RetrogeneDB ID: retro_dnov_217

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_271:242429..242794(-)
• Located in intron of: ENSDNOG00000009371

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAP1B
• Ensembl ID: ENSDNOG00000019724
• Aliases: None
• Description: RAP1B, member of RAS oncogene family [Source:HGNC Symbol;Acc:9857]

Sequence

>retro_dnov_217
GTGCGCGAGTGCAAGCTAATAGTCTTTGGTTCAGGGGGCGTGGGGAAGTCTGCTTTGACAGGTCAATTTATTCAGGGAAT
TTTTGTTGAAAAACATGATCTAGCAATAGAAGAATCCTACAGAAAGCAAGCTGAAGTGGAATGTCAACAGCGTACACTTG
AAATCCTGGACAGAGCAGTGACAGAACAATTTACAGTGATGAGGGATTTGAATATGAAGAATGGCCAAGGGTTTGCACTA
GTATATTCAATTACAGCTCAGTCCATACTTAATGACTTATAGGACCTGAGGGAACAGACTTTATGGGTTAAGGACACAGA
AGATGTGCCATGATTTTGGTTGGCAAAAAATGTGACCTGGAAGAG

Alignment

ORF - retro_dnov_217 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.61 %
• Parental protein coverage: 78.06 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MREYKLVVLGSGGVGKSALTVQFVQGIFVEKYDPTIEDSYRKQVEVDAQQCMLEILDTAGTEQFTAMRDL
          .RE.KL.V.GSGGVGKSALT.QF.QGIFVEK.D..IE.SYRKQ.EV..QQ..LEILD.A.TEQFT.MRDL
Retrocopy VRECKLIVFGSGGVGKSALTGQFIQGIFVEKHDLAIEESYRKQAEVECQQRTLEILDRAVTEQFTVMRDL

Parental  YMKNGKGFALVYSITAQSTFNDLQDLREQIL-RKDTDDVP-MILVGNKCDLED
          .MKNG.GFALVYSITAQS..NDL.DLREQ.L..KDT.DVP.MILVG.KCDLE.
Retrocopy NMKNGQGFALVYSITAQSILNDL*DLREQTLWVKDTEDVP<MILVGKKCDLEE

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	0.19 RPM	6.81 RPM
SRP012922_cerebellum	0.00 RPM	1.92 RPM
SRP012922_heart	0.00 RPM	1.16 RPM
SRP012922_kidney	0.00 RPM	4.38 RPM
SRP012922_liver	0.00 RPM	4.33 RPM
SRP012922_lung	0.15 RPM	8.25 RPM
SRP012922_quadricep_muscle	0.00 RPM	1.38 RPM
SRP012922_spleen	0.00 RPM	15.68 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_217 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 19 parental genes, and 57 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008637	1 retrocopy	retro_amel_103,
Cavia porcellus	ENSCPOG00000008272	4 retrocopies	retro_cpor_1194, retro_cpor_632, retro_cpor_739, retro_cpor_85,
Dasypus novemcinctus	ENSDNOG00000007809	5 retrocopies	retro_dnov_101, retro_dnov_1617, retro_dnov_1764, retro_dnov_628, retro_dnov_94,
Dasypus novemcinctus	ENSDNOG00000015293	3 retrocopies	retro_dnov_1358, retro_dnov_154, retro_dnov_2354,
Dasypus novemcinctus	ENSDNOG00000017413	1 retrocopy	retro_dnov_573,
Dasypus novemcinctus	ENSDNOG00000019724	18 retrocopies	retro_dnov_1243, retro_dnov_1249, retro_dnov_1323, retro_dnov_1395, retro_dnov_1574, retro_dnov_1710, retro_dnov_1763, retro_dnov_1841, retro_dnov_186, retro_dnov_1976, retro_dnov_2033, retro_dnov_217 , retro_dnov_2679, retro_dnov_298, retro_dnov_318, retro_dnov_719, retro_dnov_761, retro_dnov_84,
Erinaceus europaeus	ENSEEUG00000010052	1 retrocopy	retro_eeur_327,
Echinops telfairi	ENSETEG00000000242	1 retrocopy	retro_etel_11,
Gorilla gorilla	ENSGGOG00000025649	1 retrocopy	retro_ggor_2836,
Loxodonta africana	ENSLAFG00000016460	1 retrocopy	retro_lafr_482,
Microcebus murinus	ENSMICG00000013148	1 retrocopy	retro_mmur_116,
Macaca mulatta	ENSMMUG00000011442	2 retrocopies	retro_mmul_1151, retro_mmul_1863,
Oryctolagus cuniculus	ENSOCUG00000029552	5 retrocopies	retro_ocun_1132, retro_ocun_1200, retro_ocun_597, retro_ocun_636, retro_ocun_796,
Otolemur garnettii	ENSOGAG00000005746	2 retrocopies	retro_ogar_2260, retro_ogar_272,
Pongo abelii	ENSPPYG00000004751	1 retrocopy	retro_pabe_3403,
Pan troglodytes	ENSPTRG00000005197	3 retrocopies	retro_ptro_1812, retro_ptro_2383, retro_ptro_2877,
Rattus norvegicus	ENSRNOG00000007048	4 retrocopies	retro_rnor_2479, retro_rnor_870, retro_rnor_871, retro_rnor_872,
Sus scrofa	ENSSSCG00000021148	1 retrocopy	retro_sscr_1125,
Sus scrofa	ENSSSCG00000030014	2 retrocopies	retro_sscr_435, retro_sscr_909,