RetrogeneDB ID: retro_dnov_1971

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_39534:6069..7015(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: POT1
• Ensembl ID: ENSDNOG00000010344
• Aliases: None
• Description: protection of telomeres 1 [Source:HGNC Symbol;Acc:17284]

Sequence

>retro_dnov_1971
TCCGGATTACTATCACTATATGAGGTAGAAATATGTCAACAACTATCTGCAACAATACTTGCAGATCATCAGTATTTGGA
GAAAACCCCATTGGGTGATATTTTGAAACAAAAAGCCCCTCAACAGATTGTATTCAAGCAAAACTGAGGTCATATAAACC
CAAAAGACTCTGAATCCGTTAAACTTCATTGTCCTAAATGTCTTTCACTGCAAGATGTTCCTCATGACAGCGATTTAGAT
AGCATTTAGCAAAATGGTGCAACTAGAACCCCAGATACCAAACTACAAAATACATCATTATATGATTCAGACATGTGGAC
CACTAAAGATCAAGGAGAACAAAAAGTAGCTGTTCATTTTTGTGAGAAATAATGGTATTCTCCCACTGTCAAATAACTGT
CTAATTTCGATAAAAGGAGGTACACTCAGTGAAATCTGCAATCCCTCAAACAAGTTTCATAGTATAATTCCTGTGAGATC
TGGTGCCAAAGACCTGAACTCCTCAGCATTTCAGCACTATTCCTTATACAAAGAAAAGTACACCACTATGGGTGTAAGCA
GTGTTCTAGCTTGAAGCCAATCAAAATCTAAACTCCCTCAATGGTAAAACATTTTGGATTCCTTCTTCTGTGGCAGAAGT
ACTGTGTATTGTACTTCCCCAATCTGTGTTTGTTATGACATTTACTCTTGACGATGAAACAGGAATTCTTGAAGCTTTTC
TCATGGATTCTGACAAATTCTTTCAGATTCCAGCATCAGAAATCCTAACCAGTGATGACCTTCAGAAAAGTATGGATATG
ATCATGGATATGTTTTGTCCTTCAGAAATAAAAACTGATGTTACCCATGGTTGGAATGCTTCATCAAGTCACATAATGTC
ACAAATGGAATGGAACAGCCAATTTGCTATCAGACTTTTGATAGCACAGTTGCAGAAGATCTTATC

Alignment

ORF - retro_dnov_1971 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.37 %
• Parental protein coverage: 50.24 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SGSVSLYEVERCQQLSATILTDHQYLGKTPLCDILKQKAPQQYRIRAKLRSYKPRRLFESVKLHCPKCRS
          SG..SLYEVE.CQQLSATIL.DHQYL.KTPL.DILKQKAPQQ...........P....ESVKLHCPKC.S
Retrocopy SGLLSLYEVEICQQLSATILADHQYLEKTPLGDILKQKAPQQIVFKQN*GHINPKDS-ESVKLHCPKCLS

Parental  LQDVPHEGDLDTILRDGATRTPDTKLQNTSLYDSEMWTTKDQGERKVAVHF-VKNNGILPLSNNCLILIE
          LQDVPH..DLD.I...GATRTPDTKLQNTSLYDS.MWTTKDQGE.KVAVHF.V.NNGILPLSNNCLI.I.
Retrocopy LQDVPHDSDLDSI*QNGATRTPDTKLQNTSLYDSDMWTTKDQGEQKVAVHF>VRNNGILPLSNNCLISIK

Parental  GGTLSEICNLSNKFHSVIPVRSGAEDL-ELLNLSAPFLIQRKIHHYGCKQCSSLKPI-QNLNSLVDKTSW
          GGTLSEICN.SNKFHS.IPVRSGA.DL.ELL..SA.FLIQRK.HHYGCKQCSSLKPI.QNLNSL..KT.W
Retrocopy GGTLSEICNPSNKFHSIIPVRSGAKDL<ELLSISALFLIQRKVHHYGCKQCSSLKPI<QNLNSLNGKTFW

Parental  IPSSVAEVLGIVPLQYVFVMTFTLDDGTGVLEAFLMDSDKFFQIPASEILTSDDLQKSMDMIMDMFCPPE
          IPSSVAEVL.IV..Q.VFVMTFTLDD.TG.LEAFLMDSDKFFQIPASEILTSDDLQKSMDMIMDMFCP.E
Retrocopy IPSSVAEVLCIVLPQSVFVMTFTLDDETGILEAFLMDSDKFFQIPASEILTSDDLQKSMDMIMDMFCPSE

Parental  IKID-AYPWLECFIKSYNVINETEQQICYQIFDTTVAEDLI
          IK.D..YPWLECFIKS.NV.N..EQ.ICYQ.FD.TVAEDLI
Retrocopy IKTD<CYPWLECFIKSHNVTNGMEQPICYQTFDSTVAEDLI

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	10.11 RPM
SRP012922_cerebellum	0.00 RPM	8.66 RPM
SRP012922_heart	0.00 RPM	3.48 RPM
SRP012922_kidney	0.00 RPM	5.75 RPM
SRP012922_liver	0.00 RPM	4.95 RPM
SRP012922_lung	0.00 RPM	11.91 RPM
SRP012922_quadricep_muscle	0.00 RPM	5.54 RPM
SRP012922_spleen	0.00 RPM	19.23 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_1971 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	ENSDNOG00000010344	1 retrocopy	retro_dnov_1971 ,
Oryctolagus cuniculus	ENSOCUG00000010617	1 retrocopy	retro_ocun_148,