RetrogeneDB ID: retro_dnov_1803

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_31165:83017..83804(+)
• 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_1803
TCTTCAAAGGAGTTTTCCGTAGAACCAGTCCCCTGTATGGGCTTCTCCACTTCCTCTTATTCTTGTGATGGGAAGAAAAA
AGTGAACTCTTATGAAGAAGTCGAACAAAATAAATACTCTGACTTAGTACAGTCCATCTTGTCATTAATACGCCATGCTC
AGACCCCAGAATCACTATTTGAGGAAGATGCTTTATTCTATGGGCCTGTGAATAAGCATAAGCCCCCAAAGCAAGGTGAT
CAAGCAAGAATTACATATAACTGTCTTCCTCTTTTCAATCTAGAGAGAAGTGTAACATCAAATTCAGGTGACTCTTCAAT
TCCTTTGAAAATCCCTTTGAAAAAGAATGTGATACCAAGCGTGACCCAGGTCCTTCAACAGTCCATGACAACACAAGAGA
TCTTCTGTTTGGAGAGGTGGAAGCAGAGGATGATTCTGGAGCTGGGGGAAGATGGCTTTGCAGAATATACTTCAAACACA
TTTCTATAAAGGAAATGGTTCCATGAAGCCTTGGAAAGCCTACTTTTACCCCAGGGAAACTTGAAAGAGAGAGATGAAAA
AATCTCCTCGAATCTGGCTACATTGAGTGTCCAGCATATTCTGGAAGATGTCAGTGGTGTGCAAATGCTTGAAAGTGCTG
TTCAGCATGAGGCCCTAAAGATGTAGGACTGCTGGACTGTGTGGCTAAGTATCAGGGCAAGCTGTGTGTGATCGATTGGA
AGACATCAGAAAAAACAAAGCTTATATCCAAAATACATTTGACAACCCGCTGCAAGTACTAGCACAC

Alignment

ORF - retro_dnov_1803 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.94 %
• Parental protein coverage: 76.61 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SSKGFSVEPAPCVGFSTSSYACNRKKKVNSYEEVDQDKYSDLVQSVLSFRRHAQTPESLFEEDAFLYGPV
          SSK.FSVEP.PC.GFSTSSY.C..KKKVNSYEEV.Q.KYSDLVQS.LS..RHAQTPESLFEEDA..YGPV
Retrocopy SSKEFSVEPVPCMGFSTSSYSCDGKKKVNSYEEVEQNKYSDLVQSILSLIRHAQTPESLFEEDALFYGPV

Parental  SKRKPPKQGDPARIPRNWLPLFNPERSVTSNTIDSPIPLKIPLKKNVIPSVTRVLQQTMTPQQVFCLERW
          .K.KPPKQGD.ARI..N.LPLFN.ERSVTSN..DS.IPLKIPLKKNVIPSVT.VLQQ.MT.Q..FCLERW
Retrocopy NKHKPPKQGDQARITYNCLPLFNLERSVTSNSGDSSIPLKIPLKKNVIPSVTQVLQQSMTTQEIFCLERW

Parental  KQRMILELGEDGFAEYTSNIFLQRKQLHE--ESILSLQGNLKEKDEKNLLESGYIKSVQHILEDVSGVRA
          KQRMILELGEDGFAEYTSN.FL.RK..HE..ES.L..QGNLKE.D...........SVQHILEDVSGV..
Retrocopy KQRMILELGEDGFAEYTSNTFL*RKWFHEALESLLLPQGNLKERD-EKISSNLATLSVQHILEDVSGVQM

Parental  LESAVQHEALKY-VGLLDCVAEYXXXXCVIDWKTSEKP-KPFIQNTFDNPLQVVAY
          LESAVQHEALK..VGLLDCVA.Y....CVIDWKTSEK..K..IQNTFDNPLQV.A.
Retrocopy LESAVQHEALKM<VGLLDCVAKYQGKLCVIDWKTSEKT<KAYIQNTFDNPLQVLAH

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	0.17 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_1803 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,