RetrogeneDB ID: retro_dnov_2402

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_716:17335..17794(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDNOG00000017624
• Aliases: None
• Description: None

Sequence

>retro_dnov_2402
AAGCCAGCCAGGGAGGAGGTTACAAGAGCCACTGACACAAGGGAAAAAAGATAAAGAAGATATGATTTGTGTAGAGAAGG
ATGCCAGGGAAAGAATTCCAGTATTTGATAAGCACAGGGAAAAAAGACCATCTGCAGGAACAGCTGAGGAAGATATGGGA
GTCAAGTCCATAAAACGTTGAAAAGTTTGGCAGATTACATTAAAAAGTCTCTTCTTGCAAAGAGGAAAAGATATAAAATG
AACACCAGTGATTTGCTCAATGCCAGTAACCAGATAATTGATCATGTTTGGAAAACACAGCAAGAGCAATGGAAGAATCT
TAATTATGAATATTTTTAGCAGTTTCCAGTTTTCTTTCAACAGTGGGATATAGATGTGCAGAAAGCTGGGGAACAAGAAG
AAAAACCAAATGATATGTTTTAACAACAACGGAAGAATTTTCAACAATCTAGAATTATT

Alignment

ORF - retro_dnov_2402 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.59 %
• Parental protein coverage: 83.78 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KPAMEDQVIRVYDF-GKEDKKDLDGSEEGIVEEKFPVIDKHGKKRPCTEMIETDMG-GEVHNMLERFGAD
          KPA.E..V.R..D..GK.DK.D....E.....E..PV.DKH..KRP.....E.DMG...VH..L......
Retrocopy KPAREE-VTRATDT>GKKDKEDMICVEKD-ARERIPVFDKHREKRPSAGTAEEDMG<SQVHKTLKSLADY

Parental  INKTLLAKRKRLEVYTKASLKTSNQKIEHFWKVQQEQRQKLNQEYSQQFLTLFQQWEVDVQKAEEQEEKL
          I.K.LLAKRKR....T...L..SNQ.I.H.WK.QQEQ...LN.EY..QF...FQQW..DVQKA.EQEEK.
Retrocopy IKKSLLAKRKRYKMNTSDLLNASNQIIDHVWKTQQEQWKNLNYEYF*QFPVFFQQWDIDVQKAGEQEEKP

Parental  ANIFRQQQKIFQQSRIV
          ...F.QQ.K.FQQSRI.
Retrocopy NDMF*QQRKNFQQSRII

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	1.36 RPM
SRP012922_cerebellum	0.00 RPM	13.06 RPM
SRP012922_heart	0.00 RPM	0.70 RPM
SRP012922_kidney	0.00 RPM	0.55 RPM
SRP012922_liver	0.00 RPM	0.00 RPM
SRP012922_lung	0.00 RPM	1.83 RPM
SRP012922_quadricep_muscle	0.00 RPM	0.00 RPM
SRP012922_spleen	0.00 RPM	2.75 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_2402 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 12 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013389	2 retrocopies	retro_chof_1384, retro_chof_2693,
Callithrix jacchus	ENSCJAG00000001658	1 retrocopy	retro_cjac_2710,
Cavia porcellus	ENSCPOG00000001202	1 retrocopy	retro_cpor_686,
Dasypus novemcinctus	ENSDNOG00000017387	2 retrocopies	retro_dnov_2623, retro_dnov_739,
Dasypus novemcinctus	ENSDNOG00000017624	3 retrocopies	retro_dnov_2294, retro_dnov_2402 , retro_dnov_420,
Echinops telfairi	ENSETEG00000007664	1 retrocopy	retro_etel_1510,
Myotis lucifugus	ENSMLUG00000010711	2 retrocopies	retro_mluc_1098, retro_mluc_1839,
Mus musculus	ENSMUSG00000067764	1 retrocopy	retro_mmus_1085,
Mus musculus	ENSMUSG00000072479	1 retrocopy	retro_mmus_1782,
Otolemur garnettii	ENSOGAG00000024543	1 retrocopy	retro_ogar_633,
Rattus norvegicus	ENSRNOG00000017224	1 retrocopy	retro_rnor_1728,
Ictidomys tridecemlineatus	ENSSTOG00000001853	1 retrocopy	retro_itri_931,