RetrogeneDB ID: retro_dnov_1582

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_23924:36385..36795(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TPD52L2
• Ensembl ID: ENSDNOG00000014930
• Aliases: None
• Description: tumor protein D52-like 2 [Source:HGNC Symbol;Acc:12007]

Sequence

>retro_dnov_1582
ATAGATCCTGCAAGCCATGATATCAATTTAAATTCTCCTAACAAGGGTTTGCTGTTCAACTTCATGACAGACATCCCTGT
TGACACAGGCATTGCTGCCCAGACTCCTGCTGTTGAGGTTCTCAAGGAGGTTGAGGAGGAGGAGCTCAGGGCTGAGCTTG
CCAAGGTGGAAGAGGAAATTGTCACTCTGTGTCAGGTCCTGGCAGCCAAGGAACAGCACTGTGGGGAACTGAAAAGAAAG
CTGGGCCTCTCTGCTTGGAGGGACTGAGGCAGAACCTGTCCCAGGGTTAATGTGATATGCAGGTTTTTAATGTCTACGTG
AAAACTTCTGAGAAACTGGCAGAGTGGAATGAAAAAGAGACACAGTCACACATCTACAAAATGACTCAGGAATCTCTCTC
ACAGGCAGGG

Alignment

ORF - retro_dnov_1582 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.54 %
• Parental protein coverage: 59.57 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MDPAGQDINLNSPNKGLLSDSMTDVPVDTGVAARTPAVEGLTEAEEEELRAELAKVEEEIVTLRQVLAAK
          .DPA..DINLNSPNKGLL...MTD.PVDTG.AA.TPAVE.L.E.EEEELRAELAKVEEEIVTL.QVLAAK
Retrocopy IDPASHDINLNSPNKGLLFNFMTDIPVDTGIAAQTPAVEVLKEVEEEELRAELAKVEEEIVTLCQVLAAK

Parental  ERHCGELKRKLGLSA-LEGLKQNLTRSWHDVQVSNAYVKTSEKLGEWNEKVTQSDLYRKTQETLSQAG
          E.HCGELKRKLGLSA.LEGL.QNL.....D.QV.N.YVKTSEKL.EWNEK.TQS..Y..TQE.LSQAG
Retrocopy EQHCGELKRKLGLSA<LEGLRQNLSQG*CDMQVFNVYVKTSEKLAEWNEKETQSHIYKMTQESLSQAG

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	31.11 RPM
SRP012922_cerebellum	0.00 RPM	19.52 RPM
SRP012922_heart	0.00 RPM	15.55 RPM
SRP012922_kidney	0.00 RPM	9.58 RPM
SRP012922_liver	0.00 RPM	15.48 RPM
SRP012922_lung	0.00 RPM	29.17 RPM
SRP012922_quadricep_muscle	0.00 RPM	15.75 RPM
SRP012922_spleen	0.00 RPM	24.49 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_1582 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000003663	1 retrocopy	retro_acar_36,
Dasypus novemcinctus	ENSDNOG00000014930	1 retrocopy	retro_dnov_1582 ,
Dasypus novemcinctus	ENSDNOG00000017379	2 retrocopies	retro_dnov_1294, retro_dnov_1451,
Equus caballus	ENSECAG00000021789	1 retrocopy	retro_ecab_69,
Otolemur garnettii	ENSOGAG00000013689	1 retrocopy	retro_ogar_3142,