RetrogeneDB ID: retro_dnov_199

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_2546:39001..39392(-)
• Located in intron of: ENSDNOG00000017242

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARPC5
• Ensembl ID: ENSDNOG00000010375
• Aliases: None
• Description: actin related protein 2/3 complex, subunit 5, 16kDa [Source:HGNC Symbol;Acc:708]

Sequence

>retro_dnov_199
ATGTGGAAGAACACGGTGTCGTCAGTCTGGTTCCAGAAGGTGGACATGGATGAGTATGACAAGAACAAGTTTGTGGACCA
GGACAATGGAGGTGATAACTAGGCTGGGCCAGACGAGGGCGAGAAGGACTCTAGCCTGTGGCAAGGAAACATGACAGCTG
CTCTACAGGCAGCTCTGAAAAATCTCCCTATCAACAACAAGAGTCAGGCGGTGAAGGATCGGGCAGGCAGCATCGTCCTG
AAGGTGCTCATCTCTTTTAAAGTTAATGATATTAAAAAGGCAGTTCAATCTCTGGACAAGAGTGGTGTGGAACTCCTAAT
AAAGTGTATCTATAAAGGCTTTGAGAACCCCTCTTCACAATAGTAGTGCTGTTTTGCAATGGCATGAAAAG

Alignment

ORF - retro_dnov_199 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.78 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSKNTVSSARFRKVDVDEYDENKFVDEEDGGDGQAGPDEGEVDSCLRHSVTGNMTAALQAALKNPPINTK
          M.KNTVSS..F.KVD.DEYD.NKFVD...GGD..AGPDEGE.DS.L.....GNMTAALQAALKN.PIN.K
Retrocopy MWKNTVSSVWFQKVDMDEYDKNKFVDQDNGGDN*AGPDEGEKDSSLWQ---GNMTAALQAALKNLPINNK

Parental  SQAVKDRAGSIVLKVLISFKANDIEKAVQSLDKNGVDLLMKYIYKGFESPSD-NSSAVLLQWHEK
          SQAVKDRAGSIVLKVLISFK.NDI.KAVQSLDK.GV.LL.K.IYKGFE.PS..NSSAV.LQWHEK
Retrocopy SQAVKDRAGSIVLKVLISFKVNDIKKAVQSLDKSGVELLIKCIYKGFENPSS>NSSAV-LQWHEK

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	102.87 RPM
SRP012922_cerebellum	0.27 RPM	25.71 RPM
SRP012922_heart	0.00 RPM	10.91 RPM
SRP012922_kidney	0.00 RPM	21.36 RPM
SRP012922_liver	0.00 RPM	40.25 RPM
SRP012922_lung	0.15 RPM	71.63 RPM
SRP012922_quadricep_muscle	0.00 RPM	6.23 RPM
SRP012922_spleen	0.00 RPM	121.44 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_199 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 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000560	2 retrocopies	retro_chof_1502, retro_chof_783,
Dasypus novemcinctus	ENSDNOG00000010375	3 retrocopies	retro_dnov_1277, retro_dnov_199 , retro_dnov_2495,
Echinops telfairi	ENSETEG00000014969	1 retrocopy	retro_etel_1922,
Monodelphis domestica	ENSMODG00000007194	1 retrocopy	retro_mdom_968,
Mus musculus	ENSMUSG00000008475	1 retrocopy	retro_mmus_281,
Rattus norvegicus	ENSRNOG00000028062	1 retrocopy	retro_rnor_1873,