RetrogeneDB ID: retro_dnov_1187

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_159647:2322..3032(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IL13RA1
• Ensembl ID: ENSDNOG00000011001
• Aliases: None
• Description: interleukin 13 receptor, alpha 1 [Source:HGNC Symbol;Acc:5974]

Sequence

>retro_dnov_1187
AGTGTTTCTGTTGAAAACCTCTACAAAAAAAGGGCATGGAATCCTCCTGACGGAGCCAACCCGAATTGCAGTCTATGGTA
TTTTAGTCACTTTGGCAAAAAAGAGGTTAAGAAAATGCTCCAGAAATTCATGTTCAAAAGAAGTACTCCTGAATGAGAGG
ATTTGTCTGCAGGTGGGGTCCCAGTGTAGCAGCAATTAAAGTGAGAAGCCTAATATTTTGGTGGAAAGGTGTATCTCACC
ACCTGAAGGTGACCCTGAGTCTGCTGTGACTGAGCTGTAATGTGTATGTCACAACCTGAACTATATGAAATGTTCATGGC
TGTCGGGAAAGAACACAAATCCTGATACTAACTATACTTTCTACTATTGGCACAGCAGTCTGGAAAACATTCTTCAATGT
GAAAACATCTATAAAGAAGGTCAACACATTGGATGTTCCTTTGATCTTAAAGTAAAGGATTCCAGTTTTGAACAACATAG
TTTGCAAATAATGGTCAGGGATAATGAAGGAAAAATTAGGCCTCCCTTCAATCAAAATAGTGCCTTTAACTTCCCAAGTG
AAACCTGATCCTCTGCATGTTAAATATCTTTTCCTTCCAAAAGGGTGGTTTGTATGTGGAATGGGAGAATCCACAGAAAT
TTCCTAGCAGATGCTTATCTTATCTAGCAGAGGTAATAACAGCCAAAGTGAGAATCCTTTTATTTCCAAT

Alignment

ORF - retro_dnov_1187 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.66 %
• Parental protein coverage: 61.4 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  SVSVENLCTIKWTWNLPEGANPNCSLWYFSCFGNKEDKII-APETHR-SKEVPLNERICLQVGSQCSSNE
          SVSVENL...K..WN.P.GANPNCSLWYFS.FG.KE.K...APE.H..SKEV.LNERICLQVGSQCSSN.
Retrocopy SVSVENLYK-KRAWNPPDGANPNCSLWYFSHFGKKEVKKM<APEIHV<SKEVLLNERICLQVGSQCSSN*

Parental  SEKPSILVEKCISPPEGDPESAVTELQCVCHNLNYMKCSWLPGKNTSPDTNYTLYYWHSSLGKILQCENI
          SEKP.ILVE.CISPPEGDPESAVTEL.CVCHNLNYMKCSWL.GKNT.PDTNYT.YYWHSSL..ILQCENI
Retrocopy SEKPNILVERCISPPEGDPESAVTEL*CVCHNLNYMKCSWLSGKNTNPDTNYTFYYWHSSLENILQCENI

Parental  YREGQHISCSFDLKVKDSSFEQHSLQIVVRDD-KGKIK-PSFKIVPLTSRVKPDPPHVKYL-SFQKGGLY
          Y.EGQHI.CSFDLKVKDSSFEQHSLQI.VRD..K.K...PS.KIVPLTS.VKPDP.HVKYL.SFQKGGLY
Retrocopy YKEGQHIGCSFDLKVKDSSFEQHSLQIMVRDN>KEKLGLPSIKIVPLTSQVKPDPLHVKYL>SFQKGGLY

Parental  VEWENPQNFPSRCLSYQVEV-NNSETEKPFIFN
          VEWENPQ.FPSRCLSY..EV.NNS..E.PFI.N
Retrocopy VEWENPQKFPSRCLSYLAEV<NNSQSENPFISN

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	70.98 RPM
SRP012922_cerebellum	0.00 RPM	2.61 RPM
SRP012922_heart	0.00 RPM	5.80 RPM
SRP012922_kidney	0.00 RPM	13.69 RPM
SRP012922_liver	0.00 RPM	88.24 RPM
SRP012922_lung	0.00 RPM	21.69 RPM
SRP012922_quadricep_muscle	0.00 RPM	2.42 RPM
SRP012922_spleen	0.00 RPM	48.99 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_1187 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	ENSDNOG00000011001	1 retrocopy	retro_dnov_1187 ,
Rattus norvegicus	ENSRNOG00000013170	1 retrocopy	retro_rnor_838,