RetrogeneDB ID: retro_dnov_438

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_470:11897..12477(+)
• Located in intron of: ENSDNOG00000012411

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHAC1
• Ensembl ID: ENSDNOG00000017531
• Aliases: None
• Description: ChaC, cation transport regulator homolog 1 (E. coli) [Source:HGNC Symbol;Acc:28680]

Sequence

>retro_dnov_438
GACCCTCCAGTGCTGTGGATTTTTGGGTACAGCTCCCTGGTGTGGAACCCAACTTCGCCTTCACAACAGCTGCGTGGGCT
TCATGTGTGGCCACAGCCGCCTCTACTGGCAGGGAGACATCTTCCACTGGGGCAGTGACAAGATGCCTGGCCATGTGGTG
ACCCTCCTTGAAGACTGTGATGAGCATTGTGCTTGGGGCATGGAACACCAGGTTTGAGGCGAGCAGGTGAATGAGGCCCT
GAAGTACCTGAACATGCATGAGGTGGTACTCAGTGGCTGAGACACCAAGCAGGTCACTTTCTGCCCCAGGACACCTCTGA
CCAGCCACTGAAGACCTTGGCCTACACGGCCACCCCACAGAACCCTGACTACCTGGGCCCTGTGCCTGGAAGCCATTGCC
ACAAAGATCCTGGTCTGCTGAGTCTTCTCAGGCCACAACCTGGCATACGTGTTGTGCCTGGAAGACTTCACACAGCTCTG
TGGGCTCCAAGTACATGACAAGTACCTGGCGGCGATGGTGGATGCCATGGGTATCATGCTGCCCTGCTCCTGCCTCACCA
AGCAGGCTCTGGCACTGGTC

Alignment

ORF - retro_dnov_438 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.5 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  DRPALWIFGYGYVM-ERPDFAFS-DSQVDFVRDYSRRFWQRDTFHRGSDKMPGRVVTLLED-GEGCTWGV
          D.P.LWIFGY.......P.FAF...S.V.F....SR..WQ.D.FH.GSDKMPG.VVTLLED..E.C.WG.
Retrocopy DPPVLWIFGYSSLV<VEPNFAFT<NSCVGFMCGHSRLYWQGDIFHWGSDKMPGHVVTLLEDCDEHCAWGM

Parental  AYQVRGEQVNEALKYLNVREAVLGGYDTKEVTFCP-QDTPDQPLKALAYVAT-PQNPGYLGPAPE-EAIA
          ..QV.GEQVNEALKYLN..E.VL.G.DTK.VTFCP.QDT.DQPLK.LAY.AT.P..P...GP....EAIA
Retrocopy EHQV*GEQVNEALKYLNMHEVVLSG*DTKQVTFCP<QDTSDQPLKTLAYTAT<PTEP*LPGPCAW<EAIA

Parental  TQILACRGFSGHNLEYLLRLADFMQLCGPQAQDEHLEAIVDAVGTKLPCFCPTEQALALV
          T.IL.C..FSGHNL.Y.L.L.DF.QLCG.Q..D..L.A.VDA.G..LPC.C.T.QALALV
Retrocopy TKILVC*VFSGHNLAYVLCLEDFTQLCGLQVHDKYLAAMVDAMGIMLPCSCLTKQALALV

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	0.58 RPM	1.36 RPM
SRP012922_cerebellum	0.14 RPM	3.57 RPM
SRP012922_heart	0.23 RPM	1.16 RPM
SRP012922_kidney	0.00 RPM	1.10 RPM
SRP012922_liver	0.00 RPM	1.55 RPM
SRP012922_lung	0.61 RPM	2.75 RPM
SRP012922_quadricep_muscle	0.00 RPM	0.17 RPM
SRP012922_spleen	0.23 RPM	0.46 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_438 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000017531	1 retrocopy	retro_dnov_438 ,
Otolemur garnettii	ENSOGAG00000024541	1 retrocopy	retro_ogar_3206,
Tursiops truncatus	ENSTTRG00000011476	2 retrocopies	retro_ttru_1747, retro_ttru_945,