RetrogeneDB ID: retro_dnov_284

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_3261:28365..29131(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PAICS
• Ensembl ID: ENSDNOG00000013413
• Aliases: None
• Description: phosphoribosylaminoimidazole carboxylase, phosphoribosylaminoimidazole succinocarboxamide synthetase [Source:HGNC Symbol;Acc:8587]

Sequence

>retro_dnov_284
GATGATGCTGATATTGATCCACGGTGGTATCAGAAACAGCTAATTGCTGCAAAATTTTGCTTGGCTGAACTAGTTAAAAG
CAAACTGAAGTGGATATCATGTGTCATGCTACACAGGCAATTTCTAACGTTCTGGAAAAATCTTGGTTGCCACAGAACTG
CGTACTGTTTGATATGAAGATTGAATTCAGTGTTAATGTAACCACCAAAGAAATTGTTCTTGTTGATGTTATTGATGATG
GTTCCTGGAGACTCTGACCATCAGGAGATTGAAGCCCTCAAAAAGATAAGCAGTCTTATCATGATGTGAAGAAACTAACT
CCTGATGGACTCCAGGTGATAAAGAAATTTTTGAGTGGGTTGCTGAGTAAAGTTGTTTCTGAAATCAGAAAATCAGTGCA
TGACTGTAGTACTGAGGGCCCAACTTCTGATCTTAGTCACTATGAAAAAATCAAGAAGCCATGTGTAAATTTTGGCATTC
TATGTGAACTTTGGTAATCTCTGCCCATAAAAGACCATATGAAACTCTGAGGACTAAAGTCAAATATGAAGCAAAGGGAA
TGGTATTCCTACTGTCTGTGGCAGTAGCAGGCAGAAGGAATGATTTAGAGCTAGTATTGTCTGGTAACACTGCATATCCA
GTTATCAGTTGTCCTTCCCTCACACAAGACTGGGGAGCTCAGGATGTGTGGTCTTCTCTTCAAATACCCAGTAGTCTTGG
TTGTTTGACAATACTTTCTTCAGAAGGTTCAGCTCAGTGAGCTAGC

Alignment

ORF - retro_dnov_284 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.79 %
• Parental protein coverage: 57.14 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  DDANNDPQWSEEQLIAAKFCFAGLVIG-QTEVDIMSHATQAIFEILEKSWLSQNCALVDMKIEFGVNITS
          DDA..DP.W...QLIAAKFC.A.LV...QTEVDIM.HATQAI...LEKSWL.QNC.L.DMKIEF.VN.T.
Retrocopy DDADIDPRWYQKQLIAAKFCLAELVKS<QTEVDIMCHATQAISNVLEKSWLPQNCVLFDMKIEFSVNVTT

Parental  KEIVLADVIDNDSWRLWPSGDRSQQKDKQLYRDLKEVTPEGLQMVKK-NFEWVAD-RQLLLRSESRCRVV
          KEIVL.DVID..SWRL.PSGD.S.QKDKQ.Y.D.K..TP.GLQ..KK..FEWVA....L.L.SE..C..V
Retrocopy KEIVLVDVIDDGSWRL*PSGD*SPQKDKQSYHDVKKLTPDGLQVIKK<IFEWVAE<VKLFLKSENQCMTV

Parental  VLM-GSTSDLGHCEKIKKACGNFGIPCEL-RVTSAHKGPDQTLRIKAEYEG-GCIRTVFVAVAGRSNGLG
          VL..G.TSDL.H.EKIKK.C.NFGI.CEL..V.SAHK.P..TLR.K..YE..G......VAVAGR.N.L.
Retrocopy VLR<GPTSDLSHYEKIKKPCVNFGILCEL<LVISAHKRPYETLRTKVKYEAKGMVFLLSVAVAGRRNDLE

Parental  PVLSGNTAYPVINCPPLTPEWGAQDVWSSLRLPSGLGCSTILSPEGSAQFAA
          .VLSGNTAYPVI.CP.LT..WGAQDVWSSL..PS.LGC.TILS.EGSAQ.A.
Retrocopy LVLSGNTAYPVISCPSLTQDWGAQDVWSSLQIPSSLGCLTILSSEGSAQ*AS

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	88.29 RPM
SRP012922_cerebellum	0.00 RPM	50.31 RPM
SRP012922_heart	0.00 RPM	46.64 RPM
SRP012922_kidney	0.00 RPM	110.07 RPM
SRP012922_liver	0.00 RPM	140.25 RPM
SRP012922_lung	0.00 RPM	83.54 RPM
SRP012922_quadricep_muscle	0.00 RPM	52.27 RPM
SRP012922_spleen	0.00 RPM	100.73 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_284 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 15 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010577	1 retrocopy	retro_btau_508,
Cavia porcellus	ENSCPOG00000010749	1 retrocopy	retro_cpor_969,
Dasypus novemcinctus	ENSDNOG00000013413	1 retrocopy	retro_dnov_284 ,
Echinops telfairi	ENSETEG00000015242	2 retrocopies	retro_etel_1918, retro_etel_341,
Homo sapiens	ENSG00000128050	3 retrocopies	retro_hsap_3802, retro_hsap_3915, retro_hsap_3927,
Gorilla gorilla	ENSGGOG00000024392	1 retrocopy	retro_ggor_2643,
Mus musculus	ENSMUSG00000029247	6 retrocopies	retro_mmus_1748, retro_mmus_2750, retro_mmus_2858, retro_mmus_3126, retro_mmus_653, retro_mmus_971,
Nomascus leucogenys	ENSNLEG00000008786	2 retrocopies	retro_nleu_1274, retro_nleu_2156,
Otolemur garnettii	ENSOGAG00000003575	2 retrocopies	retro_ogar_2138, retro_ogar_865,
Procavia capensis	ENSPCAG00000008531	1 retrocopy	retro_pcap_172,
Pan troglodytes	ENSPTRG00000016081	2 retrocopies	retro_ptro_2662, retro_ptro_2670,
Rattus norvegicus	ENSRNOG00000002101	3 retrocopies	retro_rnor_1891, retro_rnor_2768, retro_rnor_804,
Tupaia belangeri	ENSTBEG00000006751	1 retrocopy	retro_tbel_3697,
Tarsius syrichta	ENSTSYG00000010497	2 retrocopies	retro_tsyr_2170, retro_tsyr_329,
Drosophila melanogaster	FBgn0020513	1 retrocopy	retro_dmel_82,