVFVAIAFITMMIISLAWLIFYYI
          TGNI.VIMISYPKGREILDLVQKGIPVKMSIGLGTRHVQEFVSGQSVVFVAIAFITMMIISLAWL....I
Retrocopy TGNIVVIMISYPKGREILDLVQKGIPVKMSIGLGTRHVQEFVSGQSVVFVAIAFITMMIISLAWLTLNSI

Parental  QRFLY-TGSQFGNQSHRKETKKV-IGQLPLHTVKXXXXGINIDAENCAVCIENFKVKDVIRILPCKHIFH
          Q...Y......G.....K...K..IGQLPLH..K....GINIDAENCAV.IENFKVKD.IRILPCKHIFH
Retrocopy QFPIY<LAQGLGIRAIDKKLRKL<IGQLPLHIGKHGEKGINIDAENCAVYIENFKVKDIIRILPCKHIFH

Parental  RTCIDPWLLDHRTCPMCKLDVIKALGYWGEPEDVQEMPASESTPGSASAANLSTALQDDDRSDRNNLPSS
          RTCIDP.LLDH.TCP.CKLDVIKALGYWGEPEDVQEMP..EST.GS.SAANLS..LQ.D.RSD.NNLPSS
Retrocopy RTCIDPRLLDHQTCPVCKLDVIKALGYWGEPEDVQEMPTPESTCGSVSAANLSSILQ-DVRSDKNNLPSS

Parental  STNESVSQVNASFKEDAGENTALLETGSSDPQRGGPVS
          STNESV.QVNASFKEDAGENTALLE.G.SDPQ..GPVS
Retrocopy STNESVPQVNASFKEDAGENTALLEMGTSDPQHDGPVS

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	3.11 RPM	28.78 RPM
SRP012922_cerebellum	0.14 RPM	3.44 RPM
SRP012922_heart	0.23 RPM	3.71 RPM
SRP012922_kidney	2.19 RPM	25.46 RPM
SRP012922_liver	0.46 RPM	8.98 RPM
SRP012922_lung	2.75 RPM	35.43 RPM
SRP012922_quadricep_muscle	0.69 RPM	6.58 RPM
SRP012922_spleen	2.75 RPM	35.83 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_534 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 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012057	2 retrocopies	retro_chof_290, retro_chof_555,
Dasypus novemcinctus	ENSDNOG00000011956	3 retrocopies	retro_dnov_2168, retro_dnov_534 , retro_dnov_580,
Dasypus novemcinctus	ENSDNOG00000014687	1 retrocopy	retro_dnov_139,
Macropus eugenii	ENSMEUG00000014821	1 retrocopy	retro_meug_417,
Myotis lucifugus	ENSMLUG00000007110	1 retrocopy	retro_mluc_1684,
Rattus norvegicus	ENSRNOG00000013946	2 retrocopies	retro_rnor_1406, retro_rnor_2527,
Tursiops truncatus	ENSTTRG00000016450	1 retrocopy	retro_ttru_351,