RetrogeneDB ID: retro_dnov_2157

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_5164:81580..82186(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PQLC3
• Ensembl ID: ENSDNOG00000015960
• Aliases: None
• Description: PQ loop repeat containing 3 [Source:HGNC Symbol;Acc:28503]

Sequence

>retro_dnov_2157
ATGGGCTCGGGGCTGCTGTGGTTCTGCTACTGGAGCACGCTGGGCGTATGCGCCGTGCTCAAGCTGCGGCAGATCTCGGC
TCTGCTGGCGGCGCGTGGCGCGCGGGCCCTCAGCGTCCCGAGTTTACTTCTGGAGCTGGCGGGGTTCCTGGTGTTCCTCC
GGTACCAGTGCTACTACAGCTACCCACTGCTGACATACCTGGAGTATCCCATCATCATCGCTCAAGATATCCTCCTACTC
TGCGTCTTCCATTTTAATGGGAACGTGAAACAGGTTGCTCCATACTTTGCTGTATTTTTGTCTTCTTGGTTTGTCCTCAC
TCTGCAGAAGTGGATCATAGACCTGGCCATGAATTTATCTACTTTCATTAGCGCGGCCAGTAAATTTGCACAACTCCAGT
ATCTGTGGAAGACAAAGGACTCAGGAGCAGTGAGTGCTCTAACTTGGAGCCTCTCTTCACACACCTGTGCAACAAGAATA
CTATCAACCTTAATGACCACCAATGATCTTACAATTCTTATCCGTTTTGTGATCATGCTGGCTTTAAACATATGGGTAAC
AGCTACAATACTTCACTACGGGAAGATGAGCACTGTAAGGACTGAA

Alignment

ORF - retro_dnov_2157 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.77 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGPGLLWFCHWSTLGVCAALKLPQISALLAARGARGLSVPSLLLELTEFLVFLRYQCYYGYPLLTYLEYP
          MG.GLLWFC.WSTLGVCA.LKL.QISALLAARGAR.LSVPSLLLEL..FLVFLRYQCYY.YPLLTYLEYP
Retrocopy MGSGLLWFCYWSTLGVCAVLKLRQISALLAARGARALSVPSLLLELAGFLVFLRYQCYYSYPLLTYLEYP

Parental  IIIAQDIILLLCIFHFKGNVKQAAPYFAVXXXXXXXXXXXXXXXXXXXNLSTFISAASKFAQLQYLWKTK
          IIIAQDI.LLLC.FHF.GNVKQ.APYFAV...................NLSTFISAASKFAQLQYLWKTK
Retrocopy IIIAQDI-LLLCVFHFNGNVKQVAPYFAVFLSSWFVLTLQKWIIDLAMNLSTFISAASKFAQLQYLWKTK

Parental  DSGAVSALTWSLSSYTCATRIVTTLMTTNDLTILIRFVIMLALNIWVTATILHYRKMNTVKTE
          DSGAVSALTWSLSS.TCATRI..TLMTTNDLTILIRFVIMLALNIWVTATILHY.KM.TV.TE
Retrocopy DSGAVSALTWSLSSHTCATRILSTLMTTNDLTILIRFVIMLALNIWVTATILHYGKMSTVRTE

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	3.31 RPM	30.34 RPM
SRP012922_cerebellum	2.89 RPM	77.12 RPM
SRP012922_heart	0.93 RPM	12.99 RPM
SRP012922_kidney	13.14 RPM	151.41 RPM
SRP012922_liver	0.93 RPM	9.91 RPM
SRP012922_lung	4.28 RPM	53.15 RPM
SRP012922_quadricep_muscle	0.52 RPM	6.23 RPM
SRP012922_spleen	6.52 RPM	72.45 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_2157 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 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006017	3 retrocopies	retro_chof_1902, retro_chof_2195, retro_chof_717,
Callithrix jacchus	ENSCJAG00000006801	1 retrocopy	retro_cjac_3969,
Dasypus novemcinctus	ENSDNOG00000015960	1 retrocopy	retro_dnov_2157 ,
Macropus eugenii	ENSMEUG00000009376	1 retrocopy	retro_meug_1167,
Mus musculus	ENSMUSG00000045679	2 retrocopies	retro_mmus_1352, retro_mmus_2875,