RetrogeneDB ID: retro_mmus_3337

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 9:52078254..52078683(-)
• Located in intron of: ENSMUSG00000032050

Retrocopy information

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

Parental gene information

• Parental gene symbol: Rps19
• Ensembl ID: ENSMUSG00000040952
• Aliases: Rps19, Dsk3
• Description: ribosomal protein S19 [Source:MGI Symbol;Acc:MGI:1333780]

Sequence

>retro_mmus_3337
CCTGGAGTTACTGTAAAAGGCATAAACCAGGAGCTGGTCAGAGCTCTGGTAGCCTTCCTCAAAATGTCTGGGAAGCTGAG
AGTCCCCGAATGGATGGATGCAGTCAAGGCTGGCCAAACATAAAGAGTTTGCCCCATATGATGAGAACTGGTTCTACACA
TGAGCCTCTTCCACAGCACGGCACCTGCACCTCATGGGGGTACAGGGCTTGGTTCCATGACCAAGATCTACAAAGGACGA
CAGAGAAACTGTGTCAGGTCCAACCACTTCAGCAGAGGCTTTAAGAGTGTGGCCCACTGGGTCCTCCAAACTCTGGAGGG
GCTGAAAATGGTAGGAAAGGACCAAGATCGAGGCCACAAGCTAACACCTCAGAGACAAAGAGATCTGGACAGAATCGTTG
GACAGTCGGCAGCTGCCAACAAGAAGCAT

Alignment

ORF - retro_mmus_3337 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.08 %
• Parental protein coverage: 99.31 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PGVTVKDVNQQEFVRALAAFLKKSGKLKVPEWVDTVK-LAKHKELAPYDENWFYTRAASTARHLYL-RGG
          PGVTVK..NQ.E.VRAL.AFLK.SGKL.VPEW.D.VK.LAKHKE.APYDENWFYT.A.STARHL.L..GG
Retrocopy PGVTVKGINQ-ELVRALVAFLKMSGKLRVPEWMDAVK>LAKHKEFAPYDENWFYT*ASSTARHLHL<HGG

Parental  AGVGSMTKIYGGRQRNGVRPSHFSRGSKSVARRVLQALEGLKMVEKDQDGGRKLTPQGQRDLDRIAGQVA
          .G.GSMTKIY.GRQRN.VR..HFSRG.KSVA..VLQ.LEGLKMV.KDQD.G.KLTPQ.QRDLDRI.GQ.A
Retrocopy TGLGSMTKIYKGRQRNCVRSNHFSRGFKSVAHWVLQTLEGLKMVGKDQDRGHKLTPQRQRDLDRIVGQSA

Parental  AANKKH
          AANKKH
Retrocopy AANKKH

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	0.14 RPM	27.33 RPM
SRP007412_cerebellum	0.04 RPM	7.38 RPM
SRP007412_heart	0.06 RPM	33.18 RPM
SRP007412_kidney	0.27 RPM	20.48 RPM
SRP007412_liver	0.19 RPM	25.26 RPM
SRP007412_testis	0.14 RPM	11.30 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_3337 was not detected

EST

No EST(s) were mapped for retro_mmus_3337 retrocopy.

TSS

No TSS is located nearby retro_mmus_3337 retrocopy 5' end.

Lab

• Experiment type: PCR amplification
• Forward primer: TAGCCACGTTCCAGCAGTAG (20 nt long)
• Reverse primer: CCCAGCATCCTTTGTTCTAA (20 nt long)
• Annealing temperature: 55 °C
• (Expected) product size: 522
• Electrophoresis gel image:
• Additional comment: Pfu DNA Polymerase; pooled mouse cDNA; 40 cycles of PCR

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3337 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 63 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000028485	10 retrocopies	retro_cfam_1017, retro_cfam_1074, retro_cfam_1155, retro_cfam_1251, retro_cfam_1377, retro_cfam_149, retro_cfam_1998, retro_cfam_2212, retro_cfam_249, retro_cfam_499,
Callithrix jacchus	ENSCJAG00000020243	5 retrocopies	retro_cjac_1968, retro_cjac_2004, retro_cjac_2094, retro_cjac_2324, retro_cjac_3,
Dasypus novemcinctus	ENSDNOG00000002376	4 retrocopies	retro_dnov_1084, retro_dnov_1124, retro_dnov_1838, retro_dnov_2456,
Equus caballus	ENSECAG00000009738	2 retrocopies	retro_ecab_263, retro_ecab_815,
Macaca mulatta	ENSMMUG00000013429	8 retrocopies	retro_mmul_1201, retro_mmul_1358, retro_mmul_1807, retro_mmul_2007, retro_mmul_2443, retro_mmul_404, retro_mmul_607, retro_mmul_691,
Monodelphis domestica	ENSMODG00000010067	3 retrocopies	retro_mdom_1531, retro_mdom_1888, retro_mdom_883,
Mustela putorius furo	ENSMPUG00000007164	4 retrocopies	retro_mputfur_1071, retro_mputfur_1148, retro_mputfur_1470, retro_mputfur_1503,
Mus musculus	ENSMUSG00000040952	15 retrocopies	retro_mmus_1206, retro_mmus_1207, retro_mmus_1528, retro_mmus_1711, retro_mmus_1713, retro_mmus_2095, retro_mmus_2295, retro_mmus_2535, retro_mmus_2850, retro_mmus_3337 , retro_mmus_3499, retro_mmus_639, retro_mmus_643, retro_mmus_684, retro_mmus_899,
Otolemur garnettii	ENSOGAG00000026255	3 retrocopies	retro_ogar_1315, retro_ogar_1663, retro_ogar_2305,
Rattus norvegicus	ENSRNOG00000048199	3 retrocopies	retro_rnor_221, retro_rnor_299, retro_rnor_51,
Sus scrofa	ENSSSCG00000003042	3 retrocopies	retro_sscr_1064, retro_sscr_308, retro_sscr_58,
Ictidomys tridecemlineatus	ENSSTOG00000003502	3 retrocopies	retro_itri_256, retro_itri_751, retro_itri_872,