RetrogeneDB ID: retro_dnov_2040

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_43843:39321..39660(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GLIPR2
• Ensembl ID: ENSDNOG00000008950
• Aliases: None
• Description: GLI pathogenesis-related 2 [Source:HGNC Symbol;Acc:18007]

Sequence

>retro_dnov_2040
TATTCTGAGGCCCTGGCCAGCACAAGGATCCTCAAGCACAGCCTGGAATCCAGTCATGGACAGTGTGGGGAGAACCTGGC
ATGGGCGTCCTACGATTGGACAGGAAAAGAGGTGGCCGATAGATGGTACAGTGAAATCAAGAACTACAACTTCCAGCAGC
CTGGCTTCACCTTGGGGACTGGACACTTGACAGCCATGGTATGGAAGAATACAAAGAAGATGAGAGTGGGAAAGGCATCT
GCAAGTGACGGGTCCTCCTTTGTGGTGGCCAGATACTTCCCAGCAGGGAATGTTGTCAATCAGGGCTACTTTGAAGAAAA
TGTCCTGCCTCCAAAGAAG

Alignment

ORF - retro_dnov_2040 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.5 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YSEALASTRILKHSPESSRGQCGENLAWASYDQTGKEVADRWYSEIKNYNFQQPGFTSGTXXXXXMVWK-
          YSEALASTRILKHS.ESS.GQCGENLAWASYD.TGKEVADRWYSEIKNYNFQQPGFT.GT.....MVWK.
Retrocopy YSEALASTRILKHSLESSHGQCGENLAWASYDWTGKEVADRWYSEIKNYNFQQPGFTLGTGHLTAMVWKN

Parental  TKKMGVGKASASDGSSFVVARYFPEGNVVNQGYFEENVLPPKR
          TKKM.VGKASASDGSSFVVARYFP.GNVVNQGYFEENVLPPK.
Retrocopy TKKMRVGKASASDGSSFVVARYFPAGNVVNQGYFEENVLPPKK

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	14.20 RPM	14.00 RPM
SRP012922_cerebellum	0.27 RPM	0.27 RPM
SRP012922_heart	1.16 RPM	0.93 RPM
SRP012922_kidney	0.27 RPM	0.27 RPM
SRP012922_liver	0.93 RPM	0.46 RPM
SRP012922_lung	6.41 RPM	7.33 RPM
SRP012922_quadricep_muscle	1.56 RPM	1.04 RPM
SRP012922_spleen	10.19 RPM	10.42 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_2040 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 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000030686	1 retrocopy	retro_cfam_428,
Dasypus novemcinctus	ENSDNOG00000008950	1 retrocopy	retro_dnov_2040 ,
Dipodomys ordii	ENSDORG00000012831	1 retrocopy	retro_dord_342,
Felis catus	ENSFCAG00000012762	2 retrocopies	retro_fcat_115, retro_fcat_1587,
Microcebus murinus	ENSMICG00000017673	1 retrocopy	retro_mmur_1525,
Myotis lucifugus	ENSMLUG00000011791	2 retrocopies	retro_mluc_1145, retro_mluc_475,
Mus musculus	ENSMUSG00000028480	1 retrocopy	retro_mmus_2458,
Rattus norvegicus	ENSRNOG00000014838	1 retrocopy	retro_rnor_2217,
Tupaia belangeri	ENSTBEG00000009276	2 retrocopies	retro_tbel_1646, retro_tbel_4682,