RetrogeneDB ID: retro_dnov_604

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_6726:847762..848220(+)
• Located in intron of: ENSDNOG00000012556

Retrocopy information

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

Parental gene information

• Parental gene symbol: GINS2
• Ensembl ID: ENSDNOG00000008760
• Aliases: None
• Description: GINS complex subunit 2 (Psf2 homolog) [Source:HGNC Symbol;Acc:24575]

Sequence

>retro_dnov_604
AATTTGAGACCTTTTAACCCTGGCTTACCAGTCAAAGTGCCTCTTGATGAGGCAACTAACCTGAAACAATGCAGAGGTGT
CAGTTGATACCTCCTGAAAGGACAGATTTAGAGAAGTTGGAGGATAACTGGGACCGTGAAAGAAAGCAAGAAACTTTTAT
CCCAATGTCCAGTCCTTACTACAGATAACTGACCAAACTCCTACTAAATCATGTTTAAGACAACATTTCAAAAGCAAATG
AGACTGAGACTCTGGTCAAAGGTATGTGGGACATTCACATAGTTAAACTTTGGTTCTCTACTGACAGCTTGGTAAAGCAA
TGGGAGGCACATGCCAAGTTGAACAACTTGACCCTAACAGAGTTTAACACCAGTGGAGCATTCCTCACTCAAGTGCTTGG
TCACATGTACAAGATCTTCAAAAATCTCCAGCCTTCTGGAAGTACCCAGTCTCAGGAC

Alignment

ORF - retro_dnov_604 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.48 %
• Parental protein coverage: 82.61 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DLGPFNPGLPVEVPLWLAINLKQ-RQKCRLIL-EWMDVEKLEANRDHERKEETFTPMPSPYYMELTKLLL
          .L.PFNPGLPV.VPL..A.NLKQ..Q.C.LI..E..D.EKLE.N.D.ERK.ETF.PM.SPYY..LTKLLL
Retrocopy NLRPFNPGLPVKVPLDEATNLKQ<MQRCQLIPPERTDLEKLEDNWDRERKQETFIPMSSPYYR*LTKLLL

Parental  NHASDNIPKADEIRTLVKDVWDTRIAKLRVSADSFVKQQEAHAKLDNLTLMEMNTSGAFLTQALGHMYKL
          NH..DNI.KA.E..TLVK..WD..I.KL..S.DS.VKQ.EAHAKL.NLTL.E.NTSGAFLTQ.LGHMYK.
Retrocopy NHV*DNISKANETETLVKGMWDIHIVKLWFSTDSLVKQWEAHAKLNNLTLTEFNTSGAFLTQVLGHMYKI

Parental  RTNLQPSESTQSQD
          ..NLQPS.STQSQD
Retrocopy FKNLQPSGSTQSQD

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	5.83 RPM
SRP012922_cerebellum	0.00 RPM	2.89 RPM
SRP012922_heart	0.00 RPM	1.62 RPM
SRP012922_kidney	0.00 RPM	1.37 RPM
SRP012922_liver	0.00 RPM	0.46 RPM
SRP012922_lung	0.00 RPM	2.14 RPM
SRP012922_quadricep_muscle	0.00 RPM	2.60 RPM
SRP012922_spleen	0.00 RPM	8.81 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_604 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 14 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017303	1 retrocopy	retro_cjac_3309,
Dasypus novemcinctus	ENSDNOG00000008760	4 retrocopies	retro_dnov_1034, retro_dnov_166, retro_dnov_2424, retro_dnov_604 ,
Homo sapiens	ENSG00000131153	1 retrocopy	retro_hsap_2477,
Gallus gallus	ENSGALG00000028131	1 retrocopy	retro_ggal_22,
Gorilla gorilla	ENSGGOG00000009069	2 retrocopies	retro_ggor_1542, retro_ggor_960,
Macropus eugenii	ENSMEUG00000014703	1 retrocopy	retro_meug_1479,
Microcebus murinus	ENSMICG00000016691	1 retrocopy	retro_mmur_342,
Macaca mulatta	ENSMMUG00000020594	1 retrocopy	retro_mmul_596,
Pongo abelii	ENSPPYG00000007616	2 retrocopies	retro_pabe_1826, retro_pabe_896,
Pan troglodytes	ENSPTRG00000008430	1 retrocopy	retro_ptro_1433,
Pteropus vampyrus	ENSPVAG00000004944	1 retrocopy	retro_pvam_762,
Sarcophilus harrisii	ENSSHAG00000015249	1 retrocopy	retro_shar_382,
Sus scrofa	ENSSSCG00000002663	1 retrocopy	retro_sscr_883,
Tupaia belangeri	ENSTBEG00000006220	1 retrocopy	retro_tbel_1328,