RetrogeneDB ID: retro_dnov_1742

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_28291:7887..9113(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000006894
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: LINS
• Ensembl ID: ENSDNOG00000009790
• Aliases: None
• Description: lines homolog (Drosophila) [Source:HGNC Symbol;Acc:30922]

Sequence

>retro_dnov_1742
ATATTGTCTAGCAAACTGAGTTCCATGCAAAGGAGAAATACAGTGATATCATTAAAATTCTTTTAAAATCATCTGAAGTG
GATTCTAAATTAATCTCTATGTTCCAGAATTCAGATAAATTGGTATCTCACATGGCTGCAAAGTGCCTCGCATTGCTTCT
GTATTTCCAACTGAGGGAGAAGATAACATTAAGTAATTCCTGGATTGCTTTTTGTCAGAAAAATCTTTCTGAGTACCCTG
AAAGTGATAAGATAGCTTGCTGTCTCTGCACTCTTACAGTTGTAATAAAAGAAATCCTTAAAGATACATGTTCACAAAAA
CCAGAAATTCTAAAGCAGTTCCTGGCTCCTTTTGACACTACTTTTGAAGTATTTTACAACTCCTTATTTTCTCAGCATTT
TGAAAACTGCCGTGATACTTCTAAAATAATAAACAGCTTGATGAGTTTCCTGGAATTGCTTGAACTTCTTATAGCCACCA
GAATCTACCTAAAGTTACATTTCACTTGCCAGAGGATTTTATTTTTGAGACCTTCTTGTGTGCTAGACATTATTACCTGG
CCCACTCAGGCTTTCGTCAAAAAGAAGTTCATCGTATTTGTTAAAAAGTGCCTTCTCTGTAAAGTGGGTGAAGACCTCTT
TCCTGGATCTGTCCCTGCCTTAATGCTACCAGATAATCATTTAGAAGTGGATATGTTGGCTTTAGCTAATGCCATTTTAC
ATGCTGTGAATTTGGGGATGTTGAGGACATTATCTATTCATGGAAAACCTTCCTACTTTGGAGGCAATGAAGTTCAGCCT
GGATGTGGAAGTATCTCTGGTCCAGATCAAGCAATCCTTAGAGCAGTGAGCTTAGTTTTAATTAAATCCTTAGAAATCAA
GTTTCAAAATTGTACTTCAGCAAATGAAATGAAAGTTGACTTGCAGAGATTCATGTCTGAGTTATTTACCTTCTTAAAGC
CTCATCTTCAGCCCTCTCTGCAATTACATAATCCCTGTGAGTGGCTCTCCAGGATCTTCATAGAACAAGATGATGACATG
CTGGAGGCTGCCAAGGCATCCCTGGGCATCTACCTCAAGTTCAGCAGAGAATGTTGTAAAGCTACTGAAAACTTGACCCA
AGAAAAAGTAAGGTGGAACCATCACACACACGAAAATGGCTATAATCCTCACTGTATTTTCTTATTCTTCTTAAAAAATA
TAGAATTTGATTTTAGCGTTCTTCTT

Alignment

ORF - retro_dnov_1742 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.05 %
• Parental protein coverage: 55.87 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ILSSK-TKFHTKENYSDIIKILLKSSKVDSKLISMFQNSDKLVSHMAAKCLALLLYFQLREKITLSNSWI
          ILSSK.T.FH.KE.YSDIIKILLKSS.VDSKLISMFQNSDKLVSHMAAKCLALLLYFQLREKITLSNSWI
Retrocopy ILSSK<TEFHAKEKYSDIIKILLKSSEVDSKLISMFQNSDKLVSHMAAKCLALLLYFQLREKITLSNSWI

Parental  AFCQKNLSEYPESDKIACCLCTLTVVIKEILKDTCSQKPEILKQFLAPFDTTFEVFYNSLFSQHFENCRD
          AFCQKNLSEYPESDKIACCLCTLTVVIKEILKDTCSQKPEILKQFLAPFDTTFEVFYNSLFSQHFENCRD
Retrocopy AFCQKNLSEYPESDKIACCLCTLTVVIKEILKDTCSQKPEILKQFLAPFDTTFEVFYNSLFSQHFENCRD

Parental  TSKIINSLMSFLELLELLIATRIYLKLHFTCQRILFLRPSCVLDIITWPTQAFVKKKFIVFVKKCLLCKV
          TSKIINSLMSFLELLELLIATRIYLKLHFTCQRILFLRPSCVLDIITWPTQAFVKKKFIVFVKKCLLCKV
Retrocopy TSKIINSLMSFLELLELLIATRIYLKLHFTCQRILFLRPSCVLDIITWPTQAFVKKKFIVFVKKCLLCKV

Parental  GEDLFPGSVPALMLPDNHLEVDMLALANAILHAVNLGMLRTLSIHGKPSYFGGNEVQPGCGSISGPDQAI
          GEDLFPGSVPALMLPDNHLEVDMLALANAILHAVNLGMLRTLSIHGKPSYFGGNEVQPGCGSISGPDQAI
Retrocopy GEDLFPGSVPALMLPDNHLEVDMLALANAILHAVNLGMLRTLSIHGKPSYFGGNEVQPGCGSISGPDQAI

Parental  LRAVSLVLIKSLEIKFQNCTSANEMKVDLQRFMSELFTFLKPHLQPSLQLHDPCEWLSRIFIEQDDDMLE
          LRAVSLVLIKSLEIKFQNCTSANEMKVDLQRFMSELFTFLKPHLQPSLQLH.PCEWLSRIFIEQDDDMLE
Retrocopy LRAVSLVLIKSLEIKFQNCTSANEMKVDLQRFMSELFTFLKPHLQPSLQLHNPCEWLSRIFIEQDDDMLE

Parental  AAKASLGIYLKFSRECCKATENLTQEKVRWNHHTHENGYNPHCIFLFFLKNIGFDFTVLL
          AAKASLGIYLKFSRECCKATENLTQEKVRWNHHTHENGYNPHCIFLFFLKNI.FDF.VLL
Retrocopy AAKASLGIYLKFSRECCKATENLTQEKVRWNHHTHENGYNPHCIFLFFLKNIEFDFSVLL

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	5.25 RPM	13.22 RPM
SRP012922_cerebellum	3.02 RPM	9.90 RPM
SRP012922_heart	0.23 RPM	5.80 RPM
SRP012922_kidney	4.11 RPM	8.49 RPM
SRP012922_liver	2.48 RPM	8.51 RPM
SRP012922_lung	4.89 RPM	12.22 RPM
SRP012922_quadricep_muscle	2.42 RPM	7.10 RPM
SRP012922_spleen	5.15 RPM	16.71 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_1742 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.

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000009790	1 retrocopy	retro_dnov_1742 ,
Monodelphis domestica	ENSMODG00000012160	1 retrocopy	retro_mdom_134,