RetrogeneDB ID: retro_dnov_2332

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_65008:2640..2990(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GABARAPL2
• Ensembl ID: ENSDNOG00000002240
• Aliases: None
• Description: GABA(A) receptor-associated protein-like 2 [Source:HGNC Symbol;Acc:13291]

Sequence

>retro_dnov_2332
CTGAAGTGGATGTGCACGGAGGACCATCGGTGGAATAAGGCTGCGTGGAATCCGCTAAGATCGGAGCAACAATATCCCGA
CCAGGTTCCGGTGATTGTGGAAAAAGTCTCAGGCTCTCAGCTTGTTCACATTGACAAGCGAAAGTACGTGGTTCCATCTG
ATATCACTGTGGCTCAATTCATGTGGATCATCAGGAAAAGGACCCAGCTTCCTTCTGAAAAGGCAGTCTTCCTGTTTGTG
GATAGGACAGTCCCACAGTCCAGCCTAACCGTGGGACAGCTCTATGAGAAGGAAAAGGATGAAGATGGATTCTCGTATGT
GGCCTACAGCAGGAGAACACTTTTGGCGTC

Alignment

ORF - retro_dnov_2332 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.5 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MKWMFKEDH-SLEHRCVESAKIRA-KYPDRVPVIVEKVSGSQIVDIDKRKYLVPSDITVAQFMWIIRKRI
          .KWM..EDH.S.E..CVESAKI.A..YPD.VPVIVEKVSGSQ.V.IDKRKY.VPSDITVAQFMWIIRKR.
Retrocopy LKWMCTEDH<SVE*GCVESAKIGA>QYPDQVPVIVEKVSGSQLVHIDKRKYVVPSDITVAQFMWIIRKRT

Parental  QLPSEKAIFLFVDKTVPQSSLTMGQLYEKEKDEDGFLYVAYS-GENTFGV
          QLPSEKA.FLFVD.TVPQSSLT.GQLYEKEKDEDGF.YVAYS..ENTFGV
Retrocopy QLPSEKAVFLFVDRTVPQSSLTVGQLYEKEKDEDGFSYVAYS<QENTFGV

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	35.39 RPM
SRP012922_cerebellum	0.00 RPM	99.80 RPM
SRP012922_heart	0.00 RPM	48.96 RPM
SRP012922_kidney	0.00 RPM	65.98 RPM
SRP012922_liver	0.00 RPM	27.25 RPM
SRP012922_lung	0.00 RPM	73.00 RPM
SRP012922_quadricep_muscle	0.00 RPM	90.18 RPM
SRP012922_spleen	0.00 RPM	100.15 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_2332 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 18 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005453	2 retrocopies	retro_amel_1054, retro_amel_1238,
Canis familiaris	ENSCAFG00000031455	1 retrocopy	retro_cfam_639,
Callithrix jacchus	ENSCJAG00000014253	1 retrocopy	retro_cjac_146,
Dasypus novemcinctus	ENSDNOG00000002240	2 retrocopies	retro_dnov_1755, retro_dnov_2332 ,
Dasypus novemcinctus	ENSDNOG00000010228	7 retrocopies	retro_dnov_1008, retro_dnov_1024, retro_dnov_1335, retro_dnov_165, retro_dnov_2435, retro_dnov_2604, retro_dnov_913,
Erinaceus europaeus	ENSEEUG00000011134	1 retrocopy	retro_eeur_337,
Homo sapiens	ENSG00000034713	1 retrocopy	retro_hsap_4115,
Gorilla gorilla	ENSGGOG00000012299	2 retrocopies	retro_ggor_2761, retro_ggor_342,
Loxodonta africana	ENSLAFG00000017065	2 retrocopies	retro_lafr_234, retro_lafr_543,
Microcebus murinus	ENSMICG00000011981	1 retrocopy	retro_mmur_1473,
Myotis lucifugus	ENSMLUG00000015112	1 retrocopy	retro_mluc_1207,
Macaca mulatta	ENSMMUG00000005759	2 retrocopies	retro_mmul_2369, retro_mmul_540,
Mustela putorius furo	ENSMPUG00000009894	1 retrocopy	retro_mputfur_993,
Mus musculus	ENSMUSG00000031950	5 retrocopies	retro_mmus_2637, retro_mmus_2655, retro_mmus_3240, retro_mmus_456, retro_mmus_506,
Nomascus leucogenys	ENSNLEG00000013048	2 retrocopies	retro_nleu_1560, retro_nleu_580,
Pongo abelii	ENSPPYG00000007565	2 retrocopies	retro_pabe_3368, retro_pabe_372,
Pan troglodytes	ENSPTRG00000008362	2 retrocopies	retro_ptro_250, retro_ptro_2794,
Rattus norvegicus	ENSRNOG00000019425	1 retrocopy	retro_rnor_57,