RetrogeneDB ID: retro_dnov_2585

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_88038:3137..3416(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDE6D
• Ensembl ID: ENSDNOG00000000568
• Aliases: None
• Description: phosphodiesterase 6D, cGMP-specific, rod, delta [Source:HGNC Symbol;Acc:8788]

Sequence

>retro_dnov_2585
TGCACAGCAGCGTCCCTGGAACTGAACTTCCCTTCTGCAGAGCAGGTGGGAAAATCCAACCTGCGACAGAAAGTGGACGT
GGGAGGGCGAGGCCTGGAAGAACGATCCTGCGCGCTGGCTGTGGCCCTTACCGCCACGTGTACCTGGCAGGCCTTGGTGG
GGGCGCACCTGAGTCCCAGATGATGCCGGCCAGTGCCTGACCTGGGAGTGCCATCGTGCGAACAGAGCTTTCCTGACAAT
GATCTTGTAAGCACGTCCAGAGTGAGGCTTTTCTACGTT

Alignment

ORF - retro_dnov_2585 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.67 %
• Parental protein coverage: 63.33 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  CKAVSRELNFSSAEQMEKFRLEQKVYFKGQCLEEWFFEFGFVIPNSTNTWQSLIEA-APESQMMPASVLT
          C.A.S.ELNF.SAEQ..K..L.QKV...G..LEE............T.TWQ.L..A.APESQMMPAS...
Retrocopy CTAASLELNFPSAEQVGKSNLRQKVDVGGRGLEERSCALAVAL-TATCTWQALVGA<APESQMMPASA*P

Parental  GNVIIETK-FFDDDLLVSTSRVRLFYV
          G..I..T..F.D.D.LVSTSRVRLFYV
Retrocopy GSAIVRTE>FPDND-LVSTSRVRLFYV

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	6.61 RPM
SRP012922_cerebellum	0.00 RPM	15.67 RPM
SRP012922_heart	0.00 RPM	6.73 RPM
SRP012922_kidney	0.00 RPM	7.12 RPM
SRP012922_liver	0.00 RPM	3.25 RPM
SRP012922_lung	0.00 RPM	11.15 RPM
SRP012922_quadricep_muscle	0.00 RPM	6.92 RPM
SRP012922_spleen	0.00 RPM	10.07 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_2585 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000012101	1 retrocopy	retro_acar_157,
Dasypus novemcinctus	ENSDNOG00000000568	1 retrocopy	retro_dnov_2585 ,
Felis catus	ENSFCAG00000002232	1 retrocopy	retro_fcat_317,
Macropus eugenii	ENSMEUG00000006427	1 retrocopy	retro_meug_1355,
Oryctolagus cuniculus	ENSOCUG00000010403	1 retrocopy	retro_ocun_182,
Pteropus vampyrus	ENSPVAG00000004743	1 retrocopy	retro_pvam_544,
Tursiops truncatus	ENSTTRG00000009165	1 retrocopy	retro_ttru_82,