RetrogeneDB ID: retro_dnov_580

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_6461:4606..5334(-)
• Located in intron of: None

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_580
GTGGTAATTATGGTTAACCACCCAAAAGGACAAGAAATTTTGCATCTGGTGCATAAAGGAATTCCAATAAAAAGTTTCCA
CTGGACTTGGCACTGGCCATGTGCAGTAATTCAAAAGCAGCTAGTCTGTAGTGTTTGTGGCCATTGCTTTCATCACCACG
GTGATCATCTCACAAGCCTGGCTGATATTTTACTATACACAACATTTCCTATATACTGGCTCATAGTTTGGAAATCAGAT
CTGTAGAAAAGGAACTAATTACATTATTGGCCAGCTTCCACCTCATACTGTAAAGCATGGAGAAAAGGGAATCAACATTG
ATGCTGAAAATTGTGCAGTATATATTGATATTTTTTAAGTAAAGGATAGTATCAGAATTCTGCCTTGCCAGCATATTTTT
CATAGAACGTTTATTGATCTATGGCTTTTGGATTGCTGAATTTGTCCAATGTGTAAGTCTGATGTCTTCAAAGCCCTGGG
ATATTGGGGAGAGCCTGAGAATGTGCAGGAGATGCCTGCTCCAGAATCACTCCCCTGGAAGTATATCTGCTGCAAATTTG
AGTAGTACTTTACAAGATGATGACATATGGGTTAGAAACAACTTACCATTGTCTTCCACTAATGAATTTGTGACACAGGT
TAATGCCAGTTTTAAAGAAGTTGCAGGTGAAAACACAGAGTTATTAGAAATGGGAAGAATTGACCCTCAGCATGGCAGAC
TAGTATCC

Alignment

ORF - retro_dnov_580 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.54 %
• Parental protein coverage: 98.78 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IVIMISYPKGREILDLVQKGIPVK-MSIGLGTRHVQEFVSGQSVVFVAIAFITMMIISLAWLIFYYIQRF
          .VIM...PKG.EIL.LV.KGIP.K..S.GLGT.HVQ.F.S..SVVFVAIAFIT..IIS.AWLIFYY.Q.F
Retrocopy VVIMVNHPKGQEILHLVHKGIPIK>VSTGLGTGHVQ*FKSS*SVVFVAIAFITTVIISQAWLIFYYTQHF

Parental  LYTGSQFGNQSHRKETKKVIGQLPLHTVKXXXXGINIDAENCAVCIENFKVKDVIRILPCKHIFHRTCID
          LYTGS.FGNQ..RK.T...IGQLP.HTVK....GINIDAENCAV.I..F.VKD.IRILPC.HIFHRT.ID
Retrocopy LYTGS*FGNQICRKGTNYIIGQLPPHTVKHGEKGINIDAENCAVYIDIF*VKDSIRILPCQHIFHRTFID

Parental  PWLLDHRTCPMCKLDVIKALGYWGEPEDVQEMPASES-TPGSASAANLSTALQDDDRSDRNNLPSSSTNE
          .WLLD...CPMCK.DV.KALGYWGEPE.VQEMPA.ES..PGS.SAANLS..LQDDD...RNNLP.SSTNE
Retrocopy LWLLDC*ICPMCKSDVFKALGYWGEPENVQEMPAPES>SPGSISAANLSSTLQDDDIWVRNNLPLSSTNE

Parental  SVSQVNASFKEDAGENTALLETGSSDPQRGGPVS
          .V.QVNASFKE.AGENT.LLE.G..DPQ.G..VS
Retrocopy FVTQVNASFKEVAGENTELLEMGRIDPQHGRLVS

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	28.78 RPM
SRP012922_cerebellum	0.00 RPM	3.44 RPM
SRP012922_heart	0.00 RPM	3.71 RPM
SRP012922_kidney	0.00 RPM	25.46 RPM
SRP012922_liver	0.00 RPM	8.98 RPM
SRP012922_lung	0.00 RPM	35.43 RPM
SRP012922_quadricep_muscle	0.00 RPM	6.58 RPM
SRP012922_spleen	0.00 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_580 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,