RetrogeneDB ID: retro_dnov_1076

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_14393:10485..11170(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM173B
• Ensembl ID: ENSDNOG00000002277
• Aliases: None
• Description: family with sequence similarity 173, member B [Source:HGNC Symbol;Acc:27029]

Sequence

>retro_dnov_1076
GGTGGCTGTTCACCTCTGGAAGCACTTGAAGAGGAAAAACAATCAGGATATGCTCTCCCTATAAGTTTTGAAGCCAACAG
TCTGAAGAAAAGAAATTGAGGGTTCTTGTTTACTGGGATTGTTGGTGGGTCATTCATGGCCTCATATGCTGTAGCCACAC
CCTTCATAATATCAGCCCTTCGAAAAGTTTGTTTGCCTTTTGTCCCTGCAACTCCCAAGTAGATTGAACCTGTGGTGACA
GTGTTGTGCTGCAGAAGAGGCTCCGTGGTGGACACTTGGAGTGGCGACAGATGTGTCATGATAGCAGCTACAAAGGAAGA
ATTCACAGCCCTTTGCTGTGAATTAAATCCATGGCTGATTTGGTACTGCAGGTACCACGTGGATGAGAAGGTATACACAA
ATCTGCCAAATTTTGTATTTCAGATTTGCGGACAGTTACTTTTTCACACTACACAAACATTGTTATTTTGGGGGTGCCTC
AGATGATGCCGCTGCTGGAGAGGAAACTTGAACTTGAGCTTGGCGAGGATGCCAGAGTCATTGCTTGTGGGTTCTCTTTC
CTGTGCTGCACTGAGACCACGTCGCTGGGGAGGGGATAGATGCCATGTAGGCCTGTGATGCGGGCATGTTTAAAGAAAGT
GGAAGGAAACCTGCCGTAGTGGGGCGTTCATAGTTGGTCACTCAG

Alignment

ORF - retro_dnov_1076 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.4 %
• Parental protein coverage: 98.28 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GGGSPLEALEEESQLGTVLPTRFEASSLKKRKWGFLFTGIVGGSLVAVYAVATPFIIPALRKICLPFVPA
          GG.SPLEALEEE.Q.G..LP..FEA.SLKKR..GFLFTGIVGGS..A.YAVATPFII.ALRK.CLPFVPA
Retrocopy GGCSPLEALEEEKQSGYALPISFEANSLKKRN*GFLFTGIVGGSFMASYAVATPFIISALRKVCLPFVPA

Parental  TPKQIENVMTMLRCRRGSVVDIGSGDGRIVIAAAKEGFTAVGYELNPWLVWYSRYRAWQ-EGVHKSAKFY
          TPK.IE.V.T.L.CRRGSVVD..SGD....IAA.KE.FTA...ELNPWL.WY.RY.....EG.HKSAKF.
Retrocopy TPK*IEPVVTVLCCRRGSVVDTWSGDRCVMIAATKEEFTALCCELNPWLIWYCRYHVDE<EGIHKSAKFC

Parental  ISDLWKVTFSGYTNVVIFGVPQMMPLLERKLELELGQDARVIACRFPFPCWIPA-HVTGEGIDTVWAYDV
          ISDL..VTFS.YTN.VI.GVPQMMPLLERKLELELG.DARVIAC.F.F.C.....HV.GEGID...A.D.
Retrocopy ISDLRTVTFSHYTNIVILGVPQMMPLLERKLELELGEDARVIACGFSFLCCTET<HVAGEGIDAM*ACDA

Parental  GTFGGSRWRPGRVERSQLAAR
          G.F..S...P..V.RS.L...
Retrocopy GMFKESGRKPAVVGRS*LVTQ

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	0.39 RPM	6.81 RPM
SRP012922_cerebellum	0.41 RPM	5.50 RPM
SRP012922_heart	0.93 RPM	3.94 RPM
SRP012922_kidney	0.00 RPM	4.11 RPM
SRP012922_liver	0.93 RPM	4.02 RPM
SRP012922_lung	0.31 RPM	3.05 RPM
SRP012922_quadricep_muscle	0.17 RPM	4.67 RPM
SRP012922_spleen	0.00 RPM	2.63 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_1076 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000002277	1 retrocopy	retro_dnov_1076 ,
Homo sapiens	ENSG00000150756	1 retrocopy	retro_hsap_1105,
Macaca mulatta	ENSMMUG00000020111	1 retrocopy	retro_mmul_858,
Nomascus leucogenys	ENSNLEG00000011587	1 retrocopy	retro_nleu_198,
Oryctolagus cuniculus	ENSOCUG00000025588	1 retrocopy	retro_ocun_1244,
Pan troglodytes	ENSPTRG00000016724	1 retrocopy	retro_ptro_692,