RetrogeneDB ID: retro_dnov_2386

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_6989:67181..67855(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDNOG00000018857
• Aliases: None
• Description: None

Sequence

>retro_dnov_2386
CTTTCTCAAATGGAATATGGGCACTCAAAGAATCTCATTTATCGAGATGTTAAGCCAGAGAACTTCCTGATTGGCCGACA
AGGCAATAAGAAAGAGCATGTTATACACATTATAGACTTTGGACTGGCCAAGGAATACATTGACCCTGAAACCAAAAAAC
ACATACCTTATAGAGAGCACAAAAGTTTAACTGGAACTGTGAGATATATGTCTATCAACACGCATCTTGGCAAAGAGCAA
AGCCGTCTGATGATTTGGAAGCCCCAGGCCATATGTTCACGTATTTCCTTCGAGGCAGCCTACTCTGGCAAAAACTCAAG
GCTGATACATTAGAAGAGAGATATCAAAAGATTGGTGACACCAAAAGAAATACTCCCATTGAAGCTCTCTGTAAGAACTT
TCCAGAGGAGATGGCAACCTATCTTCGATATGTTAGGCGATTAGACTTCTTTGAAAAGCCTGACTACAAATACTTACGGA
CTCTCTTCACAGAACTCTTTGAAAGGAAAGGCTGTACCTTTGACTAAGCCTACGATTGAGTCGGGAGGCCTATTCCTACT
CCAGTAGGATCAGTTCATGTAGCTTCTGGTGCATCTGCAATAACTCGAGAAAGCCACACACACAGGGAGCGGCCATCACA
ACAGCAGCCTCTTCGAAATCAGACTGCATCGTCA

Alignment

ORF - retro_dnov_2386 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.59 %
• Parental protein coverage: 53.44 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LSRMEYVHSKNLIYRDVKPENFLIGRQGNKKEHVIHIIDFGLAKEYIDPETKKHIPYREHKSLTGTARYM
          LS.MEY.HSKNLIYRDVKPENFLIGRQGNKKEHVIHIIDFGLAKEYIDPETKKHIPYREHKSLTGT.RYM
Retrocopy LSQMEYGHSKNLIYRDVKPENFLIGRQGNKKEHVIHIIDFGLAKEYIDPETKKHIPYREHKSLTGTVRYM

Parental  SINTHLGKEQSR-RDDLEALGHMFMYFLRGSLPWQGLKADTLKERYQKIGDTKRNTPIEALCENFPEEMA
          SINTHLGKEQSR..DDLEA.GHMF.YFLRGSL.WQ.LKADTL.ERYQKIGDTKRNTPIEALC.NFPEEMA
Retrocopy SINTHLGKEQSR<SDDLEAPGHMFTYFLRGSLLWQKLKADTLEERYQKIGDTKRNTPIEALCKNFPEEMA

Parental  TYLRYVRRLDFFEKPDYEYLRTLFTDLFERKGYTFDYAYDWVGRPIPTPVGSVHVDSGASAITRESHTHR
          TYLRYVRRLDFFEKPDY.YLRTLFT.LFERKG.TFD.AYD.VGRPIPTPVGSVHV.SGASAITRESHTHR
Retrocopy TYLRYVRRLDFFEKPDYKYLRTLFTELFERKGCTFD*AYD*VGRPIPTPVGSVHVASGASAITRESHTHR

Parental  ERPSQQQPLRNQVVSS
          ERPSQQQPLRNQ..SS
Retrocopy ERPSQQQPLRNQTASS

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	1.17 RPM	9.14 RPM
SRP012922_cerebellum	0.41 RPM	8.52 RPM
SRP012922_heart	0.00 RPM	0.93 RPM
SRP012922_kidney	0.00 RPM	1.10 RPM
SRP012922_liver	0.00 RPM	1.86 RPM
SRP012922_lung	0.15 RPM	3.05 RPM
SRP012922_quadricep_muscle	0.00 RPM	1.04 RPM
SRP012922_spleen	0.69 RPM	3.43 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_2386 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010080	3 retrocopies	retro_chof_1577, retro_chof_2058, retro_chof_216,
Dasypus novemcinctus	ENSDNOG00000007923	1 retrocopy	retro_dnov_2552,
Dasypus novemcinctus	ENSDNOG00000018857	1 retrocopy	retro_dnov_2386 ,
Rattus norvegicus	ENSRNOG00000016620	1 retrocopy	retro_rnor_2267,
Tupaia belangeri	ENSTBEG00000003013	1 retrocopy	retro_tbel_17,