RetrogeneDB ID: retro_dnov_2508

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_81171:242..666(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2E2
• Ensembl ID: ENSDNOG00000005448
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2E 2 [Source:HGNC Symbol;Acc:12478]

Sequence

>retro_dnov_2508
ATTCAGAAGGAACTAGTCGAAATAATCCTTGATTCTCCTCCTAACTGCAGTGCTGGGCCTAAAGGAGATAACATTTATGA
GTGGAGATAGACTATATTTGGTCCACCAGGTTCTGTATATGAAGGTGGTATGTTTTATCTGGATATCACATTTTCATCAG
ATCATCCATGTAAACCACCAAAGTTACTTTTCACACTAGAATATATCATTGCAAAATCAACAATCAGGGAGTCATCTGTC
TGGACATTCTTAAAGACAACTGGAGTCCCTCTTTGACTATCTCAAAGGTCTGGCTGTCTATTTGTTCCCTTTTGACAGAT
TGCAATCCTGAAGATCCTTGGTTGGAAGCATAGCCACTCAGTATTTGACCAAAAGAGTAGAACCAGACAGGATACCTAGA
GAGTGGACCTAGAGATATGCAACA

Alignment

ORF - retro_dnov_2508 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.94 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IQKELAEITLDPPPNCSAGPKGDNIYEWRSTILGPPGSVYEGGVFFLDITFSPDYPFKPP-KVTFRTRIY
          IQKEL.EI.LD.PPNCSAGPKGDNIYEWR.TI.GPPGSVYEGG.F.LDITFS.D.P.KPP.KVTF.TRIY
Retrocopy IQKELVEIILDSPPNCSAGPKGDNIYEWR*TIFGPPGSVYEGGMFYLDITFSSDHPCKPP<KVTFHTRIY

Parental  HCNINSQGVICLDILKDNWSPALTISKVLLSICSLLTDCNPADP-LVGSIATQYMTNRAEHDRMARQWTK
          HC.IN.QGVICLDILKDNWSP.LTISKV.LSICSLLTDCNP.DP.LVGSIATQY.T.R.E.DR..R.WT.
Retrocopy HCKINNQGVICLDILKDNWSPSLTISKVWLSICSLLTDCNPEDP<LVGSIATQYLTKRVEPDRIPREWT*

Parental  RYAT
          RYAT
Retrocopy RYAT

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	6.81 RPM
SRP012922_cerebellum	0.14 RPM	13.33 RPM
SRP012922_heart	0.00 RPM	5.10 RPM
SRP012922_kidney	0.00 RPM	6.84 RPM
SRP012922_liver	0.15 RPM	1.24 RPM
SRP012922_lung	0.15 RPM	10.23 RPM
SRP012922_quadricep_muscle	0.00 RPM	3.98 RPM
SRP012922_spleen	0.11 RPM	11.56 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_2508 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 11 parental genes, and 53 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010341	2 retrocopies	retro_chof_1304, retro_chof_674,
Ciona intestinalis	ENSCING00000006860	1 retrocopy	retro_cint_33,
Dasypus novemcinctus	ENSDNOG00000005448	7 retrocopies	retro_dnov_1217, retro_dnov_1281, retro_dnov_1360, retro_dnov_156, retro_dnov_2026, retro_dnov_2508 , retro_dnov_424,
Dasypus novemcinctus	ENSDNOG00000009320	30 retrocopies	retro_dnov_1061, retro_dnov_1125, retro_dnov_113, retro_dnov_114, retro_dnov_1167, retro_dnov_1193, retro_dnov_1198, retro_dnov_1257, retro_dnov_141, retro_dnov_1544, retro_dnov_1752, retro_dnov_1761, retro_dnov_1831, retro_dnov_1862, retro_dnov_1912, retro_dnov_1934, retro_dnov_1995, retro_dnov_2084, retro_dnov_2135, retro_dnov_2289, retro_dnov_2362, retro_dnov_2457, retro_dnov_2622, retro_dnov_436, retro_dnov_574, retro_dnov_750, retro_dnov_795, retro_dnov_83, retro_dnov_889, retro_dnov_917,
Dasypus novemcinctus	ENSDNOG00000013821	1 retrocopy	retro_dnov_537,
Felis catus	ENSFCAG00000007748	2 retrocopies	retro_fcat_1582, retro_fcat_913,
Microcebus murinus	ENSMICG00000016799	3 retrocopies	retro_mmur_1075, retro_mmur_15, retro_mmur_419,
Myotis lucifugus	ENSMLUG00000025144	1 retrocopy	retro_mluc_712,
Ochotona princeps	ENSOPRG00000010615	2 retrocopies	retro_opri_329, retro_opri_788,
Tursiops truncatus	ENSTTRG00000005156	1 retrocopy	retro_ttru_1075,
Vicugna pacos	ENSVPAG00000007007	3 retrocopies	retro_vpac_108, retro_vpac_315, retro_vpac_425,