RetrogeneDB ID: retro_dnov_1635

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_25085:551..1500(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRNT1
• Ensembl ID: ENSDNOG00000008837
• Aliases: None
• Description: tRNA nucleotidyl transferase, CCA-adding, 1 [Source:HGNC Symbol;Acc:17341]

Sequence

>retro_dnov_1635
CATGAAGAAAATTTTGAAATTACTGCACTCTGGATTGACGTCACCACTGATGGAAGACATGCTGAGGTAGAATTCACAAC
TGACTGGAAGAAAGATGCTGAGTGCACAGATCTCACTAAAAATTCTATGTTTTTAAGTTTTGATAGTACCTTATTTGACT
ACTTTAATGGTTATGAAGATTTAAAAAACAAGAAAGTTAGATTTGTTGGACATGCTAAACCAAGAATTTAAGATTATCTT
CAAATTTTAAGGTATTTCAGGTTTTGTGGGAGAATTGTAGAAAAACCTGGTGACCATGATCCTGAGACTTTAGAAGCAAT
TGTTGAAAATGCAAAAGGATTGGCTGGAATATCAGGAGAGAGGATTTGGGTGGAACTGAGGAAAGTTCTTGTTGATAACC
ATGTAAATCACTTGATTCATCTTATGTATAATCTTGATGTGGCTCCTTACATAGGTTTACCTACTAATGCAAATTTGGAA
GAATTTGACTAAGTCAGTAAATATGCTGAAGGTTTTTCACCAAAGCCAATGACACTCTTGGCCTCATTATTCAAAGTACA
GGATGATGTCACAAAATTGGATTGGAGGTTGAAGATTTCAAAAGAAGAGAAAAACTTTGGCTTATTTATAATTAAAAATA
GGAAGGATTTAATTAAAGCAAAGGATAGTTCAGAACCATTGAAACCCTTTAAGGACTTCATTATAGATTCTAGGGAGCCT
GATGCGATTACTCGCGTATGTGAGCTACTGAAGTACCAAGGATAGCATTGTCTTCTAAAGGAAATGCAGCAGTGGTCCAT
TCCTCTATTTCCTGTAAGTGGCCATGACATCAGAAAAGTGGGCATTTCTTCAGGAAAGAAAATTGGAGCTCTATTGCAAC
AGTTGTGAGAACAGTGGGAAAAAAGTGGGTTACCCAATGGAAAAAGATGAACTTTTGAGTTATATAAAG

Alignment

ORF - retro_dnov_1635 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.68 %
• Parental protein coverage: 73.04 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  HEENFEITTLRIDVTTDGRHAEVEFTTDWQKDAERRDLTINSMFLGFDGTLFDYFNGYEDLKNKKVRFVG
          HEENFEIT.L.IDVTTDGRHAEVEFTTDW.KDAE..DLT.NSMFL.FD.TLFDYFNGYEDLKNKKVRFVG
Retrocopy HEENFEITALWIDVTTDGRHAEVEFTTDWKKDAECTDLTKNSMFLSFDSTLFDYFNGYEDLKNKKVRFVG

Parental  HAKQRIQEDYLRILRYFRFYGRIVEKPGDHDPETLEAIAENAKGLAGISGERIWVELRKILVGNHVNHLI
          HAK.RI..DYL.ILRYFRF.GRIVEKPGDHDPETLEAI.ENAKGLAGISGERIWVELRK.LV.NHVNHLI
Retrocopy HAKPRI*-DYLQILRYFRFCGRIVEKPGDHDPETLEAIVENAKGLAGISGERIWVELRKVLVDNHVNHLI

Parental  HLMYDLDVAPYIGLPANANLEEFDKVCKYAEGFSPKPMTVLASLFKVQDDVIKLDLRLKISREEKNLGLF
          HLMY.LDVAPYIGLP.NANLEEFD.V.KYAEGFSPKPMT.LASLFKVQDDV.KLD.RLKIS.EEKN.GLF
Retrocopy HLMYNLDVAPYIGLPTNANLEEFD*VSKYAEGFSPKPMTLLASLFKVQDDVTKLDWRLKISKEEKNFGLF

Parental  IVKNRKDLIKATDSSEPLKPYKDFIIDSREPDAITRVCELLKYQGEHCLLKEMQQWSIPPFPVSGHDIRK
          I.KNRKDLIKA.DSSEPLKP.KDFIIDSREPDAITRVCELLKYQG.HCLLKEMQQWSIP.FPVSGHDIRK
Retrocopy IIKNRKDLIKAKDSSEPLKPFKDFIIDSREPDAITRVCELLKYQG*HCLLKEMQQWSIPLFPVSGHDIRK

Parental  VGISSGKEIGALLQQLREQWKKS-GYQMEKDELLSYVK
          VGISSGK.IGALLQQL.EQW.KS.GY.MEKDELLSY.K
Retrocopy VGISSGKKIGALLQQL*EQWEKS>GYPMEKDELLSYIK

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	1.56 RPM	19.64 RPM
SRP012922_cerebellum	1.65 RPM	23.92 RPM
SRP012922_heart	0.70 RPM	13.92 RPM
SRP012922_kidney	0.00 RPM	14.24 RPM
SRP012922_liver	0.31 RPM	13.31 RPM
SRP012922_lung	1.83 RPM	18.02 RPM
SRP012922_quadricep_muscle	1.38 RPM	12.12 RPM
SRP012922_spleen	0.92 RPM	19.92 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_1635 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 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015466	1 retrocopy	retro_cjac_1512,
Dasypus novemcinctus	ENSDNOG00000008837	1 retrocopy	retro_dnov_1635 ,
Echinops telfairi	ENSETEG00000018177	2 retrocopies	retro_etel_1871, retro_etel_905,
Homo sapiens	ENSG00000072756	2 retrocopies	retro_hsap_246, retro_hsap_2598,
Gorilla gorilla	ENSGGOG00000015286	1 retrocopy	retro_ggor_300,
Nomascus leucogenys	ENSNLEG00000003226	1 retrocopy	retro_nleu_856,
Petromyzon marinus	ENSPMAG00000002236	1 retrocopy	retro_pmar_17,
Pongo abelii	ENSPPYG00000013702	3 retrocopies	retro_pabe_1916, retro_pabe_2721, retro_pabe_412,
Pan troglodytes	ENSPTRG00000014564	1 retrocopy	retro_ptro_1522,