RetrogeneDB ID: retro_dnov_2542

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_84148:2756..3185(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RHEB
• Ensembl ID: ENSDNOG00000016493
• Aliases: None
• Description: Ras homolog enriched in brain [Source:HGNC Symbol;Acc:10011]

Sequence

>retro_dnov_2542
ACTTTTACAAAACTGATCACAGTAAATGGACAAGAGTATCATCTTCAACTTGTGGACACAGCTGGACAAGATGAATATTC
CATCTTTCCTCAGACATACTCCATAGATATTAATGGTTATATTCTTGTGTACTCTGTTACATCAATCAAAAGCTTTGAAG
TGATTAAAGTTATCCATGGCAAATTGTTGGATATGGTGGGGGAAGTTCAAATACCTATTATGTTGGTTGGGAGTAAGAAA
GACTTACATATGGAAAGGGTGATCAGTTATGAAGAAGGGCAAGCATTAGCAGAATCTTGGAATGCAGCTTTTTTGGAATC
TTCTGCTAAAGAAAATCAGACTGCTGTTGACATTTTTAGAAGGATAATTTTGGAGGCTGAAAAAATTGATGGGGCAGCTT
CACAAGGAAAGTCTTCATGCTCAGTGATG

Alignment

ORF - retro_dnov_2542 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.2 %
• Parental protein coverage: 86.14 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TFTKLITVNGQEYHLQLVDTAGQDEYSIFPQTYSIDINGYILVYSVTSIKSFEVIKVIHGKLLDMVGKVQ
          TFTKLITVNGQEYHLQLVDTAGQDEYSIFPQTYSIDINGYILVYSVTSIKSFEVIKVIHGKLLDMVG.VQ
Retrocopy TFTKLITVNGQEYHLQLVDTAGQDEYSIFPQTYSIDINGYILVYSVTSIKSFEVIKVIHGKLLDMVGEVQ

Parental  IPIMLVGNKKDLHMERVISYEEGKALAESWNAAFLESSAKENQTAVDVFRRIILEAEKIDGAASQGKSSC
          IPIMLVG.KKDLHMERVISYEEG.ALAESWNAAFLESSAKENQTAVD.FRRIILEAEKIDGAASQGKSSC
Retrocopy IPIMLVGSKKDLHMERVISYEEGQALAESWNAAFLESSAKENQTAVDIFRRIILEAEKIDGAASQGKSSC

Parental  SVM
          SVM
Retrocopy SVM

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	0.58 RPM	38.12 RPM
SRP012922_cerebellum	3.30 RPM	71.35 RPM
SRP012922_heart	0.23 RPM	42.69 RPM
SRP012922_kidney	2.19 RPM	84.88 RPM
SRP012922_liver	0.93 RPM	47.99 RPM
SRP012922_lung	2.14 RPM	65.21 RPM
SRP012922_quadricep_muscle	0.17 RPM	53.83 RPM
SRP012922_spleen	1.14 RPM	77.03 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_2542 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 13 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000031861	1 retrocopy	retro_btau_373,
Callithrix jacchus	ENSCJAG00000020414	1 retrocopy	retro_cjac_1694,
Cavia porcellus	ENSCPOG00000007541	2 retrocopies	retro_cpor_287, retro_cpor_787,
Dasypus novemcinctus	ENSDNOG00000016493	1 retrocopy	retro_dnov_2542 ,
Homo sapiens	ENSG00000106615	2 retrocopies	retro_hsap_568, retro_hsap_570,
Gorilla gorilla	ENSGGOG00000014675	1 retrocopy	retro_ggor_149,
Loxodonta africana	ENSLAFG00000000691	1 retrocopy	retro_lafr_471,
Macropus eugenii	ENSMEUG00000011774	1 retrocopy	retro_meug_172,
Myotis lucifugus	ENSMLUG00000004309	2 retrocopies	retro_mluc_2140, retro_mluc_857,
Mus musculus	ENSMUSG00000028945	1 retrocopy	retro_mmus_1779,
Oryctolagus cuniculus	ENSOCUG00000013173	1 retrocopy	retro_ocun_1309,
Ictidomys tridecemlineatus	ENSSTOG00000004544	2 retrocopies	retro_itri_1251, retro_itri_1357,
Tarsius syrichta	ENSTSYG00000001286	2 retrocopies	retro_tsyr_1174, retro_tsyr_1848,