RetrogeneDB ID: retro_dnov_1572

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_23739:39460..39889(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDNOG00000008670
• Aliases: None
• Description: None

Sequence

>retro_dnov_1572
ACCACAGCTGTGCAAATTGGAATAATTGGTGGAACAGGCCTGAATGATCCAGAAATTTTAGAAGGAAGAGCCGAAAAATA
TGTGGATACTCCATTTGGCAAGCCAACCAATGCCTTCGTGTGAGGGAGATAAAAAATGTTGGTTGTGTCCTTCTTGCAAA
GCTTGGGAGGTAGCACATCATCGTGGCTTCAAAAGTCAACTAGCAGGTGAATATCTGGCCCTTGAAGGAGGAGGGCTGTA
CTGTGTCATTGTGACCACAGCTTGTGGCTCCTTGAGGGAGGAGGTTCAGCCCAGCAATATTGTCATTATTGATCAGTTCA
TGGACAGGGCCACCACAAAGCCTAAGCCTTTCTATGATGAAGTCGTTCCTGGACCAGAGGAGTGGGTCGTGTTCCAATGG
TTGAGTCATTGTGCCCCAAAACGAGCGAG

Alignment

ORF - retro_dnov_1572 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.07 %
• Parental protein coverage: 51.06 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TTAVKIGIIGGTGLDDPDILEGRTEKYVDTPFGKPSDALILGK-IKNVDCVLLARHGRQHTIMPSKVNYQ
          TTAV.IGIIGGTGL.DP.ILEGR.EKYVDTPFGKP..A...G..IKNV.CVLLA..GR.H.I..SKVN.Q
Retrocopy TTAVQIGIIGGTGLNDPEILEGRAEKYVDTPFGKPTNAFV*GR<IKNVGCVLLAKLGR*HIIVASKVN*Q

Parental  ANIWALKEEGCS-HVIVTTACGSLREEIQPGDIVIIDQFIDRTTVRPQTFYDG-SHSCTRGVCHIPMAEP
          .NIW.LKEEGC...VIVTTACGSLREE.QP..IVIIDQF.DR.T..P..FYD..S.S.TRGV...PM.E.
Retrocopy VNIWPLKEEGCT<CVIVTTACGSLREEVQPSNIVIIDQFMDRATTKPKPFYDE<SRSWTRGVGRVPMVES

Parental  FCPKTRE
          .CPKT.E
Retrocopy LCPKTSE

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	4.67 RPM
SRP012922_cerebellum	0.00 RPM	3.02 RPM
SRP012922_heart	0.00 RPM	3.25 RPM
SRP012922_kidney	0.00 RPM	2.46 RPM
SRP012922_liver	0.00 RPM	1.70 RPM
SRP012922_lung	0.00 RPM	2.75 RPM
SRP012922_quadricep_muscle	0.00 RPM	7.96 RPM
SRP012922_spleen	0.00 RPM	5.27 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_1572 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 13 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000025929	1 retrocopy	retro_btau_1049,
Choloepus hoffmanni	ENSCHOG00000002224	1 retrocopy	retro_chof_772,
Callithrix jacchus	ENSCJAG00000008021	2 retrocopies	retro_cjac_187, retro_cjac_950,
Cavia porcellus	ENSCPOG00000000825	1 retrocopy	retro_cpor_375,
Dasypus novemcinctus	ENSDNOG00000008670	1 retrocopy	retro_dnov_1572 ,
Echinops telfairi	ENSETEG00000013214	1 retrocopy	retro_etel_588,
Macropus eugenii	ENSMEUG00000015381	2 retrocopies	retro_meug_807, retro_meug_917,
Microcebus murinus	ENSMICG00000015072	1 retrocopy	retro_mmur_927,
Macaca mulatta	ENSMMUG00000001137	1 retrocopy	retro_mmul_1549,
Ornithorhynchus anatinus	ENSOANG00000013963	1 retrocopy	retro_oana_38,
Oryctolagus cuniculus	ENSOCUG00000012289	2 retrocopies	retro_ocun_1355, retro_ocun_341,
Otolemur garnettii	ENSOGAG00000007889	1 retrocopy	retro_ogar_3285,
Ochotona princeps	ENSOPRG00000001259	1 retrocopy	retro_opri_792,