RetrogeneDB ID: retro_dnov_2102

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_47818:10691..11366(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP6AP2
• Ensembl ID: ENSDNOG00000006109
• Aliases: None
• Description: ATPase, H+ transporting, lysosomal accessory protein 2 [Source:HGNC Symbol;Acc:18305]

Sequence

>retro_dnov_2102
TTAAGATCACCAGGGTCTGTTGTTTTCCATGATGGAAATTGGCCCATACCATGAGAGTGAATCCCAGATGTGGCTGCATT
GTCCATGGGCTTCTCTGTGAAAGAAGACCTTTCTTGGCCAGGGCTTGCAGTGGGTAACCTATTCCATTATCCTTGAGCTA
CCGTTATGGTGATGGTGAAGGGGGTGGACAAACTGGCTTTACCCCCAGGTAGTGTCATCTCATACCCTTTGGAGAACGCA
GTTCCTTTTAGTCTTGACAGTGTTGCAAATTCCATTCATTCCTTATTTTCTGAAGAAACACCTGTAGTTTTGCAGTTGGC
TCTCAGTGAGGAAAGAGTCTATATGGTGGGAAAGGCAAACTCAGTTTTTGAAGACCTTTCAGTAACATTATGACAGCTCG
GTAATCGCCTGTTTCAAGAAAACACTATTCTCAATTCATTTCCCTTCAATTCTCTGAGTAGGAATAATGAAGTTGACCTA
CTCTTCCTTTCTGAACTGCAAGTGCTACATGATATTTCAAGTTTGTTGTCTCGACATAAGCATCTAGCCAAGGATCATTC
TCCTGATTTATATTCCCTGGAGCTGGCAGGTTTGGATGAAATTGGGAAACGTTATGGGGAAGACTCTGAACAATTCAGAG
ATGCATCTAAGATTCTGGTTGATGCTCTGCAAAAG

Alignment

ORF - retro_dnov_2102 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.22 %
• Parental protein coverage: 66.67 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LRSPGSVVFRDGNWPIPGERIPDVAALSMGFSVKEDLSWPGLAVGNLFHRPRATVMVMVKGVDKLALPPG
          LRSPGSVVF.DGNWPIP.E.IPDVAALSMGFSVKEDLSWPGLAVGNLFH.P.ATVMVMVKGVDKLALPPG
Retrocopy LRSPGSVVFHDGNWPIP*E*IPDVAALSMGFSVKEDLSWPGLAVGNLFHYP*ATVMVMVKGVDKLALPPG

Parental  SVISYPLENAVPFSLDSVANSIHSLFSEETPVVLQLAPSEERVYMVGKANSVFEDLSVTLRQLRNRLF-E
          SVISYPLENAVPFSLDSVANSIHSLFSEETPVVLQLA.SEERVYMVGKANSVFEDLSVTL.QL.NRLF.E
Retrocopy SVISYPLENAVPFSLDSVANSIHSLFSEETPVVLQLALSEERVYMVGKANSVFEDLSVTL*QLGNRLFQE

Parental  NSVLXXXXXXXXXXXXXXXXXXXXELQVLHDISSLLSRHKHLAKDHSPDLYSLELAGLDEIGKRYGEDSE
          N..L....................ELQVLHDISSLLSRHKHLAKDHSPDLYSLELAGLDEIGKRYGEDSE
Retrocopy NTILNSFPFNSLSRNNEVDLLFLSELQVLHDISSLLSRHKHLAKDHSPDLYSLELAGLDEIGKRYGEDSE

Parental  QFRDASKILVDALQK
          QFRDASKILVDALQK
Retrocopy QFRDASKILVDALQK

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	21.59 RPM
SRP012922_cerebellum	16.50 RPM	26.67 RPM
SRP012922_heart	3.48 RPM	5.57 RPM
SRP012922_kidney	22.18 RPM	40.25 RPM
SRP012922_liver	7.59 RPM	10.53 RPM
SRP012922_lung	12.68 RPM	25.50 RPM
SRP012922_quadricep_muscle	2.42 RPM	4.15 RPM
SRP012922_spleen	14.54 RPM	31.71 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_2102 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000006109	1 retrocopy	retro_dnov_2102 ,
Homo sapiens	ENSG00000182220	1 retrocopy	retro_hsap_280,
Gorilla gorilla	ENSGGOG00000000532	1 retrocopy	retro_ggor_323,
Myotis lucifugus	ENSMLUG00000001159	1 retrocopy	retro_mluc_1613,
Macaca mulatta	ENSMMUG00000012762	1 retrocopy	retro_mmul_561,
Nomascus leucogenys	ENSNLEG00000001441	1 retrocopy	retro_nleu_1491,
Pongo abelii	ENSPPYG00000020251	1 retrocopy	retro_pabe_389,
Pan troglodytes	ENSPTRG00000021803	1 retrocopy	retro_ptro_233,