RetrogeneDB ID: retro_dnov_530

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_5795:221476..221977(+)
• Located in intron of: ENSDNOG00000006120

Retrocopy information

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

Parental gene information

• Parental gene symbol: BCCIP
• Ensembl ID: ENSDNOG00000002939
• Aliases: None
• Description: BRCA2 and CDKN1A interacting protein [Source:HGNC Symbol;Acc:978]

Sequence

>retro_dnov_530
GAAGTGAATATTTAATTTGGAGCTTACACCATCTCAGATAACAATTATGATGGAATTAAGAAATTACTACACCAACTCTT
CCTAAAGGCTCCTGTGAATACTGCAGAACTAACAGATCTCGTCATACAACAGAGCCACACTGGGAGTGTGACTACACAAA
CAGATGTTTCAGAAGGCAGCGATGATGAGGTGGATGTTGATGAAGATGAGAGTTTTGGTTTCTTAAGTCTTTTAAATTTA
ACTCAATGAAAGGGTACCCAGTGTGCTGAGCAAATTAAAGTGTTGATTCTAAGCTTCTGGGAGAACTGTGAAAAGAGCAT
GGTTGAACAGCTGGGCAAGTTTTTTAATGACTCCACCAAGCCGGTGGGCTTGCTGCTGAGTGAAAGAATCATTAATGTGA
TCTCCCTGTCCATGCACCAGCAACTTCAGAAAGAACTGACCGAGGCACACAAAACGAACAAGCCACATGGGAAGTGTTGC
TGTTACCTTCTAAATTCTAAA

Alignment

ORF - retro_dnov_530 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.36 %
• Parental protein coverage: 66.28 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EVNIEFEAYSISDNDYDGIKKLLHQLFLKAPVNTAELTNLLVQQNHIGSVIKQTDVSEDSDDDVEVDEDE
          EVNI.F.AY.ISDN.YDGIKKLLHQLFLKAPVNTAELT.L..QQ.H.GSV..QTDVSE.SDD.V.VDEDE
Retrocopy EVNI*FGAYTISDNNYDGIKKLLHQLFLKAPVNTAELTDLVIQQSHTGSVTTQTDVSEGSDDEVDVDEDE

Parental  IFGFISLLNLTERKGTQCAEQIKELILSFCEKNCEKSMVEQLDKLLNDTTKPVGLLLSERFINVPPQIAL
          .FGF.SLLNLT..KGTQCAEQIK.LILSF.E.NCEKSMVEQL.K..ND.TKPVGLLLSER.INV...I.L
Retrocopy SFGFLSLLNLTQ*KGTQCAEQIKVLILSFWE-NCEKSMVEQLGKFFNDSTKPVGLLLSERIINV---ISL

Parental  PMHQQLQKELAEAHKMNKPCGKCCFYLMISK
          .MHQQLQKEL.EAHK.NKP.GKCC.YL..SK
Retrocopy SMHQQLQKELTEAHKTNKPHGKCCCYLLNSK

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	0.39 RPM	35.78 RPM
SRP012922_cerebellum	1.10 RPM	23.37 RPM
SRP012922_heart	0.00 RPM	21.11 RPM
SRP012922_kidney	1.37 RPM	23.27 RPM
SRP012922_liver	0.00 RPM	17.18 RPM
SRP012922_lung	0.31 RPM	24.74 RPM
SRP012922_quadricep_muscle	0.00 RPM	24.58 RPM
SRP012922_spleen	0.00 RPM	34.91 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_530 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 8 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012873	1 retrocopy	retro_cfam_1356,
Callithrix jacchus	ENSCJAG00000012411	1 retrocopy	retro_cjac_2838,
Dasypus novemcinctus	ENSDNOG00000002939	1 retrocopy	retro_dnov_530 ,
Macaca mulatta	ENSMMUG00000008541	1 retrocopy	retro_mmul_472,
Oryctolagus cuniculus	ENSOCUG00000008761	1 retrocopy	retro_ocun_843,
Otolemur garnettii	ENSOGAG00000010901	1 retrocopy	retro_ogar_1184,
Ictidomys tridecemlineatus	ENSSTOG00000011828	4 retrocopies	retro_itri_1004, retro_itri_1130, retro_itri_1513, retro_itri_559,
Tupaia belangeri	ENSTBEG00000002570	4 retrocopies	retro_tbel_1259, retro_tbel_1260, retro_tbel_2963, retro_tbel_3044,