RetrogeneDB ID: retro_dnov_748

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_104287:6991..7552(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SBDS
• Ensembl ID: ENSDNOG00000016904
• Aliases: None
• Description: Shwachman-Bodian-Diamond syndrome [Source:HGNC Symbol;Acc:19440]

Sequence

>retro_dnov_748
CCAACGAACCAGATCCGCCTAACTAATGTGGCCGTAGTACGAATGAAGCGCGGCAGGAAGCGCTTCGAAATCGCTTGCTA
CAAAAATAAAGTCGTAGGCTGGAGGAGTGGCATGGAAAAAGACCTTGACGAAGTTCTGTAGACCCACTCAGTGTTTGTAA
ATGTTTCTAAAGGTCAGGTTGCAAAGAAGGAAGAGCTCATCAGCGCATTTGACACAGATGACCGAACTGAAGTCTGTAAG
CAGATTTTGACTAAAGAAGAGGTTCAAATATTATATAAAGAACGGCACAGGCAGCTGGAGCAGATGTTTAGAGACATTGC
AACAATTGTAGCAGACAAATGTGTGAATCCTGAAACAAAGAGGCCGTACGCTGTTATCTTTATTGACAGAGCCATGAAGG
ACACCCACTATTCAGTCAAAACCAACAAGAGTACAAAACAGCAGGCGTTGGAAGTGATAAAGCAGTTAGAAGAGAAAATG
AAGATAGAACGTGCTCACATGATACTTCGATTCATTATTCCAGTGAACAAAGGGAAGAAGCTGAAAGAAAAGTTAAAGCC
A

Alignment

ORF - retro_dnov_748 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.7 %
• Parental protein coverage: 74.8 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PTNQIRLTNVAVVRMKRAGKRFEIACYKNKVVGWRSGVEKDLDEVLQTHSVFVNVSKGQVAKKEDLVSAF
          PTNQIRLTNVAVVRMKR..KRFEIACYKNKVVGWRSG.EKDLDEVL.THSVFVNVSKGQVAKKE.L.SAF
Retrocopy PTNQIRLTNVAVVRMKRGRKRFEIACYKNKVVGWRSGMEKDLDEVL*THSVFVNVSKGQVAKKEELISAF

Parental  GTDDQTEICKQILTKGEVQVSDKERHTQLEQMFRDIATIVADKCVNPETKRPYTVILIERAMKDIHYSVK
          .TDD.TE.CKQILTK.EVQ...KERH.QLEQMFRDIATIVADKCVNPETKRPY.VI.I.RAMKD.HYSVK
Retrocopy DTDDRTEVCKQILTKEEVQILYKERHRQLEQMFRDIATIVADKCVNPETKRPYAVIFIDRAMKDTHYSVK

Parental  TNKSTKQQALEVIKQLKEKMKIERAHMRLRFILPLNEGKKLKEKLKP
          TNKSTKQQALEVIKQL.EKMKIERAHM.LRFI.P.N.GKKLKEKLKP
Retrocopy TNKSTKQQALEVIKQLEEKMKIERAHMILRFIIPVNKGKKLKEKLKP

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	104.04 RPM
SRP012922_cerebellum	0.00 RPM	84.54 RPM
SRP012922_heart	0.00 RPM	44.78 RPM
SRP012922_kidney	0.00 RPM	127.59 RPM
SRP012922_liver	0.00 RPM	73.07 RPM
SRP012922_lung	0.00 RPM	100.80 RPM
SRP012922_quadricep_muscle	0.00 RPM	89.14 RPM
SRP012922_spleen	0.00 RPM	74.97 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_748 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.

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003795	2 retrocopies	retro_chof_1999, retro_chof_623,
Callithrix jacchus	ENSCJAG00000004283	1 retrocopy	retro_cjac_3984,
Dasypus novemcinctus	ENSDNOG00000016904	1 retrocopy	retro_dnov_748 ,
Loxodonta africana	ENSLAFG00000008763	1 retrocopy	retro_lafr_920,
Monodelphis domestica	ENSMODG00000006644	1 retrocopy	retro_mdom_2004,
Mus musculus	ENSMUSG00000025337	1 retrocopy	retro_mmus_950,
Otolemur garnettii	ENSOGAG00000009011	1 retrocopy	retro_ogar_3368,
Ochotona princeps	ENSOPRG00000008721	6 retrocopies	retro_opri_1179, retro_opri_154, retro_opri_363, retro_opri_484, retro_opri_698, retro_opri_957,
Rattus norvegicus	ENSRNOG00000000888	1 retrocopy	retro_rnor_686,
Ictidomys tridecemlineatus	ENSSTOG00000022203	1 retrocopy	retro_itri_1763,