RetrogeneDB ID: retro_dnov_158

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_2218:58840..59152(+)
• Located in intron of: ENSDNOG00000018299

Retrocopy information

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

Parental gene information

• Parental gene symbol: GOLT1B
• Ensembl ID: ENSDNOG00000013576
• Aliases: None
• Description: golgi transport 1B [Source:HGNC Symbol;Acc:20175]

Sequence

>retro_dnov_158
TTATCGACACCCAGAGTTTTATTCGTGGCTGGCTTGGCTTTTGTAATTGGTTTAGAAAGAACATTCAGATTCTTCTTCCA
AAAACACAAAATGAAAGCTACAGGATTTTTCCTGGGTGGTGTGTTTGTAGTCCTTATTGGTTGGCCTTTGATAGGCATGA
TCTTTGAAATTTATGGATTCTTTCTCTTGTTCAGGGGATTCTTTTCTGTGGTAGGTGGCTTTATTAGAAGAGTGTCAGTC
CTGGGATCTCTCTTGAATTTACCTGGAATCAGATCATTTGTAGATAAAGTTGGAGAAAGCAACAATATGGTA

Alignment

ORF - retro_dnov_158 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.27 %
• Parental protein coverage: 75.36 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LAIGNVLFVAGLAFVIGLERTFRFFFQKHKMKATGFFLGGVFVVLIGWPLIGMIFEIYGFFLLFRGFFPV
          L....VLFVAGLAFVIGLERTFRFFFQKHKMKATGFFLGGVFVVLIGWPLIGMIFEIYGFFLLFRGFF.V
Retrocopy LSTPRVLFVAGLAFVIGLERTFRFFFQKHKMKATGFFLGGVFVVLIGWPLIGMIFEIYGFFLLFRGFFSV

Parental  VVGFIRRVPVLGSLLNLPGIRSFVDKVGESNNMV
          V.GFIRRV.VLGSLLNLPGIRSFVDKVGESNNMV
Retrocopy VGGFIRRVSVLGSLLNLPGIRSFVDKVGESNNMV

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	5.06 RPM
SRP012922_cerebellum	0.00 RPM	3.85 RPM
SRP012922_heart	0.00 RPM	3.71 RPM
SRP012922_kidney	0.00 RPM	0.82 RPM
SRP012922_liver	0.00 RPM	2.48 RPM
SRP012922_lung	0.00 RPM	7.33 RPM
SRP012922_quadricep_muscle	0.00 RPM	2.60 RPM
SRP012922_spleen	0.00 RPM	4.35 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_158 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 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016231	1 retrocopy	retro_amel_604,
Canis familiaris	ENSCAFG00000012256	1 retrocopy	retro_cfam_1835,
Dasypus novemcinctus	ENSDNOG00000013576	2 retrocopies	retro_dnov_158 , retro_dnov_1730,
Felis catus	ENSFCAG00000028655	1 retrocopy	retro_fcat_1782,
Loxodonta africana	ENSLAFG00000000965	1 retrocopy	retro_lafr_416,
Oryctolagus cuniculus	ENSOCUG00000008797	1 retrocopy	retro_ocun_1706,
Otolemur garnettii	ENSOGAG00000004756	1 retrocopy	retro_ogar_3234,
Ictidomys tridecemlineatus	ENSSTOG00000006352	1 retrocopy	retro_itri_1786,
Tarsius syrichta	ENSTSYG00000009234	1 retrocopy	retro_tsyr_567,