RetrogeneDB ID: retro_dnov_1300

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_177771:3157..3500(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PLGRKT
• Ensembl ID: ENSDNOG00000004320
• Aliases: None
• Description: plasminogen receptor, C-terminal lysine transmembrane protein [Source:HGNC Symbol;Acc:23633]

Sequence

>retro_dnov_1300
CTGGAAAGGCAGCTAATGATGTAGAATGAAAATGAGGGAACGACAAATAGCCAAGCAGATTGCTTGGTCTCAGGAATTCC
ACAGATATTTTGGGACTTTCTTTGGCATTGCAGCCATCTCTTTAATAGCTGGAGTTATAAAAAAGAAAAAAGCAGCCTTC
CTCTTCCCTGTCATTCCATTAGGCTTTGTCTTTATCTACCAGTATAATTGGGGCTATGGAACCCTTCTACAGAGAATGAA
AGGTGAAGCAGAGAATATATTGGAAACAGGAAAGAGAAAGTTACAGCTGCCAAGAGGAATGCCATCAGTTTTGAAAGTCT
TGAAAAAGCCAGAAAGGAAAGAG

Alignment

ORF - retro_dnov_1300 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.83 %
• Parental protein coverage: 94.17 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LERQLMMQNE-MRERQIAMQIAWSREFLKYFGTFFGMAAISLTAGAIKKKKPAILFPIVPLGFIFTYQCD
          LERQLMM.NE.MRERQIA.QIAWS.EF..YFGTFFG.AAISL.AG.......A.LFP..PLGF.F.YQ..
Retrocopy LERQLMM*NE>MRERQIAKQIAWSQEFHRYFGTFFGIAAISLIAGVXXXXXAAFLFPVIPLGFVFIYQYN

Parental  LGYGTLLQRMKGEAENILETEKSKLQLPGGM-ITFESLEKARREQ
          .GYGTLLQRMKGEAENILET.K.KLQLP.GM......L.K..R..
Retrocopy WGYGTLLQRMKGEAENILETGKRKLQLPRGMPSVLKVLKKPERKE

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	22.95 RPM
SRP012922_cerebellum	0.00 RPM	2.75 RPM
SRP012922_heart	0.00 RPM	10.67 RPM
SRP012922_kidney	0.00 RPM	7.39 RPM
SRP012922_liver	0.00 RPM	5.88 RPM
SRP012922_lung	0.00 RPM	7.18 RPM
SRP012922_quadricep_muscle	0.00 RPM	15.58 RPM
SRP012922_spleen	0.00 RPM	6.07 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_1300 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000004320	1 retrocopy	retro_dnov_1300 ,
Dipodomys ordii	ENSDORG00000000109	1 retrocopy	retro_dord_553,
Otolemur garnettii	ENSOGAG00000003280	1 retrocopy	retro_ogar_2243,
Sarcophilus harrisii	ENSSHAG00000001757	1 retrocopy	retro_shar_822,