RetrogeneDB ID: retro_dnov_2610

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_89948:4414..4937(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZDHHC4
• Ensembl ID: ENSDNOG00000009165
• Aliases: None
• Description: zinc finger, DHHC-type containing 4 [Source:HGNC Symbol;Acc:18471]

Sequence

>retro_dnov_2610
GCACAGATATTTTCGTGTCTAATTCCAGTGTGTCTTCAGAGAGCCAGGCAAAGATCGCTCCACTACCTCTTCATATGCAA
ACCCACACCTTCCTTGCCCCGCAACCTCATCTCATCTTGCACGGGATGGTTTCTTCTGAATACATCTGGGAAATACCTGA
CTACTGTCCAGAACTGAAGTTCTCCTTATATTACTTTCTTCTGCCCTATCTGCTACTGTCTGTAAACCTGTGTTTTTTTC
CCCTAAGTTGTATAACCAACCCTGGGACTATAACAAAAGCAAATGGATGGCTGCTTCTTCAAGTTTATGAATTCGAGGAA
GTGATTCATCTACAGAACCTGAGATGCTCCACTTGTGACAGAAGGAAACCAGCTTGATCTGAGCACTGCAGAGTGTGTCA
CTGGTGTGAGCACCGTTTCGAGCATCACAGTGCTTGGGTGTACAACAGCATTAGCACCTAGGATACCAGTACTTCCACAT
CCACCTCTTGACAGTGACGGCCTCGGCATGTTTCAAATCCAGT

Alignment

ORF - retro_dnov_2610 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.71 %
• Parental protein coverage: 50.29 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AQIFSCIIPECLQKAMQRLLHYF-LHTRNHTFVVL--HLSLQGMVYTEYTWEILGYCQELEFSLYYLLLP
          AQIFSC.IP.CLQ.A.QR.LHY..LH...HTF.....HL.L.GMV..EY.WEI..YC.EL.FSLYY.LLP
Retrocopy AQIFSCLIPVCLQRARQRSLHYL<LHMQTHTFLAPQPHLILHGMVSSEYIWEIPDYCPELKFSLYYFLLP

Parental  YLLLFVNLCFFALSCVSNPGTVTKANELLLLQVYGFDEVMFLKNTRCPTCDLKKPARSKHCSVCNRCVHR
          YLLL.VNLCFF.LSC..NPGT.TKAN..LLLQVY.F.EV..L.N.RC.TCD..KPA.S.HC.VC..C.HR
Retrocopy YLLLSVNLCFFPLSCITNPGTITKANGWLLLQVYEFEEVIHLQNLRCSTCDRRKPA*SEHCRVCHWCEHR

Parental  FDHHCVWVNNCIGAWNA-RYFLIYLLTLTASAASLAS
          F.HH..WV.N.I.......YF.I.LLT.TASA....S
Retrocopy FEHHSAWVYNSIST*DT<QYFHIHLLTVTASACFKSS

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	35.78 RPM
SRP012922_cerebellum	0.00 RPM	23.37 RPM
SRP012922_heart	0.00 RPM	20.88 RPM
SRP012922_kidney	0.00 RPM	26.56 RPM
SRP012922_liver	0.31 RPM	13.31 RPM
SRP012922_lung	0.00 RPM	22.60 RPM
SRP012922_quadricep_muscle	0.00 RPM	38.42 RPM
SRP012922_spleen	0.00 RPM	21.86 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_2610 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 11 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009547	1 retrocopy	retro_btau_643,
Dasypus novemcinctus	ENSDNOG00000009165	1 retrocopy	retro_dnov_2610 ,
Homo sapiens	ENSG00000136247	1 retrocopy	retro_hsap_1193,
Macaca mulatta	ENSMMUG00000015545	1 retrocopy	retro_mmul_1283,
Nomascus leucogenys	ENSNLEG00000015607	1 retrocopy	retro_nleu_2081,
Pongo abelii	ENSPPYG00000017352	1 retrocopy	retro_pabe_993,
Pan troglodytes	ENSPTRG00000018915	1 retrocopy	retro_ptro_3038,
Pteropus vampyrus	ENSPVAG00000016104	2 retrocopies	retro_pvam_1175, retro_pvam_758,
Ictidomys tridecemlineatus	ENSSTOG00000011605	1 retrocopy	retro_itri_1054,
Tursiops truncatus	ENSTTRG00000005001	1 retrocopy	retro_ttru_179,
Vicugna pacos	ENSVPAG00000011480	1 retrocopy	retro_vpac_177,