RetrogeneDB ID: retro_mmus_1867

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 19:30351935..30352229(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Dpy30
• Ensembl ID: ENSMUSG00000024067
• Aliases: Dpy30, 2810410M20Rik, C87842
• Description: dpy-30 homolog (C. elegans) [Source:MGI Symbol;Acc:MGI:1913560]

Sequence

>retro_mmus_1867
GAGTCAGTGGAAATGCTGGAGAGACAGACACAGGTTGCAGAAAACCCTCTCTCTGAGTATGGGCTCACAGACAACGTTGA
GAGGAGAGTCAAAAATGAGAAGATTAATGCAGAAAAATCATCAAAACAAAAGATGGGCCTACAGTCCTTGCTCACCCCTT
GCTGCCTGGACCAGACAGCCATGCCTACCTTATTATAGGGACTTGCTATGCTTGCAAAGGAATGACTGCCAAACCCCATG
GAATTTATAGCATCTTATCTTTTAAAAAATAAGGCATAGTTTGAAGATTGAAAT

Alignment

ORF - retro_mmus_1867 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.51 %
• Parental protein coverage: 98.99 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ESEQMLEGQTQVAENPHSEYGLTDSVERIVENEKINAEKSSKQKVDLQSLPTRAYLDQTVVPILLQGLAV
          ES..MLE.QTQVAENP.SEYGLTD.VER.V.NEKINAEKSSKQK..LQSL.T...LDQT..P.LL.GLA.
Retrocopy ESVEMLERQTQVAENPLSEYGLTDNVERRVKNEKINAEKSSKQKMGLQSLLTPCCLDQTAMPTLL*GLAM

Parental  LAKERPPNPIEFLASYLLKNKAQFEDRN
          LAKE..PNP.EF.ASYLLKNKA.FED.N
Retrocopy LAKE*LPNPMEFIASYLLKNKA*FED*N

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
SRP007412_brain	0.00 RPM	13.01 RPM
SRP007412_cerebellum	0.00 RPM	17.41 RPM
SRP007412_heart	0.00 RPM	13.79 RPM
SRP007412_kidney	0.00 RPM	18.52 RPM
SRP007412_liver	0.00 RPM	11.91 RPM
SRP007412_testis	0.05 RPM	77.94 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1867 was not detected

EST

No EST(s) were mapped for retro_mmus_1867 retrocopy.

TSS

No TSS is located nearby retro_mmus_1867 retrocopy 5' end.

Lab

retro_mmus_1867 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1867 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 19 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007768	1 retrocopy	retro_amel_89,
Canis familiaris	ENSCAFG00000005708	1 retrocopy	retro_cfam_1794,
Equus caballus	ENSECAG00000019630	1 retrocopy	retro_ecab_676,
Erinaceus europaeus	ENSEEUG00000012471	1 retrocopy	retro_eeur_239,
Echinops telfairi	ENSETEG00000006389	4 retrocopies	retro_etel_1156, retro_etel_1592, retro_etel_1796, retro_etel_682,
Felis catus	ENSFCAG00000026246	1 retrocopy	retro_fcat_1883,
Macropus eugenii	ENSMEUG00000006193	1 retrocopy	retro_meug_335,
Myotis lucifugus	ENSMLUG00000015346	2 retrocopies	retro_mluc_2327, retro_mluc_2367,
Monodelphis domestica	ENSMODG00000015481	1 retrocopy	retro_mdom_1962,
Mustela putorius furo	ENSMPUG00000005211	1 retrocopy	retro_mputfur_1063,
Mus musculus	ENSMUSG00000024067	1 retrocopy	retro_mmus_1867 ,
Oryctolagus cuniculus	ENSOCUG00000017877	1 retrocopy	retro_ocun_1751,
Otolemur garnettii	ENSOGAG00000034197	2 retrocopies	retro_ogar_3326, retro_ogar_3420,
Ochotona princeps	ENSOPRG00000011833	1 retrocopy	retro_opri_890,
Pteropus vampyrus	ENSPVAG00000005599	1 retrocopy	retro_pvam_1128,
Rattus norvegicus	ENSRNOG00000027126	1 retrocopy	retro_rnor_2141,
Ictidomys tridecemlineatus	ENSSTOG00000013372	2 retrocopies	retro_itri_361, retro_itri_75,
Tupaia belangeri	ENSTBEG00000017486	5 retrocopies	retro_tbel_1154, retro_tbel_1311, retro_tbel_1312, retro_tbel_3073, retro_tbel_4675,
Tarsius syrichta	ENSTSYG00000000146	1 retrocopy	retro_tsyr_1052,