RetrogeneDB ID: retro_dnov_2001

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_41490:8207..8733(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNAP29
• Ensembl ID: ENSDNOG00000005913
• Aliases: None
• Description: synaptosomal-associated protein, 29kDa [Source:HGNC Symbol;Acc:11133]

Sequence

>retro_dnov_2001
ATGTCAGCCTACCCCAAAAGCTACACCTCTTGACAACCACAGGGAGGATGAGGGTTACCAACAGACCCTGTGGAGGGTGC
CCTGCAATATCCCCAGTAGGCCAACAACAGGTAGCAGAGTCTGCAGCAGGAGGTGCTATGCAGGGCTGAGGCCACGCCAC
CAGCACTAGCAACAAACTCTCCTTCATTTTCAAGTCCAAGATGGTCAGGATCACCTCTTGCAAGGAACATGTCCATCAGC
AAGGAGTCTTGGAACACACAGAGAAGATGGTGGAAAAGATGGACCAAGATTTGAAGACCAGTCAGAAGCATATTAACAAC
ATGAAGAGTGTGTTTAGGGATTTTGTCAATCACTTCAAATCCAAACTGGCAGAGATGCCATTTCAACAGAATGGCACCCT
TGTCCGCCAGCACTGCAGCAAATTAAAAGAAGTCATACCTACAAGTAAAGAACAGGAGCAAAGTACTAGGCCAGCTACCC
AAACCTAAGAAAACCTGATAACTCAGACTCTATCACTGGAGGGGCT

Alignment

ORF - retro_dnov_2001 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.46 %
• Parental protein coverage: 68.92 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MSAY-PKSYNPFDDDAEDEGARPAPWEDPRDLPDWP-NDRQQSLRQEVLRRAEAT-AASTSKSLSLMYES
          MSAY.PK...P.D...EDEG.....W..P...P..P.N.R.QSL.QEVL.RAEAT.A.STS..LS....S
Retrocopy MSAY>PKA-TPLDNHREDEGYQQTLWRVPCNIPSRP<NNR*QSLQQEVLCRAEAT<ATSTSNKLSFIFKS

Parental  ERVGVASCEELI-SLGVLESTEKMVD-MDQDLKTSQKHIMNIKSMLNE-INYFKKPVKKPP-EQNGTLAP
          ..V...SC.E.....GVLE.TEKMV..MDQDLKTSQKHI.N.KS......N.FK......P..QNGTL..
Retrocopy KMVRITSCKEHVHQQGVLEHTEKMVEKMDQDLKTSQKHINNMKSVFRDFVNHFKSKLAEMPFQQNGTLVR

Parental  QTSSRLKEAITTSKEQE-SKYQASHPNLRKLDNSDSIIGGA
          Q..S.LKE.I.TSKEQE..KY.AS.PNLRK.DNSDSI.GGA
Retrocopy QHCSKLKEVIPTSKEQE<AKY*ASYPNLRKPDNSDSITGGA

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	10.31 RPM
SRP012922_cerebellum	0.00 RPM	13.20 RPM
SRP012922_heart	0.00 RPM	2.78 RPM
SRP012922_kidney	0.00 RPM	4.65 RPM
SRP012922_liver	0.00 RPM	4.02 RPM
SRP012922_lung	0.00 RPM	4.73 RPM
SRP012922_quadricep_muscle	0.00 RPM	1.90 RPM
SRP012922_spleen	0.00 RPM	6.87 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_2001 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 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015201	1 retrocopy	retro_cfam_1542,
Cavia porcellus	ENSCPOG00000003137	1 retrocopy	retro_cpor_1442,
Dasypus novemcinctus	ENSDNOG00000005913	4 retrocopies	retro_dnov_1401, retro_dnov_1855, retro_dnov_2001 , retro_dnov_2364,
Nomascus leucogenys	ENSNLEG00000000108	1 retrocopy	retro_nleu_2645,
Otolemur garnettii	ENSOGAG00000013003	1 retrocopy	retro_ogar_3493,