RetrogeneDB ID: retro_dnov_485

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_5208:23818..24091(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PFN1
• Ensembl ID: ENSDNOG00000011649
• Aliases: None
• Description: profilin 1 [Source:HGNC Symbol;Acc:8881]

Sequence

>retro_dnov_485
CCAGCTGAGGTTGGTGTTTTGGTTGGCAGAGTCTGGTCAAGTTTTTTCATGAAAGGGCTGACACTGGGGGGCCAGAAATA
TTCTGTGATCTGGGACTCACTGCTGCAGAATGGGGAATTTATCATGGATCTTCCTGCTAAGAGCACTGGTAGAACTCCCG
CCTTCAACCTCACTGTCACCATGACTGCCAAAACGCTAGTCCTGCTGATGGGCAAAGAAGGCATCTACAGTGGTTTGATC
AACAAGAAATGATATGAAATGGCCTCCCACCTG

Alignment

ORF - retro_dnov_485 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.54 %
• Parental protein coverage: 94.79 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PAEVGVLVGKDRSGLFVNGLTLGGQKCSVIRDSLLQDGEFTMDLRTKSTGGAPTFNLTVTMTAKXXXXXX
          PAEVGVLVG...S..F..GLTLGGQK.SVI.DSLLQ.GEF.MDL..KSTG..P.FNLTVTMTAK......
Retrocopy PAEVGVLVGRVWSSFFMKGLTLGGQKYSVIWDSLLQNGEFIMDLPAKSTGRTPAFNLTVTMTAKTLVLLM

Parental  XXXXXXXXXXXKECYEMASHL
          ...........K..YEMASHL
Retrocopy GKEGIYSGLINKK*YEMASHL

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	11.67 RPM	68.84 RPM
SRP012922_cerebellum	1.51 RPM	7.29 RPM
SRP012922_heart	1.62 RPM	9.75 RPM
SRP012922_kidney	2.46 RPM	22.45 RPM
SRP012922_liver	3.10 RPM	17.18 RPM
SRP012922_lung	5.19 RPM	39.40 RPM
SRP012922_quadricep_muscle	1.04 RPM	6.58 RPM
SRP012922_spleen	9.50 RPM	63.41 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_485 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.

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006193	2 retrocopies	retro_amel_1712, retro_amel_1781,
Bos taurus	ENSBTAG00000004915	1 retrocopy	retro_btau_141,
Dasypus novemcinctus	ENSDNOG00000011649	2 retrocopies	retro_dnov_1762, retro_dnov_485 ,
Equus caballus	ENSECAG00000021116	3 retrocopies	retro_ecab_171, retro_ecab_28, retro_ecab_559,
Nomascus leucogenys	ENSNLEG00000017446	6 retrocopies	retro_nleu_16, retro_nleu_1870, retro_nleu_2425, retro_nleu_2429, retro_nleu_848, retro_nleu_886,
Otolemur garnettii	ENSOGAG00000031395	3 retrocopies	retro_ogar_1680, retro_ogar_2143, retro_ogar_3351,
Pelodiscus sinensis	ENSPSIG00000004124	1 retrocopy	retro_psin_8,
Rattus norvegicus	ENSRNOG00000003975	1 retrocopy	retro_rnor_1623,
Tursiops truncatus	ENSTTRG00000001299	1 retrocopy	retro_ttru_14,