RetrogeneDB ID: retro_mmus_413

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:9802307..9802553(-)
• Located in intron of: ENSMUSG00000025915

Retrocopy information

• Ensembl ID: ENSMUSG00000046334
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Rpa3
• Ensembl ID: ENSMUSG00000012483
• Aliases: Rpa3, 14kDa, C330026P08Rik
• Description: replication protein A3 [Source:MGI Symbol;Acc:MGI:1915490]

Sequence

>retro_mmus_413
ATGAAGGACATAATGGGGCACCCCAAAGCGCGCATCAACACCAGCATGTTACCACAGTATATCGACCAGTCCGTGTGCTT
CGTGGGGAAGCTAGAAAAGATTCATCCCACTGGAAAAATGTTTATTCTTTCAGATGGAGAAGGAAAAAATGGAACCATTG
AATTGATGGAGCCACTTGACGAGGAAATCTCTGGGATTGTAGAAGTAGTTGGAAAAGTCACAGCCAAGGCGACCGTGCTC
TGTGCG

Alignment

ORF - retro_mmus_413 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.46 %
• Parental protein coverage: 67.77 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEDIMQLPKARVNASMLPQYIDRPVCFVGKLEKIHPTGKMFILSDGEGKNGTIELMEPLDEEISGIVEVV
          M.DIM..PKAR.N.SMLPQYID..VCFVGKLEKIHPTGKMFILSDGEGKNGTIELMEPLDEEISGIVEVV
Retrocopy MKDIMGHPKARINTSMLPQYIDQSVCFVGKLEKIHPTGKMFILSDGEGKNGTIELMEPLDEEISGIVEVV

Parental  GKVTAKATVLCA
          GKVTAKATVLCA
Retrocopy GKVTAKATVLCA

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	3.50 RPM
SRP007412_cerebellum	0.00 RPM	2.95 RPM
SRP007412_heart	0.06 RPM	4.42 RPM
SRP007412_kidney	0.06 RPM	4.25 RPM
SRP007412_liver	0.00 RPM	3.85 RPM
SRP007412_testis	0.00 RPM	1.97 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_413 was not detected

EST

No EST(s) were mapped for retro_mmus_413 retrocopy.

TSS

No TSS is located nearby retro_mmus_413 retrocopy 5' end.

Lab

retro_mmus_413 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_413 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 20 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016401	1 retrocopy	retro_amel_1031,
Callithrix jacchus	ENSCJAG00000000705	1 retrocopy	retro_cjac_3111,
Cavia porcellus	ENSCPOG00000011748	2 retrocopies	retro_cpor_855, retro_cpor_998,
Dasypus novemcinctus	ENSDNOG00000011718	3 retrocopies	retro_dnov_1044, retro_dnov_1824, retro_dnov_2045,
Equus caballus	ENSECAG00000007680	2 retrocopies	retro_ecab_212, retro_ecab_819,
Felis catus	ENSFCAG00000025369	1 retrocopy	retro_fcat_1287,
Homo sapiens	ENSG00000106399	2 retrocopies	retro_hsap_2179, retro_hsap_3473,
Gorilla gorilla	ENSGGOG00000022464	2 retrocopies	retro_ggor_1727, retro_ggor_2342,
Microcebus murinus	ENSMICG00000000741	1 retrocopy	retro_mmur_934,
Myotis lucifugus	ENSMLUG00000007421	1 retrocopy	retro_mluc_852,
Macaca mulatta	ENSMMUG00000000854	2 retrocopies	retro_mmul_131, retro_mmul_909,
Mus musculus	ENSMUSG00000012483	1 retrocopy	retro_mmus_413 ,
Nomascus leucogenys	ENSNLEG00000016151	2 retrocopies	retro_nleu_308, retro_nleu_340,
Oryctolagus cuniculus	ENSOCUG00000000467	1 retrocopy	retro_ocun_1097,
Otolemur garnettii	ENSOGAG00000001018	1 retrocopy	retro_ogar_113,
Pongo abelii	ENSPPYG00000017787	2 retrocopies	retro_pabe_2062, retro_pabe_2868,
Pan troglodytes	ENSPTRG00000018927	1 retrocopy	retro_ptro_2354,
Rattus norvegicus	ENSRNOG00000008309	2 retrocopies	retro_rnor_2803, retro_rnor_53,
Sus scrofa	ENSSSCG00000023886	1 retrocopy	retro_sscr_297,
Tupaia belangeri	ENSTBEG00000010930	6 retrocopies	retro_tbel_1347, retro_tbel_1876, retro_tbel_2736, retro_tbel_4029, retro_tbel_87, retro_tbel_917,