RetrogeneDB ID: retro_mmus_1326

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 15:10917442..10917821(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Pfn1
• Ensembl ID: ENSMUSG00000018293
• Aliases: Pfn1, Pfn
• Description: profilin 1 [Source:MGI Symbol;Acc:MGI:97549]

Sequence

>retro_mmus_1326
TGGGTGGAACACTTACATGGACAGTCTCTTGGCAGACCTTTAGCCATCGTTGGCTACAAGGACTCACCTTCGATCTGGGC
TGCTGTCCCCAGGAAGACTTTCATTAGCATTAAGCCAGTTGAGGTTGGTGTTTTGGTAGGCAATGGCCAGTCAAGATTTT
TCATAAATGGGCTGACACCTGGGGCCCAGAAATGTTCTGTGATGTGGTATTCACTGCTGCAGGATGGGAAATTTAAAAAG
GATCTTTGTACCAAGAACATGGAGGAGAACCTACCTTCAATGTCACTCTCACCATGACTACCAAGACACTGATACTGCTA
ATGGGCAAAAAGGTTTTCATGGTGGTTTGATCAACAAAACATGTTACGGAATGGCCTCC

Alignment

ORF - retro_mmus_1326 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.89 %
• Parental protein coverage: 90.71 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YIDSLMADGTCQDAAIVGYKDSPSVWAAVPGKTFVSITPAEVGVLVGKDRSSFFVNGLTLGGQKCSVIRD
          ....L.........AIVGYKDSPS.WAAVP.KTF.SI.P.EVGVLVG...S.FF.NGLT.G.QKCSV...
Retrocopy WVEHLHGQSLGRPLAIVGYKDSPSIWAAVPRKTFISIKPVEVGVLVGNGQSRFFINGLTPGAQKCSVMWY

Parental  SLLQDGEFTMDLRTKST-GGAPTFNVTVTMTAKTLVLLMGK-EGVHGGLINKKCYEMAS
          SLLQDG.F..DL.TK...GG.PTFNVT.TMT.KTL.LLMGK..G.HGGLINK.CY.MAS
Retrocopy SLLQDGKFKKDLCTKNM<GGEPTFNVTLTMTTKTLILLMGK<KGFHGGLINKTCYGMAS

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	61.14 RPM
SRP007412_cerebellum	0.00 RPM	77.25 RPM
SRP007412_heart	0.00 RPM	162.13 RPM
SRP007412_kidney	0.00 RPM	190.26 RPM
SRP007412_liver	0.00 RPM	177.67 RPM
SRP007412_testis	0.00 RPM	65.96 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1326 was not detected

EST

No EST(s) were mapped for retro_mmus_1326 retrocopy.

TSS

No TSS is located nearby retro_mmus_1326 retrocopy 5' end.

Lab

retro_mmus_1326 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1326 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_1623

---

Parental genes homology:

Parental genes homology involve 18 parental genes, and 50 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006193	2 retrocopies	retro_amel_1712, retro_amel_1781,
Bos taurus	ENSBTAG00000004915	1 retrocopy	retro_btau_141,
Callithrix jacchus	ENSCJAG00000011719	2 retrocopies	retro_cjac_1023, retro_cjac_1641,
Cavia porcellus	ENSCPOG00000013136	1 retrocopy	retro_cpor_1216,
Equus caballus	ENSECAG00000021116	3 retrocopies	retro_ecab_171, retro_ecab_28, retro_ecab_559,
Homo sapiens	ENSG00000108518	10 retrocopies	retro_hsap_214, retro_hsap_215, retro_hsap_221, retro_hsap_223, retro_hsap_224, retro_hsap_352, retro_hsap_446, retro_hsap_447, retro_hsap_450, retro_hsap_451,
Gorilla gorilla	ENSGGOG00000022394	3 retrocopies	retro_ggor_285, retro_ggor_289, retro_ggor_366,
Macaca mulatta	ENSMMUG00000002772	5 retrocopies	retro_mmul_407, retro_mmul_527, retro_mmul_528, retro_mmul_574, retro_mmul_732,
Mus musculus	ENSMUSG00000018293	1 retrocopy	retro_mmus_1326 ,
Nomascus leucogenys	ENSNLEG00000017446	6 retrocopies	retro_nleu_16, retro_nleu_1870, retro_nleu_2425, retro_nleu_2429, retro_nleu_848, retro_nleu_886,
Otolemur garnettii	ENSOGAG00000031395	3 retrocopies	retro_ogar_1680, retro_ogar_2143, retro_ogar_3351,
Procavia capensis	ENSPCAG00000000291	1 retrocopy	retro_pcap_27,
Pelodiscus sinensis	ENSPSIG00000004124	1 retrocopy	retro_psin_8,
Pan troglodytes	ENSPTRG00000008616	5 retrocopies	retro_ptro_185, retro_ptro_196, retro_ptro_276, retro_ptro_332, retro_ptro_333,
Rattus norvegicus	ENSRNOG00000003975	1 retrocopy	retro_rnor_1623,
Sus scrofa	ENSSSCG00000017905	1 retrocopy	retro_sscr_275,
Tursiops truncatus	ENSTTRG00000001299	1 retrocopy	retro_ttru_14,
Vicugna pacos	ENSVPAG00000005327	3 retrocopies	retro_vpac_389, retro_vpac_395, retro_vpac_457,