RetrogeneDB ID: retro_dnov_2663

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_9607:79637..80358(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CAPZB
• Ensembl ID: ENSDNOG00000018644
• Aliases: None
• Description: capping protein (actin filament) muscle Z-line, beta [Source:HGNC Symbol;Acc:1491]

Sequence

>retro_dnov_2663
AATGATCAGTGGCTGGACTGTACCTTGGACTTAATGAGGCATCTGCCTCCACAGCAAATGGAGAAAAATGGCAGCAACAC
ATTCGGCCTGGTCCCCAGTCTATGTGAAGATCTCCTGTCTTCTGTTGACAGCCACTGAAAATCATGAGACAAGGTAGTGG
GAAAGGATTACCTTTTGTGTGACTACAACAGAGACAGGGACTCCTATAGGTCACCATGAAGTAACAAGTATGACCCTCCA
TTGGAAGATGGGGCCATGCCATCTGCTCGGCAGCGAAAGCTGGAGGTGGAAGCCAATAATGCCTTTGACCAGTATCGAGA
CCTGTATTTTAAAGGTGGCATCTCCTCTGCCTACCTCTGGGATCTGGATCATGGCTTTGCTGGCATGATCCTCATAAAGG
AGGCTGGAGATGGATCAAAGAATATCAAAGGCTTCTGGGATTCCATCCATGTGGTGGAAGTGAAGGAGAAATCCAGTAGT
CACACCATCCATTGTAAGGTGACCTCCACAGTGATGCTGTGACCGCAAACAGACAAATCTGGCTCTGGCACCATGAACCT
CAGAAGCAGCCTTACCAGACAGATGGAGAAAGATGGAACTGTGAGTGACTCCTCCCCATATAGCCAACACTGGGTGCCTG
GTGGAGGACATGGACAATACAATCAGAATTACGCTGAGTGAGATCTACTTTGGAAAAGCAAAGGACGTTATTAATTGTCT
G

Alignment

ORF - retro_dnov_2663 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.95 %
• Parental protein coverage: 90.3 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SDQQLDCALDLMRRLPPQQIEKNLSDLIDLVPSLCEDLLSSVDQPLKIARDKVVGKDYLLCDYNRDGDSY
          .DQ.LDC.LDLMR.LPPQQ.EKN.S....LVPSLCEDLLSSVD...K...DKVVGKDYLLCDYNRD.DSY
Retrocopy NDQWLDCTLDLMRHLPPQQMEKNGSNTFGLVPSLCEDLLSSVDSH*K-S*DKVVGKDYLLCDYNRDRDSY

Parental  RSPWSNKYDPPLEDGAMPSARLRKLEVEANNAFDQYRDLYFEGGVSSVYLWDLDHGFAGVILIKKAGDGS
          RSP.SNKYDPPLEDGAMPSAR.RKLEVEANNAFDQYRDLYF.GG.SS.YLWDLDHGFAG.ILIK.AGDGS
Retrocopy RSP*SNKYDPPLEDGAMPSARQRKLEVEANNAFDQYRDLYFKGGISSAYLWDLDHGFAGMILIKEAGDGS

Parental  KKIKGCWDSIHVVEVQEKSSGRTAHYKLTSTVMLWLQTNKSGSGTMNLGGSLTRQMEKDEGVNDSS-PHI
          K.IKG.WDSIHVVEV.EKSS..T.H.K.TSTVML..QT.KSGSGTMNL..SLTRQMEK..G....S.PHI
Retrocopy KNIKGFWDSIHVVEVKEKSSSHTIHCKVTSTVML*PQTDKSGSGTMNLRSSLTRQMEK-DGTVSDS>PHI

Parental  AHIGRLVEDMENKIRSTLNEIYFGKTKGIVNGL
          A..G.LVEDM.N.IR.TL.EIYFGK.K...N.L
Retrocopy ANTGCLVEDMDNTIRITLSEIYFGKAKDVINCL

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	80.70 RPM
SRP012922_cerebellum	0.00 RPM	51.14 RPM
SRP012922_heart	0.00 RPM	34.57 RPM
SRP012922_kidney	0.00 RPM	36.69 RPM
SRP012922_liver	0.00 RPM	27.71 RPM
SRP012922_lung	0.00 RPM	65.82 RPM
SRP012922_quadricep_muscle	0.00 RPM	61.79 RPM
SRP012922_spleen	0.00 RPM	97.06 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_2663 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 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006715	1 retrocopy	retro_cjac_1184,
Dasypus novemcinctus	ENSDNOG00000018644	3 retrocopies	retro_dnov_1168, retro_dnov_1719, retro_dnov_2663 ,
Macropus eugenii	ENSMEUG00000002018	1 retrocopy	retro_meug_1958,
Myotis lucifugus	ENSMLUG00000012115	2 retrocopies	retro_mluc_1254, retro_mluc_2204,
Oryctolagus cuniculus	ENSOCUG00000014711	1 retrocopy	retro_ocun_1213,