RetrogeneDB ID: retro_dnov_2298

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_62010:8208..8964(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBM22
• Ensembl ID: ENSDNOG00000011166
• Aliases: None
• Description: RNA binding motif protein 22 [Source:HGNC Symbol;Acc:25503]

Sequence

>retro_dnov_2298
CACATTTGATCCTTCTGGGAGAAAGGCAAGTGTGACAGGGAGAGCCATGTCCATACAGGCATGAGAAGCCTACAGATCCA
GATGACCCCCTTGCTGATCAAATACCAAAGACCTCTATTATGGGATCAACGACCCTGTGGTAGATACGCTTCTAAAGTGG
CCTTCAGCAGTGACTCATCTGGACCCACCAGAGGGTAGAATTATTGCCATACTGTATGTTGGTGGGCTGGAAGATACCCT
TCCCAAGACAGAGCGAAGAAATCATTTCTACCAGTTTGGAGAGATTCAGTCACTGTTGTGCAGAATCAACAGTGTGCTTT
CATCCAGTCTGCCCAAGGCAGGCCGCAGAAGTAGCTGCTGAAAAATCTTTTAATAAGTTAACTGTCAATGACTGCAGATT
CAATGTAAGATAGGGAAGATCCCAAGAGGCCAGAGGAAAAGCAAAAGAGAAGGGTGGAACCGCAGACTCTGGAAGCCCGG
TAGAGTCTGCTCCAGGACTGCCAGGAGCTCTGCCTCCTCCTCCTGCAGCAGCAGAAGGAGCCTCTGCCAGCTCCTTCCAC
TTACCCCGAGTGGTTCCAGTGTGGTGGTGAACATCGCCCTGCCACCACCCCGTATTGCTCCTCGCCCACCCGCAGGGTTT
GGCCACACATGCTCCCCCCAGTGGAACCGGCCCCTCCTTTCATGAGGGCTCCAGGACCAGTCCACTGTCCTTCCCAGGGC
CTTCAGAGGATGTGGGTTCATGCTGGGAGCAGCAGC

Alignment

ORF - retro_dnov_2298 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.7 %
• Parental protein coverage: 66.67 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  HICSFWVKGECKR-GEECPYRHEKPTDPDDPLADQ-NIKDRYYGINDPVADKLLKRASTMPRLDPPEDKT
          HI.SFW.KG.C.R.GE.CPYRHEKPTDPDDPLADQ.N.KD.YYGINDPV.D.LLK..S....LDPPE...
Retrocopy HI*SFWEKGKCDR<GEPCPYRHEKPTDPDDPLADQ<NTKDLYYGINDPVVDTLLKWPSAVTHLDPPEGRI

Parental  ITTLYVGGLGDTITETDLRNHFYQFGEIRTI-TVVQRQQCAFIQFA-TRQAAEVAAEKSFNKLIVNGRRL
          I..LYVGGL.DT...T..RNHFYQFGEI.....V...Q.CAFIQ.A..RQAAEVAAEKSFNKL.VN..R.
Retrocopy IAILYVGGLEDTLPKTERRNHFYQFGEIQSL<VVQNQQ-CAFIQSA<PRQAAEVAAEKSFNKLTVNDCRF

Parental  NVKWGRSQAARGKEKEKDGTTDSGIKLEPVPGLPGALPPPPAAEEEASANYFNLP-PSGPPAVVNIALPP
          NV..GRSQ.ARGK.KEK.GT.DSG...E..PGLPGALPPPPAA.E.ASA..F.LP.PSG...VVNIAL.P
Retrocopy NVR*GRSQEARGKAKEKGGTADSGSPVESAPGLPGALPPPPAAAEGASASSFHLP<PSGSSVVVNIAL-P

Parental  PPGIAPPPPPGFG-PHMFHPMGPPPPFMRAPGPIHYPSQDPQRMGAHAGKHS
          PP.IAP.PP.GFG.PHM..P..P.PPFMRAPGP.H.PSQ..QRM..HAG..S
Retrocopy PPRIAPRPPAGFG<PHMLPPVEPAPPFMRAPGPVHCPSQGLQRMWVHAGSSS

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	23.14 RPM
SRP012922_cerebellum	0.00 RPM	30.66 RPM
SRP012922_heart	0.00 RPM	8.35 RPM
SRP012922_kidney	0.00 RPM	13.14 RPM
SRP012922_liver	0.00 RPM	12.85 RPM
SRP012922_lung	0.00 RPM	36.50 RPM
SRP012922_quadricep_muscle	0.00 RPM	12.29 RPM
SRP012922_spleen	0.00 RPM	36.63 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_2298 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 12 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018082	1 retrocopy	retro_cfam_1480,
Callithrix jacchus	ENSCJAG00000020963	6 retrocopies	retro_cjac_1338, retro_cjac_2471, retro_cjac_3342, retro_cjac_3390, retro_cjac_3934, retro_cjac_990,
Cavia porcellus	ENSCPOG00000001946	2 retrocopies	retro_cpor_280, retro_cpor_283,
Dasypus novemcinctus	ENSDNOG00000011166	1 retrocopy	retro_dnov_2298 ,
Homo sapiens	ENSG00000086589	2 retrocopies	retro_hsap_3465, retro_hsap_4273,
Gorilla gorilla	ENSGGOG00000012947	2 retrocopies	retro_ggor_2337, retro_ggor_2859,
Myotis lucifugus	ENSMLUG00000009040	2 retrocopies	retro_mluc_1453, retro_mluc_153,
Macaca mulatta	ENSMMUG00000020683	4 retrocopies	retro_mmul_1199, retro_mmul_1348, retro_mmul_1553, retro_mmul_1762,
Monodelphis domestica	ENSMODG00000009574	1 retrocopy	retro_mdom_186,
Pongo abelii	ENSPPYG00000015955	4 retrocopies	retro_pabe_1412, retro_pabe_1594, retro_pabe_2861, retro_pabe_3486,
Pan troglodytes	ENSPTRG00000017423	2 retrocopies	retro_ptro_2348, retro_ptro_2898,
Tarsius syrichta	ENSTSYG00000003939	3 retrocopies	retro_tsyr_1090, retro_tsyr_1187, retro_tsyr_1231,