RetrogeneDB ID: retro_dnov_27

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_5826:55964..57080(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000014905
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: TRAM1
• Ensembl ID: ENSDNOG00000009296
• Aliases: None
• Description: translocation associated membrane protein 1 [Source:HGNC Symbol;Acc:20568]

Sequence

>retro_dnov_27
ATGGCAATCCGCAAGAAAAGCACGAAGAACCCCCCAGTCCTCAGCCACGAATTCATCCTGCAGAATCATGCAGACATCGT
CTCCTGTGTGGGGATGGTCTTACTGCTGGGGCTTATGTTCGAGAGAACAGCAGAAGCGTCTATCGTTTTTATAACTCTTC
AGCACAGTGTTACTTTCCCTGCAGCAGAAGAACAAACTACGGAATCAACGTCCCTTTATGGTTATGGTGTCAAAGATTTG
GCCACAGTTTTTTTCTACACGCTAGTGGCAATAATTATGCACGCCACAATTCAGGAGTATGTGTTGGATAAAATTAGCAA
GCTAATGCAATTTCCCAAAACGAAACAAAGCAAATTTAATGAATCTGGTCAGCTTAGTGCATTCTACTTTGTTTCTTGTA
TTTGGGGCACATTCATTCTAATCTCTGAAAACTACATCTCAGATCCAACTCTTTTGTGGAAGGCTCGTCCCCATAACATG
ATGACATTTCAAATGAAGTTTTTCTACATATCACAGTTGGCTTACTGGCTTCATGCTTTCCCTGAACTCTACTTTCAGAA
AATCAAAAAACAAGATATCCCTCGTCAATTTATTTACATTGGGCTTCACCTCTTTCACATTGCTGGAGTTTATCTTTTAT
ATTTGAATCATCTGGGACTTGTTCTTATAATGCTGCATTATTTTGTTGAATTACTTTCCCACATTTGCGGCCTGTTTTAT
TTTCGTGATGAAAATTATCATAAAGGGTATTCTCTGTGGGCAATAGTGTTTATTTTGGGAAGACTTGTGAATTTAATTGT
TTCGGTACTCACTGTTGGCTTTCACCTTGCTAGGGCGGAGACTCAGAAGCAGGATGTCATTACTGGAAACTTCAATGTGT
TGGCTGCTAAAATTGCTGTTCTGTCATCCAGTTGCACTATCCAAGCATACATAACATGGAATTTAATTAATACTCAGCTT
CAGAAGTGGCGGGAAGAGTCTACTTTTCAGGTCCCATGTGCGAAGAAGAAACGGACAACAAGTAAAAGCAGGTCTTCTAG
AAAAGGAATTGAAAATGGAGTGGAAACTTCAAATAGAGCAGATTCTCCCCGGAATAGGAAAGAGAAATGTTCAAAT

Alignment

ORF - retro_dnov_27 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.64 %
• Parental protein coverage: 99.71 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAIRKKSTKSSLVLSHEFILQNHADIVSCVAMVFLLGLMFEITAKASIIFVTLQYNVTLPATEEQATEAA
          MAIRKKSTK...VLSHEFILQNHADIVSCV.MV.LLGLMFE.TA.ASI.F.TLQ..VT.PA.EEQ.TE..
Retrocopy MAIRKKSTKNPPVLSHEFILQNHADIVSCVGMVLLLGLMFERTAEASIVFITLQHSVTFPAAEEQTTEST

Parental  SLYYYGIKDLATVFFYMLVAIIIHAIIQEYVLDKINRRMHFSKTKHSKFNESGQLSAFYLFSCIWGTFIL
          SLY.YG.KDLATVFFY.LVAII.HA.IQEYVLDKI...M.F.KTK.SKFNESGQLSAFY..SCIWGTFIL
Retrocopy SLYGYGVKDLATVFFYTLVAIIMHATIQEYVLDKISKLMQFPKTKQSKFNESGQLSAFYFVSCIWGTFIL

Parental  FSENYISDPTILWRAYPHTLMTXXXXFFYISQLAYWFHAFPELYFQKTKKEDIPRQLVYIGLYLFHIAGA
          .SENYISDPT.LW.A.PH..MT....FFYISQLAYW.HAFPELYFQK.KK.DIPRQ..YIGL.LFHIAG.
Retrocopy ISENYISDPTLLWKARPHNMMTFQMKFFYISQLAYWLHAFPELYFQKIKKQDIPRQFIYIGLHLFHIAGV

Parental  YLLNLNHLGLVLLVLHYFVEFLFHISRLFYFSDEKY-QGFSLWAVLFVLGRLLTLILSVLTVGFGLARAE
          YLL.LNHLGLVL..LHYFVE.L.HI..LFYF.DE.Y..G.SLWA..F.LGRL..LI.SVLTVGF.LARAE
Retrocopy YLLYLNHLGLVLIMLHYFVELLSHICGLFYFRDENYHKGYSLWAIVFILGRLVNLIVSVLTVGFHLARAE

Parental  NQKLDFSTGNFNVLAVRIAVLASICITQAFMMWKFINFQLRRWREHSSFQAPTVKKKPTVTKGRSSRKG
          .QK.D..TGNFNVLA..IAVL.S.C..QA...W..IN.QL..WRE.S.FQ.P..KKK.T..K.RSSRKG
Retrocopy TQKQDVITGNFNVLAAKIAVLSSSCTIQAYITWNLINTQLQKWREESTFQVPCAKKKRTTSKSRSSRKG

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	96.26 RPM
SRP012922_cerebellum	2.20 RPM	11.68 RPM
SRP012922_heart	0.23 RPM	13.92 RPM
SRP012922_kidney	0.55 RPM	41.62 RPM
SRP012922_liver	0.00 RPM	76.47 RPM
SRP012922_lung	0.00 RPM	69.18 RPM
SRP012922_quadricep_muscle	0.00 RPM	15.58 RPM
SRP012922_spleen	0.00 RPM	135.52 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_27 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 25 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006325	1 retrocopy	retro_amel_78,
Bos taurus	ENSBTAG00000007562	1 retrocopy	retro_btau_24,
Canis familiaris	ENSCAFG00000007866	1 retrocopy	retro_cfam_15,
Callithrix jacchus	ENSCJAG00000007893	1 retrocopy	retro_cjac_168,
Dasypus novemcinctus	ENSDNOG00000009296	2 retrocopies	retro_dnov_27 , retro_dnov_906,
Dipodomys ordii	ENSDORG00000001901	1 retrocopy	retro_dord_27,
Equus caballus	ENSECAG00000018378	1 retrocopy	retro_ecab_506,
Echinops telfairi	ENSETEG00000018447	1 retrocopy	retro_etel_674,
Felis catus	ENSFCAG00000028775	1 retrocopy	retro_fcat_136,
Homo sapiens	ENSG00000067167	1 retrocopy	retro_hsap_51,
Loxodonta africana	ENSLAFG00000011625	1 retrocopy	retro_lafr_9,
Macaca mulatta	ENSMMUG00000001516	1 retrocopy	retro_mmul_235,
Monodelphis domestica	ENSMODG00000007316	1 retrocopy	retro_mdom_308,
Mustela putorius furo	ENSMPUG00000010616	1 retrocopy	retro_mputfur_558,
Mus musculus	ENSMUSG00000025935	1 retrocopy	retro_mmus_117,
Nomascus leucogenys	ENSNLEG00000011376	1 retrocopy	retro_nleu_73,
Oryctolagus cuniculus	ENSOCUG00000008734	1 retrocopy	retro_ocun_52,
Otolemur garnettii	ENSOGAG00000006379	1 retrocopy	retro_ogar_2932,
Pongo abelii	ENSPPYG00000018660	1 retrocopy	retro_pabe_169,
Pan troglodytes	ENSPTRG00000020334	1 retrocopy	retro_ptro_2081,
Rattus norvegicus	ENSRNOG00000007892	1 retrocopy	retro_rnor_287,
Sus scrofa	ENSSSCG00000006193	1 retrocopy	retro_sscr_980,
Ictidomys tridecemlineatus	ENSSTOG00000005537	1 retrocopy	retro_itri_38,
Tarsius syrichta	ENSTSYG00000013887	1 retrocopy	retro_tsyr_24,
Tursiops truncatus	ENSTTRG00000000328	1 retrocopy	retro_ttru_24,