RetrogeneDB ID: retro_dnov_1892

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_35666:13607..14054(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CAPZA2
• Ensembl ID: ENSDNOG00000005771
• Aliases: None
• Description: capping protein (actin filament) muscle Z-line, alpha 2 [Source:HGNC Symbol;Acc:1490]

Sequence

>retro_dnov_1892
TTCATCACTCATGTATGATCAGCAGAATTTTATGAAGTGTTTAATGGTGCCTGGCTACTGCTTAATAATGACAATCTTCT
CAGGGAAGGGGCAGTACATACTTTGCTTAATATAACATGGATCAGTTCACACCTGTAAAGGTAGAAAGATATGATGATCA
GGTCTTAATTACAGAATATGGTGACCTGGGTTATAGCAGATTTTTAGATCCAAGAAACAAAATTTCCTTTAAGTTTGATC
ACTTATGGAAAGAAGCAAGTGACCCCCAGCCAAGAGGAAGTAGATGGAGGACTGAAGTCTTGGACAGAATCCTGAGACAG
TGCTTTAAGGGCCTATGTGAAAGATCATTATTCCAACGGCTTCTGTACTATTTACTCTAAAACTATAGATGGGCAACAGA
CGATTATCGCACGTATTGAAAGCCACCAGTTTCAGCCTAAAAACTTC

Alignment

ORF - retro_dnov_1892 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.55 %
• Parental protein coverage: 54.58 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FIIHAPPGEFNEVFNDVRLLLNNDNLLREGAAHA-FAQYNLDQFTPVKIEGYEDQXLITEHGDLGNGKFL
          FI.H....EF.EVFN...LLLNNDNLLREGA.H..FA.YN.DQFTPVK.E.Y.DQ.LITE.GDLG...FL
Retrocopy FITHV*SAEFYEVFNGAWLLLNNDNLLREGAVHT<FA*YNMDQFTPVKVERYDDQVLITEYGDLGYSRFL

Parental  DPKNRICFKFDHLRKEATDPRP-YEAENAIESWRTSIETALRAYVKEHYPNGVCTVYGKKIDGQQTIIAC
          DP.N.I.FKFDHL.KEA.DP.P..E......SW..S...ALRAYVK.HY.NG.CT.Y.K.IDGQQTIIA.
Retrocopy DPRNKISFKFDHLWKEASDPQP>EEVDGGLKSWTES*DSALRAYVKDHYSNGFCTIYSKTIDGQQTIIAR

Parental  IESHQFQAKNF
          IESHQFQ.KNF
Retrocopy IESHQFQPKNF

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	26.45 RPM	23.73 RPM
SRP012922_cerebellum	6.05 RPM	21.72 RPM
SRP012922_heart	2.32 RPM	24.13 RPM
SRP012922_kidney	4.38 RPM	16.70 RPM
SRP012922_liver	7.12 RPM	8.98 RPM
SRP012922_lung	11.00 RPM	21.38 RPM
SRP012922_quadricep_muscle	2.60 RPM	52.44 RPM
SRP012922_spleen	26.44 RPM	31.48 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_1892 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 14 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004925	2 retrocopies	retro_chof_2296, retro_chof_680,
Cavia porcellus	ENSCPOG00000007677	1 retrocopy	retro_cpor_205,
Dasypus novemcinctus	ENSDNOG00000005771	1 retrocopy	retro_dnov_1892 ,
Dipodomys ordii	ENSDORG00000016226	1 retrocopy	retro_dord_266,
Erinaceus europaeus	ENSEEUG00000009063	5 retrocopies	retro_eeur_142, retro_eeur_167, retro_eeur_351, retro_eeur_365, retro_eeur_482,
Echinops telfairi	ENSETEG00000019711	3 retrocopies	retro_etel_1516, retro_etel_2020, retro_etel_442,
Gorilla gorilla	ENSGGOG00000012158	1 retrocopy	retro_ggor_1774,
Microcebus murinus	ENSMICG00000000707	1 retrocopy	retro_mmur_1224,
Myotis lucifugus	ENSMLUG00000007910	1 retrocopy	retro_mluc_2595,
Oryctolagus cuniculus	ENSOCUG00000003591	2 retrocopies	retro_ocun_1531, retro_ocun_873,
Pongo abelii	ENSPPYG00000017933	1 retrocopy	retro_pabe_1321,
Sus scrofa	ENSSSCG00000026942	2 retrocopies	retro_sscr_1127, retro_sscr_600,
Ictidomys tridecemlineatus	ENSSTOG00000024828	1 retrocopy	retro_itri_1561,
Tupaia belangeri	ENSTBEG00000012657	2 retrocopies	retro_tbel_2004, retro_tbel_2228,