RetrogeneDB ID: retro_dnov_1771

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_2928:11942..12438(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB28
• Ensembl ID: ENSDNOG00000007750
• Aliases: None
• Description: RAB28, member RAS oncogene family [Source:HGNC Symbol;Acc:9768]

Sequence

>retro_dnov_1771
ATGTCGGACTCTGAGAAAGAGAGCCAGGACCGGCAACTGAAAATCGTCGTGCTGGGGGACGGCACCTCCCGAGAAGACCT
CCTAGCTACGTGTTTTGCTCAAGAAACTTTTGGGAAAACAGTACAAACAAACTATAGGACTGGATTTCTTTTTGAGAAGG
ATAACATTGCCAGGAAACTTGAATGTTACTCTTCAAGTTTGGGATATAGGAGGGCAGACAATAGGAGGGAAGATGTTGGA
GAAATATATCTATGGAGCACAGGGAATCCTCTTGGTATATGATATTACAAATTATCAAAGCTTTGAGAATTTAGGAGACT
GGTATACTGTGGTGAAGAAAGTAAGTGAGGAATCAGAAACTCAGCCACTGGTTGCCTTGGTGGGCAATAAAATTGATTTG
GAGCATATGCGTACAGTAAAACCTGAAAAACACTTAAGGTTTTGCCAGGAAAATGGTTTTAGTAGCCACTTTGTCTCAGC
CAAGACAGGAGACTCT

Alignment

ORF - retro_dnov_1771 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.18 %
• Parental protein coverage: 74.66 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSDSEEESQDRQLKIVVLGDGTSGKTSLATCFAQETFGK-QYKQTIGLDFFLRRITLPGNLNVTLQVWDI
          MSDSE.ESQDRQLKIVVLGDGTS....LATCFAQETFGK.QYKQTIGLDFFLRRITLPGNLNVTLQVWDI
Retrocopy MSDSEKESQDRQLKIVVLGDGTSREDLLATCFAQETFGK>QYKQTIGLDFFLRRITLPGNLNVTLQVWDI

Parental  GGQTIGGKMLDKYIYGAQGILLVYDITNYQSFENLEDWYTVVKKVSEESETQPLVALVGNKIDLEHMRTV
          GGQTIGGKML.KYIYGAQGILLVYDITNYQSFENL.DWYTVVKKVSEESETQPLVALVGNKIDLEHMRTV
Retrocopy GGQTIGGKMLEKYIYGAQGILLVYDITNYQSFENLGDWYTVVKKVSEESETQPLVALVGNKIDLEHMRTV

Parental  KPEKHLRFCQENGFSSHFVSAKTGDS
          KPEKHLRFCQENGFSSHFVSAKTGDS
Retrocopy KPEKHLRFCQENGFSSHFVSAKTGDS

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	3.50 RPM	20.42 RPM
SRP012922_cerebellum	3.16 RPM	15.12 RPM
SRP012922_heart	6.26 RPM	28.31 RPM
SRP012922_kidney	5.48 RPM	21.63 RPM
SRP012922_liver	2.63 RPM	13.78 RPM
SRP012922_lung	5.19 RPM	25.50 RPM
SRP012922_quadricep_muscle	7.44 RPM	39.64 RPM
SRP012922_spleen	6.07 RPM	25.41 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_1771 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 16 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001523	1 retrocopy	retro_chof_1365,
Callithrix jacchus	ENSCJAG00000012136	2 retrocopies	retro_cjac_2713, retro_cjac_4126,
Dasypus novemcinctus	ENSDNOG00000007750	4 retrocopies	retro_dnov_1426, retro_dnov_1771 , retro_dnov_2419, retro_dnov_381,
Dipodomys ordii	ENSDORG00000012378	1 retrocopy	retro_dord_682,
Homo sapiens	ENSG00000157869	7 retrocopies	retro_hsap_4166, retro_hsap_4259, retro_hsap_4261, retro_hsap_4263, retro_hsap_4265, retro_hsap_4317, retro_hsap_4762,
Gorilla gorilla	ENSGGOG00000024190	1 retrocopy	retro_ggor_2966,
Macropus eugenii	ENSMEUG00000006792	4 retrocopies	retro_meug_1079, retro_meug_1182, retro_meug_1510, retro_meug_913,
Macaca mulatta	ENSMMUG00000022025	1 retrocopy	retro_mmul_1172,
Nomascus leucogenys	ENSNLEG00000016243	1 retrocopy	retro_nleu_2292,
Pongo abelii	ENSPPYG00000014610	1 retrocopy	retro_pabe_3707,
Pan troglodytes	ENSPTRG00000015920	2 retrocopies	retro_ptro_2893, retro_ptro_3171,
Rattus norvegicus	ENSRNOG00000017074	1 retrocopy	retro_rnor_1075,
Sarcophilus harrisii	ENSSHAG00000009274	1 retrocopy	retro_shar_602,
Sus scrofa	ENSSSCG00000022358	2 retrocopies	retro_sscr_482, retro_sscr_514,
Ictidomys tridecemlineatus	ENSSTOG00000004135	1 retrocopy	retro_itri_27,
Tarsius syrichta	ENSTSYG00000010939	2 retrocopies	retro_tsyr_1450, retro_tsyr_1750,