RetrogeneDB ID: retro_dnov_338

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_3790:539766..540283(+)
• Located in intron of: ENSDNOG00000014896

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRM
• Ensembl ID: ENSDNOG00000013348
• Aliases: None
• Description: spermidine synthase [Source:HGNC Symbol;Acc:11296]

Sequence

>retro_dnov_338
CAGAAGATGATTGCCAACCTGCCACTCTGCAGCCACCCCAACCCCCCCACAAGGTTTTGATCATTGGAGGTAGGGACAGG
GGCATCCTGTGGGAGGTGATGAAGTACCCCTTGATGAAGTCAGTTGCCCAGTGTGAAATCGATGAGAATGCCATCCAGGT
CTCCAAGAAATTCCTGCCTGGCATGGCCATTGGCTACTCCAGCTCGAAGCTGACCCTGCACATATGTGATGGTTTTGAGT
TTTTGAAGCAGAGCCCTTATGCGTTCCACATTATCATCACTAACTCCTCAGACCCCGTGGGTCCAGCTGAGAGCCTCTTC
AAGGAGTCCTATTACCAGCTCATGAAAACAACCCTCAAGGAGGACAGGATTCTCTATTGCCTGGGTGAATGCCAGTGGCT
GTACCTGGTCCCATCAAGGAGATAAATCTGTTCTGCAAGTCCCTCTTCCCTGTGGTGGGCTAAGCCTACTGTACCATCCC
CACCAATTTCAGTGGCCAGATTGCCTTCATGCTGTGC

Alignment

ORF - retro_dnov_338 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.43 %
• Parental protein coverage: 68.83 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QEMIANLPLCSHPD-PRKVLIIGGG-DGGVLREVVKHPSVESVVQCEIDEEVIEVSKKFLPSMAVGYSSS
          Q.MIANLPLCSHP..P.....I.GG.D.G.L.EV.K.P...SV.QCEIDE..I.VSKKFLP.MA.GYSSS
Retrocopy QKMIANLPLCSHPN<PPHKVLIIGGRDRGILWEVMKYPLMKSVAQCEIDENAIQVSKKFLPGMAIGYSSS

Parental  KLTLCVGDGFEFMKQNQDAFDVIITDSSDPMGPAESLFKESYYQLMKTALKEDGILCCQGECQWLHL-DL
          KLTL...DGFEF.KQ...AF..IIT.SSDP.GPAESLFKESYYQLMKT.LKED.IL.C.GECQWL.L...
Retrocopy KLTLHICDGFEFLKQSPYAFHIIITNSSDPVGPAESLFKESYYQLMKTTLKEDRILYCLGECQWLYL<GP

Parental  IKQMRQFCRSLFLVVGYDYCSIPT--PSQIGFMLC
          IK....FC.SLF.VVG..YC.IPT....QI.FMLC
Retrocopy IKEINLFCKSLFPVVG*AYCTIPTNFSGQIAFMLC

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	9.33 RPM
SRP012922_cerebellum	0.00 RPM	15.40 RPM
SRP012922_heart	0.00 RPM	4.64 RPM
SRP012922_kidney	0.00 RPM	9.86 RPM
SRP012922_liver	0.00 RPM	4.80 RPM
SRP012922_lung	0.31 RPM	8.25 RPM
SRP012922_quadricep_muscle	0.00 RPM	5.88 RPM
SRP012922_spleen	1.14 RPM	10.07 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_338 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 6 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002354	4 retrocopies	retro_cjac_2131, retro_cjac_2524, retro_cjac_3331, retro_cjac_4025,
Dasypus novemcinctus	ENSDNOG00000013348	1 retrocopy	retro_dnov_338 ,
Gorilla gorilla	ENSGGOG00000014385	1 retrocopy	retro_ggor_1756,
Macropus eugenii	ENSMEUG00000007002	2 retrocopies	retro_meug_1330, retro_meug_887,
Macaca mulatta	ENSMMUG00000019321	2 retrocopies	retro_mmul_1500, retro_mmul_2259,
Mus musculus	ENSMUSG00000006442	1 retrocopy	retro_mmus_3271,