RetrogeneDB ID: retro_dnov_1143

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_15322:14959..15471(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDNOG00000019288
• Aliases: None
• Description: None

Sequence

>retro_dnov_1143
GTTTTTGCCCTAACTACATCCTGGACCTCAAGACAAGTAGGAGAATGGACATTCAGTGGTACAGTAATAGACTATGAAAA
TGGTGTCATTCTTGCCATTCCCAGGGCTAAAGGGTATGTGACTGGCAGCTGCATTAAGCACATTCCAATTGCAGGACAAG
ACATAACACATTTTATTCAGCAATGCTAAGAGACGGAGAAGTAGGAATCTGTCCAGAGAAATCTCCAGAAATAGCTAAAG
CAGTAAAGGAGTGATATAGTTATGTTTGCCCCAATTTAGTAAAAGAACTTAACAAGTATGAAACAGATAGGTCATAGTGG
ATTAAGCAGTATACTAGAATCAATGCTATCTCAAGAGAATTTTCCATCAATGTTGGTTATGAGAGATTCTTTGGACACAA
AATATTTTCTCACCCAGAGTTTGCTAATCCAAACCTCACACAACCTATCTCAGAAGTTGTAGATGAAGTAACTCAGAATT
GTCCTACTGATGTCAGACTTCTTCCCTACAAA

Alignment

ORF - retro_dnov_1143 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.16 %
• Parental protein coverage: 99.42 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VLALAASWTSRQVGERTLTGIVIDSGDGVTHVIPVAEGYVIGSCIKHIPIAGRDITYFIQQ-LLREREVG
          V.AL..SWTSRQVGE.T..G.VID...GV...IP.A.GYV.GSCIKHIPIAG.DIT.FIQQ..LR..EVG
Retrocopy VFALTTSWTSRQVGEWTFSGTVIDYENGVILAIPRAKGYVTGSCIKHIPIAGQDITHFIQQ<MLRDGEVG

Parental  IPPEQSLETAKAEK--YCYICPDIVKEFGKYDVDPRRWIKQYTGINAINQKKFVIDVGYERFLGPEIFFH
          I.PE.S.E.AKA.K..Y.Y.CP..VKE..KY..D...WIKQYT.INAI....F.I.VGYERF.G..IF.H
Retrocopy ICPEKSPEIAKAVKE*YSYVCPNLVKELNKYETDRS*WIKQYTRINAIS-REFSINVGYERFFGHKIFSH

Parental  PEFANPDFMESISDVVDEVIQNCPIDVRRPLYK
          PEFANP.....IS.VVDEV.QNCP.DVR...YK
Retrocopy PEFANPNLTQPISEVVDEVTQNCPTDVRLLPYK

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	0.00 RPM
SRP012922_cerebellum	0.00 RPM	11.13 RPM
SRP012922_heart	0.00 RPM	0.00 RPM
SRP012922_kidney	0.00 RPM	0.55 RPM
SRP012922_liver	0.00 RPM	2.01 RPM
SRP012922_lung	0.00 RPM	0.76 RPM
SRP012922_quadricep_muscle	0.00 RPM	1.90 RPM
SRP012922_spleen	0.00 RPM	1.95 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_1143 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 11 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007730	5 retrocopies	retro_chof_1134, retro_chof_1204, retro_chof_1899, retro_chof_208, retro_chof_2171,
Dasypus novemcinctus	ENSDNOG00000019288	2 retrocopies	retro_dnov_1143 , retro_dnov_2539,
Homo sapiens	ENSG00000133627	7 retrocopies	retro_hsap_1676, retro_hsap_2126, retro_hsap_2540, retro_hsap_2966, retro_hsap_4334, retro_hsap_4921, retro_hsap_561,
Macropus eugenii	ENSMEUG00000004885	5 retrocopies	retro_meug_1340, retro_meug_1477, retro_meug_2105, retro_meug_330, retro_meug_899,
Nomascus leucogenys	ENSNLEG00000015688	1 retrocopy	retro_nleu_733,
Oryctolagus cuniculus	ENSOCUG00000000459	1 retrocopy	retro_ocun_320,
Otolemur garnettii	ENSOGAG00000003249	2 retrocopies	retro_ogar_1307, retro_ogar_3388,
Pongo abelii	ENSPPYG00000018206	1 retrocopy	retro_pabe_2460,
Pan troglodytes	ENSPTRG00000019897	8 retrocopies	retro_ptro_1137, retro_ptro_1479, retro_ptro_2007, retro_ptro_2952, retro_ptro_2961, retro_ptro_3052, retro_ptro_3281, retro_ptro_420,
Tupaia belangeri	ENSTBEG00000011647	2 retrocopies	retro_tbel_2820, retro_tbel_932,
Tursiops truncatus	ENSTTRG00000016334	2 retrocopies	retro_ttru_471, retro_ttru_93,