RetrogeneDB ID: retro_dnov_2242

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_57978:8455..9380(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDC7
• Ensembl ID: ENSDNOG00000006454
• Aliases: None
• Description: cell division cycle 7 [Source:HGNC Symbol;Acc:1745]

Sequence

>retro_dnov_2242
ATTAAGTTCAGCAATTTTTTAATATACTAGATACCTGAAAAAGTATGCTTTGGTAGGCTTTGGTTTGGCCCAGGGAACCC
ATGATATGAAAATAGAGGTTCTGAAATTTGTCCAGTCTTAGACTCAACAGGAAAGTTTTTCACAAAATAAGTCCCATATA
ATCACAGGAAAGAAGATTTCATTGAGTGGCCCATCATCTAAAGAGCTGAATCAGCAGCGTTTCACAAAAGCATCTGTTAA
AAGGCCCCATGCAAATGCACAAATTTATATTAAACAAGGAAAAGATGGAAAGGAGGTATCTGTAGGCCTTTCTATCCAGG
GCTCTGTTTTTGGAGAAAGAAATTTCAATACGCACAGCTCCATTTCACATGAGAGCCCTGCAGTGAAATTTATGAAGCAG
TCAAAGACTGTGGATATACTATCTAGAAAGTTAGCAACAAAAAAGAAGGCTATTTCTACAACAGTTGTAAACAGTGGTGT
GATAAGGAAAACTGCCAGTTCTTGCCCAGCTAACCTGATCTGTGACTTTTTTGCAACAGATAAAGTTTGCAGCATTTACC
TTTCAAGGCAGCAGCAAGTTGTCCCTAGGGCAGATACACCAAGATTCAGAATGCCAGAAGTTTTAAACAAAGTGCCCCAA
TCAAACCACTGCAATTGACATGTGGACTGCATGTATCATATTCCTTCCCTTGCTTAGTGGACAATATCATTTTATAAAGC
AACTGATGATTTAACTGCTTTGGCTCAAATTATGACAATTCATGGATCCAGGGAAACTATCCAGGCTACTAAAACTTTTG
GCAAGTCAATATTATGTAGCAAAGAAGTCCCAGCAAATGCCTTGAGAAAACTCTGTGAGACACTCTGGGATATAGACACT
AAAACTTCCAAATTAACAAGTGCAATACAAGGACCTACTTCTTAT

Alignment

ORF - retro_dnov_2242 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.39 %
• Parental protein coverage: 53.95 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VKPSNFL-YNRCLKKYALVDFGLAQGTHDTKIELLKLVQSEAQQQSFSQNKSHVITGNKISLSGPAPKDL
          .K.SNFL.Y.R.LKKYALV.FGLAQGTHD.KIE.LK.VQS..QQ.SFSQNKSH.ITG.KISLSGP..K.L
Retrocopy IKFSNFL>YTRYLKKYALVGFGLAQGTHDMKIEVLKFVQS*TQQESFSQNKSHIITGKKISLSGPSSKEL

Parental  NQQPITKASVKRPYTNAQIHIKQGKDGKEGSVGLSAQRSVFGERNFNIHSSISHESPAVKLMKQSKTVDV
          NQQ..TKASVKRP..NAQI.IKQGKDGKE.SVGLS.Q.SVFGERNFN.HSSISHESPAVK.MKQSKTVD.
Retrocopy NQQRFTKASVKRPHANAQIYIKQGKDGKEVSVGLSIQGSVFGERNFNTHSSISHESPAVKFMKQSKTVDI

Parental  LSRKLAT-KKTISTKVINSGVMRKTASSCPSSLICDCFATDKVCSICLSRRQQVAPRAGTPGFRAPEVL-
          LSRKLAT.KK.IST.V.NSGV.RKTASSCP..LICD.FATDKVCSI.LSR.QQV.PRA.TP.FR.PEVL.
Retrocopy LSRKLATKKKAISTTVVNSGVIRKTASSCPANLICDFFATDKVCSIYLSRQQQVVPRADTPRFRMPEVL>

Parental  TKCPNQTTAIDMWSAGVIFLSLLSGRY-PFYKATDDLTALAQIMTIRGSRETIQAAKTFGKSILCSKEVP
          TKCPNQTTAIDMW.A..IFL.LLSG.Y..FYKATDDLTALAQIMTI.GSRETIQA.KTFGKSILCSKEVP
Retrocopy TKCPNQTTAIDMWTACIIFLPLLSGQY<SFYKATDDLTALAQIMTIHGSRETIQATKTFGKSILCSKEVP

Parental  AQDLRKLCERLRGIDSKTSKLTSEIQGPASH
          A..LRKLCE.L..ID.KTSKLTS.IQGP.S.
Retrocopy ANALRKLCETLWDIDTKTSKLTSAIQGPTSY

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	8.17 RPM
SRP012922_cerebellum	0.00 RPM	16.91 RPM
SRP012922_heart	0.00 RPM	4.18 RPM
SRP012922_kidney	0.00 RPM	0.82 RPM
SRP012922_liver	0.00 RPM	1.39 RPM
SRP012922_lung	0.00 RPM	9.62 RPM
SRP012922_quadricep_muscle	0.00 RPM	0.69 RPM
SRP012922_spleen	0.00 RPM	25.64 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_2242 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000006454	1 retrocopy	retro_dnov_2242 ,
Macaca mulatta	ENSMMUG00000011010	1 retrocopy	retro_mmul_1689,