RetrogeneDB ID: retro_dnov_361

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_3980:38319..39309(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP5B
• Ensembl ID: ENSDNOG00000011289
• Aliases: None
• Description: ATP synthase subunit beta [Source:UniProtKB/TrEMBL;Acc:Q0QEP6]

Sequence

>retro_dnov_361
CTTGTGAACGTCATTGGAGAACCGGTTGATGAGAAAGCACCCACCAAAACCAAACAATTTGTTGCTATTGACACTGAGGC
TCCTGAGTTCATGGAGATGAGCGTTAAACAAGAAATTCCGATTACTGGCATCAAGATCATGAATCTGCTGCTCCCTATGC
CGAGGGTGGAAAAATTGGACCATTTGGTAATACTGGAGTCAGTAAGACAGTTCTCATCATAGATTTAATCAGCAATGTTG
CCAAAGCCCGTGGTGGTTACTCCATGTTTGCTAGAGTTGGTAAGAAGACCCAGAAGGGCAATGACTTGTACCGTGAAATG
ATTGAGTCTGATGTTGTCAAGTTAAAAGATGCTACTCCAAGGTAGCCTTGGTGTACAGTCAAATGAATGAACCACCTGGT
GTCCATGCCTGTGTAGCTCTGACTGGACTGATGGTGGCTGAATACTTTAGAGTCCAAAAAGATCAAGATGTACTGCTCTT
TATTGATAACATCTTTTGCTTCACCCAGGCAGGCTCAGAGGTGTCTGCCTTATTGGACAGAATCCCCTCTGCTGTTGGCT
TAACAGCCTACACTGGCCGCTGACATAGGTATCATTCAGGAAAGAATTACTACCACCAAGAAGGGATCTATTACCTCTGT
ACAGGCTATCTACGTGCCTGCTAATGGCTTGACTGCCCCTGCCCCTGCCACTACCATTGCCCATTTGGATGCTACCACTG
TGCTGTCCCTTACTATTGATGAGCTGGACATCTATCCAGCTGAGGAGCCTCTGGACTCCACCTCTCACATCATGGATCCC
AGCATTTGTTGGCAGTGAGCATTATGATGTTGCCCATGGGGTGCAAGAAATCCTACAGGACTACAGATTCCTTCAGGACA
TCAGTGCAATCTTGGGTATGGATGAACTTTCTGAGGAAGACAAGTTCATCGTGTCCAATGCATGGAAAATACAGCATTTC
TTTTCTCAGCCATTCCATGTTGCTGAGATC

Alignment

ORF - retro_dnov_361 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.65 %
• Parental protein coverage: 62.5 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  IMNVIGEPIDERGPIKTKQFAAIHAEAPEFMEMSVEQEILVTGIKVVDLL-APYAKGGKIGLFGGAGVGK
          ..NVIGEP.DE..P.KTKQF.AI..EAPEFMEMSV.QEI..TGIK...LL.APYA.GGKIG.FG..GV.K
Retrocopy LVNVIGEPVDEKAPTKTKQFVAIDTEAPEFMEMSVKQEIPITGIKIMNLL<APYAEGGKIGPFGNTGVSK

Parental  TVLIMELINNVAKAHGGYSVFAGVGERTREGNDLYHEMIESGVINLKDAT-SKVALVYGQMNEPPGARAR
          TVLI..LI.NVAKA.GGYS.FA.VG..T..GNDLY.EMIES.V..LKDAT.SKVALVY.QMNEPPG..A.
Retrocopy TVLIIDLISNVAKARGGYSMFARVGKKTQKGNDLYREMIESDVVKLKDAT<SKVALVYSQMNEPPGVHAC

Parental  VALTGLTVAEYFRDQEGQDVLLFIDNIFRFTQAGSEVSALLGRIPSAVGY-QPTLATDMGTMQERITTTK
          VALTGL.VAEYFR.Q..QDVLLFIDNIF.FTQAGSEVSALL.RIPSAVG..QPTLA.D.G..QERITTTK
Retrocopy VALTGLMVAEYFRVQKDQDVLLFIDNIFCFTQAGSEVSALLDRIPSAVGL>QPTLAADIGIIQERITTTK

Parental  KGSITSVQAIYVPADDLTDPAPATTFAHLDATTVLSRAIAELGIYPAVDPLDSTSRIMDPNI-VGSEHYD
          KGSITSVQAIYVPA..LT.PAPATT.AHLDATTVLS..I.EL.IYPA..PLDSTS.IMDP.I.VGSEHYD
Retrocopy KGSITSVQAIYVPANGLTAPAPATTIAHLDATTVLSLTIDELDIYPAEEPLDSTSHIMDPSI>VGSEHYD

Parental  VARGVQKILQDYKSLQDIIAILGMDELSEEDKLTVSRARKIQRFLSQPFQVAEV
          VA.GVQ.ILQDY..LQDI.AILGMDELSEEDK..VS.A.KIQ.F.SQPF.VAE.
Retrocopy VAHGVQEILQDYRFLQDISAILGMDELSEEDKFIVSNAWKIQHFFSQPFHVAEI

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	1924.65 RPM
SRP012922_cerebellum	0.00 RPM	805.16 RPM
SRP012922_heart	0.00 RPM	2616.15 RPM
SRP012922_kidney	0.00 RPM	1516.28 RPM
SRP012922_liver	0.00 RPM	815.68 RPM
SRP012922_lung	0.00 RPM	395.56 RPM
SRP012922_quadricep_muscle	0.00 RPM	2514.05 RPM
SRP012922_spleen	0.00 RPM	445.71 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_361 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 17 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000016752	1 retrocopy	retro_acar_181,
Bos taurus	ENSBTAG00000013315	1 retrocopy	retro_btau_1264,
Choloepus hoffmanni	ENSCHOG00000005350	1 retrocopy	retro_chof_1544,
Callithrix jacchus	ENSCJAG00000033571	2 retrocopies	retro_cjac_1488, retro_cjac_928,
Dasypus novemcinctus	ENSDNOG00000011289	1 retrocopy	retro_dnov_361 ,
Echinops telfairi	ENSETEG00000010208	1 retrocopy	retro_etel_2162,
Homo sapiens	ENSG00000110955	1 retrocopy	retro_hsap_2128,
Gorilla gorilla	ENSGGOG00000011596	1 retrocopy	retro_ggor_1648,
Macropus eugenii	ENSMEUG00000002875	6 retrocopies	retro_meug_1416, retro_meug_1608, retro_meug_411, retro_meug_430, retro_meug_685, retro_meug_908,
Microcebus murinus	ENSMICG00000001084	1 retrocopy	retro_mmur_495,
Macaca mulatta	ENSMMUG00000001027	1 retrocopy	retro_mmul_103,
Pongo abelii	ENSPPYG00000004668	2 retrocopies	retro_pabe_1921, retro_pabe_2032,
Pan troglodytes	ENSPTRG00000005107	1 retrocopy	retro_ptro_1557,
Sus scrofa	ENSSSCG00000000405	1 retrocopy	retro_sscr_453,
Tarsius syrichta	ENSTSYG00000009962	1 retrocopy	retro_tsyr_644,
Tursiops truncatus	ENSTTRG00000002144	1 retrocopy	retro_ttru_371,
Vicugna pacos	ENSVPAG00000004025	2 retrocopies	retro_vpac_405, retro_vpac_562,