RetrogeneDB ID: retro_dnov_756

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_105075:885..1375(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AKTIP
• Ensembl ID: ENSDNOG00000004906
• Aliases: None
• Description: AKT interacting protein [Source:HGNC Symbol;Acc:16710]

Sequence

>retro_dnov_756
TATGGACTCTATCAAGATGGTGTGTTTCAGTTTACAGATTATATGTTTGATAACTACCCAGATGATAACTGTCCACCCTT
GGGGTTTGATATTCCCACCTTTCACTGGCTAGTTGATTCCCACCTCAGGTCAGCTGCTGTGAAGAGAGCATTTGCAAAAT
GGAGGCAGAACCATAATCATATTTGGCAAGTATTAATGTATGTAAAGAGAGTTTCCTACAAGATTGCTTCAGCAAGGCCC
CTAAACCCAGAGGTTGCAGTACTGTATGAAAATGATGTTCAGCTCTTTAAAAATAAAGTACTTGACATGTTAAGGCATGC
ACTGCTCATTTGTTCACCAACCTAAATAAATAAATAAGGAGACCCTATTCAATTACCTTCTCTCCATGGAATCCTTCTGT
ACATGATGAAGCCAGAGAGAAGTGCTGACTCAGAAAAAGCCTAAAAAAGATCACAATAAAAGTGTTTATGTTGCTGGCTT
GTCGTTGGTA

Alignment

ORF - retro_dnov_756 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.02 %
• Parental protein coverage: 56.25 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  HGLYQDGVFKFTVYIPDNYPDGDCPRLVFDIPVFHPLVD-PTSGEL-DVKRAFAKWRRNHNHIWQVLMYA
          .GLYQDGVF.FT.Y..DNYPD..CP.L.FDIP.FH.LVD.PTSG.L..VKRAFAKWR.NHNHIWQVLMY.
Retrocopy YGLYQDGVFQFTDYMFDNYPDDNCPPLGFDIPTFHWLVD>PTSGQL<AVKRAFAKWRQNHNHIWQVLMYV

Parental  RRVFYKIDTASPLNPEAAVLYEKDVQLFKSKVVD-SVKVCTARLFDQPK--IEDPYAISFSPWNPSVHDE
          .RV.YKI..A.PLNPE.AVLYE.DVQLFK.KV.D..VK.CTA.LF......I..PY.I.FSPWNPSVHDE
Retrocopy KRVSYKIASARPLNPEVAVLYENDVQLFKNKVLD<HVKACTAHLFTNLNK*IRRPYSITFSPWNPSVHDE

Parental  AREK-MLTQKKPEEQHNKSVHVAGLSWV
          AREK..LTQKKP...HNKSV.VAGLS.V
Retrocopy AREK<VLTQKKPKKDHNKSVYVAGLSLV

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	33.84 RPM
SRP012922_cerebellum	0.00 RPM	49.63 RPM
SRP012922_heart	0.00 RPM	27.84 RPM
SRP012922_kidney	0.00 RPM	47.37 RPM
SRP012922_liver	0.00 RPM	16.56 RPM
SRP012922_lung	0.00 RPM	44.44 RPM
SRP012922_quadricep_muscle	0.00 RPM	56.77 RPM
SRP012922_spleen	0.00 RPM	26.55 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_756 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 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016345	1 retrocopy	retro_amel_392,
Canis familiaris	ENSCAFG00000009500	1 retrocopy	retro_cfam_1826,
Choloepus hoffmanni	ENSCHOG00000013690	2 retrocopies	retro_chof_2533, retro_chof_629,
Callithrix jacchus	ENSCJAG00000001498	1 retrocopy	retro_cjac_2895,
Cavia porcellus	ENSCPOG00000006523	1 retrocopy	retro_cpor_622,
Dasypus novemcinctus	ENSDNOG00000004906	4 retrocopies	retro_dnov_1376, retro_dnov_1776, retro_dnov_2080, retro_dnov_756 ,
Equus caballus	ENSECAG00000020381	1 retrocopy	retro_ecab_504,
Homo sapiens	ENSG00000166971	2 retrocopies	retro_hsap_1458, retro_hsap_3152,
Gorilla gorilla	ENSGGOG00000014821	1 retrocopy	retro_ggor_1122,
Microcebus murinus	ENSMICG00000010810	3 retrocopies	retro_mmur_124, retro_mmur_333, retro_mmur_985,
Microcebus murinus	ENSMICG00000016793	1 retrocopy	retro_mmur_1191,
Monodelphis domestica	ENSMODG00000025788	1 retrocopy	retro_mdom_1881,
Nomascus leucogenys	ENSNLEG00000001106	1 retrocopy	retro_nleu_2660,
Otolemur garnettii	ENSOGAG00000014495	1 retrocopy	retro_ogar_365,
Oryzias latipes	ENSORLG00000013747	1 retrocopy	retro_olat_30,
Pongo abelii	ENSPPYG00000007351	2 retrocopies	retro_pabe_1204, retro_pabe_1205,
Pan troglodytes	ENSPTRG00000008116	1 retrocopy	retro_ptro_2282,
Rattus norvegicus	ENSRNOG00000011956	1 retrocopy	retro_rnor_1611,
Tupaia belangeri	ENSTBEG00000017105	5 retrocopies	retro_tbel_1063, retro_tbel_2864, retro_tbel_3350, retro_tbel_4130, retro_tbel_853,
Tursiops truncatus	ENSTTRG00000012705	1 retrocopy	retro_ttru_348,