RetrogeneDB ID: retro_dnov_211

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_2660:179234..179849(-)
• Located in intron of: ENSDNOG00000007370

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDNOG00000008252
• Aliases: None
• Description: None

Sequence

>retro_dnov_211
GATTTCTATAATTGGCCTGATGAATCTTTTGATGAAATGGGCAGTACACTAGCTGTTCAACAATATATTCAACAGAACAT
AAGGACAGATTGCTCCAATATTGACAAAATTCTTAAACCACCTGAAGGCTGAGATGAAGGTATATGGAAGTATGAACATT
TAAGACAGTTTTGCCTTGAGCGAAATGGACTTGCTGTCAAACTTCAGAGTGAATGCTGTCCAGATACACATACTCAGATG
ACAGCAACTTAACAATGGATTTTTCTTTCTGCAGCTCATAAAACTCCAAAAGAGTGTCCTGCCATAGACTATACTAGGCA
CATGCTTGACAGGACTGCATGTCTACTGAATAGCAGTAAATATTTTCCCCACAAAGTTAGCATAAAGGAATCATCTGTAG
CAAAACTAGGACCGGTATGTTGTAGGATTTACAGAATATTTTCACATGCTTATTTTCATCATCGACAGGTATTTGATGGA
TATGAAAATGAAACATTTTTGTGTCATCAGTTTACTAAATTTGTGATGAAATATAATTTGATGTCCAAGGATAACCTGAT
TGTACCAATTTTAGAAGAAGAAGTATAGAATTCAGTTTCTGGAGAAAGTGAGGCA

Alignment

ORF - retro_dnov_211 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.41 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DFYNWPDESFDEMDSTLAVQQYIQQNIRA-CSNMDKILEPPEGQXXXXXXXXXXXQFCLELNGLAVKLQS
          DFYNWPDESFDEM.STLAVQQYIQQNIR..CSN.DKIL.PPEG............QFCLE.NGLAVKLQS
Retrocopy DFYNWPDESFDEMGSTLAVQQYIQQNIRTDCSNIDKILKPPEG*DEGIWKYEHLRQFCLERNGLAVKLQS

Parental  ECHPDTCTQMTATEQWIFLCAAHKTPKECPAIDYTRHTLDGAACLLNSNKYFPSRVSIKESSVAKLGSVC
          EC.PDT.TQMTAT.QWIFL.AAHKTPKECPAIDYTRH.LD..ACLLNS.KYFP..VSIKESSVAKLG.VC
Retrocopy ECCPDTHTQMTAT*QWIFLSAAHKTPKECPAIDYTRHMLDRTACLLNSSKYFPHKVSIKESSVAKLGPVC

Parental  RRIYRIFSHAYFHHRQIFDEYENETFLCHRFTKFVMKYNLMSKDNLIVPILEEEVQNSVSGESEA
          .RIYRIFSHAYFHHRQ.FD.YENETFLCH.FTKFVMKYNLMSKDNLIVPILEEEV.NSVSGESEA
Retrocopy CRIYRIFSHAYFHHRQVFDGYENETFLCHQFTKFVMKYNLMSKDNLIVPILEEEV*NSVSGESEA

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	11.28 RPM
SRP012922_cerebellum	0.69 RPM	9.90 RPM
SRP012922_heart	0.23 RPM	8.35 RPM
SRP012922_kidney	0.00 RPM	8.21 RPM
SRP012922_liver	0.62 RPM	6.81 RPM
SRP012922_lung	0.76 RPM	9.01 RPM
SRP012922_quadricep_muscle	1.38 RPM	7.10 RPM
SRP012922_spleen	0.46 RPM	12.36 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_211 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000884	5 retrocopies	retro_chof_1077, retro_chof_1354, retro_chof_1631, retro_chof_177, retro_chof_213,
Dasypus novemcinctus	ENSDNOG00000008252	1 retrocopy	retro_dnov_211 ,
Homo sapiens	ENSG00000115540	2 retrocopies	retro_hsap_2275, retro_hsap_906,
Latimeria chalumnae	ENSLACG00000015430	1 retrocopy	retro_lcha_112,
Oryctolagus cuniculus	ENSOCUG00000005712	1 retrocopy	retro_ocun_30,