RetrogeneDB ID: retro_dnov_1261

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_171308:3675..4496(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MGME1
• Ensembl ID: ENSDNOG00000002646
• Aliases: None
• Description: mitochondrial genome maintenance exonuclease 1 [Source:HGNC Symbol;Acc:16205]

Sequence

>retro_dnov_1261
ATAAAAATGAAGGCTTTTCGGACCATTTGTAGGCAGCTCAGAAGTTCAAAGGGGTTTTCAGTAGAACCAGCACACTGTCT
AGGTTTCTCTACTTCCTCTTACTCACATGACCAGAAGAAAAAAGTGAACTCTTGAGAAGTGGACCAAAATAAATACTCTG
GTTTAGTACAGTCTGTCTTGTCATTCAGAAGCCATGCTCAGATCCAATAATTACTATTTGAGGAAGATGCTTTATTCTAT
GGGCCTGTGAATAAGCATAAGCCCCCAAAGCAAGGTGATCAAGCAAGAATTACATATAACTGTCTTCCTCTTTTCAATCT
AGAGAGAAGTGTAACATCAAATTCAGGTGACTCTTCAATTCCTTTGAAAATCCCTTTGAAAAAGAATGTGATACCAAGCG
TGACCCAGGTCCTTCAACAGTCCATGACAACACAAGAGATCTTCTGTTTGGAGAGGTGGAAGCAGAGGATGATTCTGGAG
CTGGGGGAAGATGGCTTTGCAGAATATACTTCAAACACATTTCTATAAAGGAAATGGTTCCATGAAGCCTTGGAAAGCCT
ACTTTTACCCCAGGGAAACTTGAAAGAGAGAGATGAAAAAATCTCCTCGAATCTGGCTACATTGAGTGTCCAGCATATTC
TGGAAGATGTCAGTGGTGTGCAAATGCTTGAAAGTGCTGTTCAGCATGAGGCCCTAAAGATGTAGGACTGCTGGACTGTG
TGGCTAAGTATCATGGCAAGCTGTGTGTGATCGATTGGTAGACATCAGAAAAAACAAAGCTTATATCCCAAAATACATTT
GACAACCCGCTGCAAGTACTA

Alignment

ORF - retro_dnov_1261 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.73 %
• Parental protein coverage: 80.12 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IKMKAFQTICRQLGSSKGFSVEPAPCVGFSTSSYACNRKKKVNSYEEVDQDKYSDLVQSVLSFRRHAQTP
          IKMKAF.TICRQL.SSKGFSVEPA.C.GFSTSSY....KKKVNS.E.VDQ.KYS.LVQSVLSFR.HAQ..
Retrocopy IKMKAFRTICRQLRSSKGFSVEPAHCLGFSTSSYSHDQKKKVNS*E-VDQNKYSGLVQSVLSFRSHAQIQ

Parental  ESLFEEDAFLYGPVSKRKPPKQGDPARIPRNWLPLFNPERSVTSNTIDSPIPLKIPLKKNVIPSVTRVLQ
          ..LFEEDA..YGPV.K.KPPKQGD.ARI..N.LPLFN.ERSVTSN..DS.IPLKIPLKKNVIPSVT.VLQ
Retrocopy *LLFEEDALFYGPVNKHKPPKQGDQARITYNCLPLFNLERSVTSNSGDSSIPLKIPLKKNVIPSVTQVLQ

Parental  QTMTPQQVFCLERWKQRMILELGEDGFAEYTSNIFLQRKQLHE--ESILSLQGNLKEKDEKNLLESGYIK
          Q.MT.Q..FCLERWKQRMILELGEDGFAEYTSN.FL.RK..HE..ES.L..QGNLKE.D...........
Retrocopy QSMTTQEIFCLERWKQRMILELGEDGFAEYTSNTFL*RKWFHEALESLLLPQGNLKERD-EKISSNLATL

Parental  SVQHILEDVSGVRALESAVQHEALKY-VGLLDCVAEYXXXXCVIDWKTSEKPKPFIQNTFDNPLQVV
          SVQHILEDVSGV..LESAVQHEALK..VGLLDCVA.Y....CVIDW.TSEK.K...QNTFDNPLQV.
Retrocopy SVQHILEDVSGVQMLESAVQHEALKM<VGLLDCVAKYHGKLCVIDW*TSEKTKLISQNTFDNPLQVL

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	5.25 RPM
SRP012922_cerebellum	0.00 RPM	5.64 RPM
SRP012922_heart	0.00 RPM	8.82 RPM
SRP012922_kidney	0.00 RPM	4.65 RPM
SRP012922_liver	0.00 RPM	2.17 RPM
SRP012922_lung	0.00 RPM	7.03 RPM
SRP012922_quadricep_muscle	0.00 RPM	7.62 RPM
SRP012922_spleen	0.00 RPM	13.16 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_1261 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000002646	2 retrocopies	retro_dnov_1261 , retro_dnov_1803,
Tursiops truncatus	ENSTTRG00000016431	1 retrocopy	retro_ttru_1335,