RetrogeneDB ID: retro_dnov_2505

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_8105:88532..89070(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL8
• Ensembl ID: ENSDNOG00000009300
• Aliases: None
• Description: ribosomal protein L8 [Source:HGNC Symbol;Acc:10368]

Sequence

>retro_dnov_2505
CAGGTGGTCTTCTACGACCTGGGCAGGTTTAAGAAGTGGATGGAGATGTTCATTGCCACCAATGAATTCACGTGGGCCAG
TGCCTGTACTGTGTACTGGAGGCCCAGCTCGACATCATCAAAGTCTTCTTAGAGGGCACCATGCCCAAGGTCACTGCTGC
GTGCTGCTTGGAGAAGCCTGGTAAACTGGACAAGCTGGCCTCGGTCTCTAGGAATTAAGCCATCATCGTCTCCCACAACC
CTGAGACTGGGAAGACCCACATGAAGCTGCCCTTGGGTTTCAAGGAGGTCGTCTCCTCAGCAAAATAGCAGAAGGTGGGC
ATGGTAGCTGGTGTTGACTTCATTGATAAACCCATACTGAAGTTGGATGTAGCCTACCATAAGTACGAGGGCAAAGAAGA
AGTGCTGGCTGTGCATGTGGGTTGTGGTCATGAAACTTGTGAAACATCGCCTTCGGAGGCGGCAACCACTATTTCATTGG
CAAACTTTCCGTCATCTGCTGAGATGCGCTTGCCAGTAGCCATGTGCATCTCATTTCT

Alignment

ORF - retro_dnov_2505 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.64 %
• Parental protein coverage: 70.04 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KVVFRDPYRFKKRTELFIAAEG-IHTGQFVYCGKKAQLNIGNVLPVGTMPEGTIVCCLEEKPGDRGKLAR
          .VVF.D..RFKK..E.FIA....IH.GQ..YC...AQL.I..V...GTMP..T..CCLE.KPG...KLA.
Retrocopy QVVFYDLGRFKKWMEMFIATNE<IHVGQCLYCVLEAQLDIIKVFLEGTMPKVTAACCLE-KPGKLDKLAS

Parental  ASGNYATVISHNPETKKTRVKLPSGSKKVISSANRAVVGVVAGGGRIDKPILKAGRAYHKY-KAKRNCWP
          .S.N.A...SHNPET.KT..KLP.G.K.V.SSA....VG.VAG...IDKPILK...AYHKY..AK..CW.
Retrocopy VSRN*AIIVSHNPETGKTHMKLPLGFKEVVSSAK*QKVGMVAGVDFIDKPILKLDVAYHKY>RAKKKCWL

Parental  RVRGVAMNPVEH-PFGGGNHQHIGKPSTIRRDAPAGRKVGLIA
          ....V.M..V.H..FGGGNH..IGK.S.I..DA.A...V.LI.
Retrocopy CMWVVVMKLVKH>AFGGGNHYFIGKLSVIC*DALASSHVHLIS

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	779.43 RPM
SRP012922_cerebellum	0.00 RPM	331.85 RPM
SRP012922_heart	0.00 RPM	344.33 RPM
SRP012922_kidney	0.00 RPM	738.97 RPM
SRP012922_liver	0.00 RPM	407.92 RPM
SRP012922_lung	0.00 RPM	848.69 RPM
SRP012922_quadricep_muscle	0.00 RPM	591.08 RPM
SRP012922_spleen	0.00 RPM	1161.44 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_2505 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
Anolis carolinensis	ENSACAG00000017933	1 retrocopy	retro_acar_31,
Ailuropoda melanoleuca	ENSAMEG00000005395	1 retrocopy	retro_amel_241,
Bos taurus	ENSBTAG00000026327	1 retrocopy	retro_btau_96,
Canis familiaris	ENSCAFG00000001677	1 retrocopy	retro_cfam_1132,
Callithrix jacchus	ENSCJAG00000021388	4 retrocopies	retro_cjac_1109, retro_cjac_1169, retro_cjac_1579, retro_cjac_2047,
Cavia porcellus	ENSCPOG00000003854	2 retrocopies	retro_cpor_1006, retro_cpor_1415,
Dasypus novemcinctus	ENSDNOG00000009300	2 retrocopies	retro_dnov_2505 , retro_dnov_503,
Echinops telfairi	ENSETEG00000007104	4 retrocopies	retro_etel_1100, retro_etel_264, retro_etel_296, retro_etel_916,
Felis catus	ENSFCAG00000026288	1 retrocopy	retro_fcat_570,
Homo sapiens	ENSG00000161016	1 retrocopy	retro_hsap_2851,
Gorilla gorilla	ENSGGOG00000008164	1 retrocopy	retro_ggor_1974,
Macaca mulatta	ENSMMUG00000013379	2 retrocopies	retro_mmul_1470, retro_mmul_1531,
Mustela putorius furo	ENSMPUG00000006022	1 retrocopy	retro_mputfur_1517,
Mus musculus	ENSMUSG00000003970	2 retrocopies	retro_mmus_2004, retro_mmus_2112,
Nomascus leucogenys	ENSNLEG00000010952	2 retrocopies	retro_nleu_1603, retro_nleu_594,
Oryctolagus cuniculus	ENSOCUG00000024716	1 retrocopy	retro_ocun_146,
Pan troglodytes	ENSPTRG00000020716	1 retrocopy	retro_ptro_1931,
Rattus norvegicus	ENSRNOG00000048523	2 retrocopies	retro_rnor_122, retro_rnor_239,
Tupaia belangeri	ENSTBEG00000010363	2 retrocopies	retro_tbel_2826, retro_tbel_3453,
Tursiops truncatus	ENSTTRG00000013858	1 retrocopy	retro_ttru_1147,