RetrogeneDB ID: retro_dnov_322

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_3602:266512..267077(-)
• Located in intron of: ENSDNOG00000013864

Retrocopy information

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

Parental gene information

• Parental gene symbol: PNP
• Ensembl ID: ENSDNOG00000011630
• Aliases: None
• Description: purine nucleoside phosphorylase [Source:HGNC Symbol;Acc:7892]

Sequence

>retro_dnov_322
TGGAGGGTAAGGTTACTAGTGAGGGTTCTCCAGCTTATGGGTGTGGTATCCTAGTGTTCACCAGCGCAGCTGGAGGGCTC
AACCCCAAGGTGGGGACTGGAGATGTCACGCTGACCTGTGATCACATCAACATGCCTGGTTTCTCTCGCCAGAACTCACT
CAGAGGGCCCAATGACAAAAGGTTTAGTGATTGTTTTCCCTCCACCTGTGATGCCTATGACCATAATCTGAGGCAGAAGG
CTTATAGTGCCTGGAAACAAATGCGCGAGCAGTGAGAACTATGGGAAGGCATCTATGTGATGCTCCGTGGCCTAAGTTTG
AGACCATTGCAGAGTGTCATCTGCTACAGAAGCTGGGACTGATGCTGTTGGAATAAGTACAGTACCAAAAGTTATAGTTG
CATGGCACTATGAACTCTGAGTTTTTGGCTTCTCCCTCATCACTAACAAGGTTATCCTGAATTATGAAAGCTTAGAGATG
GCTGACCATGAGGAAGTACCAGAGGCTGGGAAACAAGCTGCACAGAAATTGGAACAGTTTTGTTTTTATTCTTATGGCTA
GCATT

Alignment

ORF - retro_dnov_322 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.91 %
• Parental protein coverage: 65.4 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  FKVTFPVRVFRLMGVDT-LVVTNAAGGLNPKFEVGDIMLIRDHINMPGFSGQNPLRGPNEERFGDRFPAM
          ..V...VRV..LMGV...LV.T.AAGGLNPK...GD..L..DHINMPGFS.QN.LRGPN..RF.D.FP..
Retrocopy WRVRLLVRVLQLMGVVS<LVFTSAAGGLNPKVGTGDVTLTCDHINMPGFSRQNSLRGPNDKRFSDCFPST

Parental  SDAYDRNLRKEAHCAWKRMGEERELQEGTYVMLGGLN-FETIAECRLLQKL-GADAVGMSTVPEVIVARH
          .DAYD.NLR..A..AWK.M.E..EL.EG.YVML.GL..FETIAEC.LLQKL.G.DAVG.STVP.VIVA.H
Retrocopy CDAYDHNLRQKAYSAWKQMREQ*ELWEGIYVMLRGLS<FETIAECHLLQKL<GTDAVGISTVPKVIVAWH

Parental  CGLRVFGFSLITNKVTLSYESLEKANHEEVLEAGKQAARKLEQ-FVSLLMASI
          ..L.VFGFSLITNKV.L.YESLE.A.HEEV.EAGKQAA.KLEQ.FV..LMASI
Retrocopy YEL*VFGFSLITNKVILNYESLEMADHEEVPEAGKQAAQKLEQ>FVFILMASI

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	52.90 RPM
SRP012922_cerebellum	0.00 RPM	10.86 RPM
SRP012922_heart	0.00 RPM	6.03 RPM
SRP012922_kidney	0.00 RPM	176.32 RPM
SRP012922_liver	0.00 RPM	24.92 RPM
SRP012922_lung	0.00 RPM	37.42 RPM
SRP012922_quadricep_muscle	0.00 RPM	3.98 RPM
SRP012922_spleen	0.11 RPM	29.07 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_322 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 20 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005373	1 retrocopy	retro_amel_1666,
Bos taurus	ENSBTAG00000012317	1 retrocopy	retro_btau_1463,
Choloepus hoffmanni	ENSCHOG00000009274	5 retrocopies	retro_chof_1328, retro_chof_1595, retro_chof_1827, retro_chof_1933, retro_chof_348,
Callithrix jacchus	ENSCJAG00000009676	2 retrocopies	retro_cjac_1195, retro_cjac_1511,
Dasypus novemcinctus	ENSDNOG00000011630	1 retrocopy	retro_dnov_322 ,
Erinaceus europaeus	ENSEEUG00000002411	1 retrocopy	retro_eeur_541,
Felis catus	ENSFCAG00000006934	1 retrocopy	retro_fcat_1368,
Homo sapiens	ENSG00000198805	1 retrocopy	retro_hsap_2282,
Gorilla gorilla	ENSGGOG00000002126	1 retrocopy	retro_ggor_1695,
Macropus eugenii	ENSMEUG00000014512	3 retrocopies	retro_meug_1282, retro_meug_1560, retro_meug_211,
Macaca mulatta	ENSMMUG00000019126	1 retrocopy	retro_mmul_287,
Mustela putorius furo	ENSMPUG00000018119	2 retrocopies	retro_mputfur_420, retro_mputfur_822,
Nomascus leucogenys	ENSNLEG00000010969	1 retrocopy	retro_nleu_1964,
Otolemur garnettii	ENSOGAG00000013344	4 retrocopies	retro_ogar_1631, retro_ogar_2141, retro_ogar_3083, retro_ogar_594,
Pongo abelii	ENSPPYG00000005567	1 retrocopy	retro_pabe_1938,
Pan troglodytes	ENSPTRG00000006095	1 retrocopy	retro_ptro_1616,
Pteropus vampyrus	ENSPVAG00000010734	1 retrocopy	retro_pvam_1302,
Rattus norvegicus	ENSRNOG00000009982	1 retrocopy	retro_rnor_891,
Tupaia belangeri	ENSTBEG00000016378	1 retrocopy	retro_tbel_4632,
Tarsius syrichta	ENSTSYG00000000748	3 retrocopies	retro_tsyr_2057, retro_tsyr_2127, retro_tsyr_235,