RetrogeneDB ID: retro_dnov_1965

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_39256:4581..5394(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MIER1
• Ensembl ID: ENSDNOG00000013550
• Aliases: None
• Description: mesoderm induction early response 1 homolog (Xenopus laevis) [Source:HGNC Symbol;Acc:29657]

Sequence

>retro_dnov_1965
TTTCAGGCATGGTTAATTTCCAGAATTTGGCCATCTGTTGAGTCTTCAAATCCAGTGGGTCCAGCAACATCAAGTGACCA
TGAATTTGATTCATCAGCCTACACGCTGGTTCATGATTTTGATGATGAATGGAAATTAGAAGAATAAATGATGGAAGGAG
AAACAAACTTCAGTTCTGAAATAGAGAATCTTGCAAGGGAAGGTGACATGCCACTTCATGAACTTCTCAGCCTTTATGGT
TATGGGGTACTGTCTGACCACCTGAAGAAGATGAAGAGGAGGAGGAAGGTGAAGAAGACAAAGAAGCTGATAATGATGAC
AACAGTGGCTGTAGTGAGGAAAATAAGTAAGAGAATATAAAGGATTCATCAGGTCAAGAGGATGAAACTCAATCTTCCAA
TGATGATTCATCACAATTGCTTCTCCAGATCCAAGGAAACAATCTGCACATGTCATTGTACACATTTTGATACAAACAGG
GAAATAAAAGAAGAATCTGAAAACCAAGATTATATTTCATCATAAGACTGGTAAAAGGAAATTATGGTGGGGTCTTTGTT
TCAAGTAGAGATTCTAGTTGGCATTTTTGGATATAAAGAAAATTTTAAAGTATATGAAAATGATGATCAGCTCTTGTGGG
ATTCTGAATATTTAATGGAAGACAAAGTGATTGCATTTCTTAAGGATGCATCTAGAAAAAGAGGTAATGAGAAAGGTATA
AAAGTAATTCCTGAAGGATCTCGCATAACAGACAATGAACAAGCTTTATGTCATTTGGTTAAATGTAATTTTGACACAGA
AGAACCATTGAGA

Alignment

ORF - retro_dnov_1965 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.21 %
• Parental protein coverage: 76.44 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  FNADKTDMMLPSVESSSPGGSATSDDHEFDPSADMLVHDFDDERTLEEEEMMEGETNFSSEIEDLARGRD
          F.A.......PSVESS.P.G.ATS.DHEFD.SA..LVHDFDDE..LEE..MMEGETNFSSEIE.LAR..D
Retrocopy FQAWLISRIWPSVESSNPVGPATSSDHEFDSSAYTLVHDFDDEWKLEE*-MMEGETNFSSEIENLAREGD

Parental  MPIHELLSLYGYD-STVRLPEEDEEGGEEEEEGEDDEDADNDDNSGCSGENKEENIKDSSGQEDETQSSN
          MP.HELLSLYGY...TV..PEED....EEEEEGE.D..ADNDDNSGCS.ENK.ENIKDSSGQEDETQSS.
Retrocopy MPLHELLSLYGYG<GTV*PPEED----EEEEEGEEDKEADNDDNSGCSEENK*ENIKDSSGQEDETQSS-

Parental  DDPSQ-SVTSQD-TQEIIRPRRCKYFDTNSEIEEESEEDEDYIPSEDWKKEIMVGSMFQAEIPVGICRYK
          .D.S.....S.D...E.I....C..FDTN.EI.EESE...DYI.S.DW.KEIMVGS.FQ.EI.VGI..YK
Retrocopy NDDSS<TIASPD<SKETICTCHCTHFDTNREIKEESE-NQDYISS*DW*KEIMVGSLFQVEILVGIFGYK

Parental  ENEKVYENDDQLLWDPEYLPEDKVIAFLKDASRRTGDEKGVEAIPEGSHIKDNEQALYELVKCSFDTEEA
          EN.KVYENDDQLLWD.EYL.EDKVIAFLKDASR..G.EKG...IPEGS.I.DNEQAL..LVKC.FDTEE.
Retrocopy ENFKVYENDDQLLWDSEYLMEDKVIAFLKDASRKRGNEKGIKVIPEGSRITDNEQALCHLVKCNFDTEEP

Parental  LR
          LR
Retrocopy LR

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	0.19 RPM	13.81 RPM
SRP012922_cerebellum	0.14 RPM	8.39 RPM
SRP012922_heart	0.00 RPM	6.26 RPM
SRP012922_kidney	0.00 RPM	7.94 RPM
SRP012922_liver	0.15 RPM	3.41 RPM
SRP012922_lung	0.31 RPM	13.59 RPM
SRP012922_quadricep_muscle	0.00 RPM	3.98 RPM
SRP012922_spleen	0.00 RPM	14.19 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_1965 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000013550	1 retrocopy	retro_dnov_1965 ,