RetrogeneDB ID: retro_mmus_1733

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 18:65342929..65343338(+)
• Located in intron of: ENSMUSG00000032845

Retrocopy information

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

Parental gene information

• Parental gene symbol: Snrpn
• Ensembl ID: ENSMUSG00000000948
• Aliases: Snrpn, 2410045I01Rik, HCERN3, Peg4, Pwcr1, SMN
• Description: small nuclear ribonucleoprotein N [Source:MGI Symbol;Acc:MGI:98347]

Sequence

>retro_mmus_1733
CCTAAGGTTAGGAAGGCAGACTGCAGAGGAATACCAGCTGGCATACCTATTCCTTACACTCCTGCTGGCTTAGCAGGCCC
CGTCTAAGGATTTGGAGGTCCCTCCCATGGAGTCAATGACTACACACGGAAGATGCATTGTAGCAGCTGCTGTGGCCTGT
GCTCCTGCCAGCACTGCTGAAGGAAGCCTCAGCCCACTATTCCCCAGGATGGAGAGCTCCACCCCACAGGTAGGTGTTGA
AAGCCCACTTCCAGGATTAGGGCTCCTCCACCTGGCATGAGACCACCCACGAACCACAAACTGGCCTCTTCCCTGCCGGA
GAGACCCTTATAGACATGCTCCCTCCAGGGTGAGATCCTTTCCATCAGCAGTTAGAGGCCCACTTCCCCAAGGAATGTGG
CCACCAAGA

Alignment

ORF - retro_mmus_1733 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.61 %
• Parental protein coverage: 56.67 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  PGVGRAAGRGVPAGVPIPQAPAGLAGPVRGVGGPSQQV-MTPQGRGTVAAAAVAATASIA-GAPTQYPPG
          P.V..A..RG.PAG.PIP..PAGLAGPV.G.GGPS..V.MT..GR..VAAA...A.AS.A.G......P.
Retrocopy PKVRKADCRGIPAGIPIPYTPAGLAGPV*GFGGPSHGV>MTTHGRCIVAAAVACAPASTAEGSLSPLFPR

Parental  RGTPPPPVGRATPPPG-IMAPPPGMRPPMG-PPIGLPPARGTPIGMPPPG-MRPPPPGIRGPPPPGMRPP
          .....P.VG...P.PG.I.APPPGMRPP...P..GL.PA..T.I.M.PPG..R..P...RGP.P.GM.PP
Retrocopy MESSTPQVGVESPLPG<IRAPPPGMRPPTN<PQTGLFPAGETLIDMLPPG<VRSFPSAVRGPLPQGMWPP

Parental  R
          R
Retrocopy R

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	414.67 RPM
SRP007412_cerebellum	0.00 RPM	294.40 RPM
SRP007412_heart	0.03 RPM	33.18 RPM
SRP007412_kidney	0.00 RPM	14.75 RPM
SRP007412_liver	0.00 RPM	6.06 RPM
SRP007412_testis	0.00 RPM	9.01 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1733 was not detected

EST

No EST(s) were mapped for retro_mmus_1733 retrocopy.

TSS

No TSS is located nearby retro_mmus_1733 retrocopy 5' end.

Lab

retro_mmus_1733 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1733 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 54 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007034	3 retrocopies	retro_amel_1048, retro_amel_714, retro_amel_839,
Bos taurus	ENSBTAG00000008251	1 retrocopy	retro_btau_620,
Canis familiaris	ENSCAFG00000010127	6 retrocopies	retro_cfam_1753, retro_cfam_1874, retro_cfam_2039, retro_cfam_627, retro_cfam_682, retro_cfam_752,
Choloepus hoffmanni	ENSCHOG00000001846	2 retrocopies	retro_chof_2275, retro_chof_385,
Cavia porcellus	ENSCPOG00000020270	1 retrocopy	retro_cpor_878,
Felis catus	ENSFCAG00000022298	2 retrocopies	retro_fcat_1390, retro_fcat_1895,
Homo sapiens	ENSG00000128739	1 retrocopy	retro_hsap_2580,
Gorilla gorilla	ENSGGOG00000003988	1 retrocopy	retro_ggor_1615,
Loxodonta africana	ENSLAFG00000009458	1 retrocopy	retro_lafr_1012,
Myotis lucifugus	ENSMLUG00000023361	3 retrocopies	retro_mluc_1192, retro_mluc_1816, retro_mluc_2156,
Macaca mulatta	ENSMMUG00000023139	1 retrocopy	retro_mmul_644,
Mustela putorius furo	ENSMPUG00000014638	1 retrocopy	retro_mputfur_1080,
Mus musculus	ENSMUSG00000000948	3 retrocopies	retro_mmus_1285, retro_mmus_1733 , retro_mmus_665,
Mus musculus	ENSMUSG00000027404	3 retrocopies	retro_mmus_2938, retro_mmus_3450, retro_mmus_554,
Oryctolagus cuniculus	ENSOCUG00000003532	4 retrocopies	retro_ocun_1291, retro_ocun_488, retro_ocun_689, retro_ocun_846,
Otolemur garnettii	ENSOGAG00000007392	5 retrocopies	retro_ogar_1179, retro_ogar_3042, retro_ogar_3060, retro_ogar_475, retro_ogar_722,
Pongo abelii	ENSPPYG00000006269	1 retrocopy	retro_pabe_1900,
Pan troglodytes	ENSPTRG00000006826	1 retrocopy	retro_ptro_1507,
Rattus norvegicus	ENSRNOG00000015976	6 retrocopies	retro_rnor_1122, retro_rnor_1314, retro_rnor_1485, retro_rnor_2161, retro_rnor_2462, retro_rnor_2517,
Sus scrofa	ENSSSCG00000028124	2 retrocopies	retro_sscr_350, retro_sscr_405,
Ictidomys tridecemlineatus	ENSSTOG00000001339	1 retrocopy	retro_itri_44,
Tursiops truncatus	ENSTTRG00000010966	5 retrocopies	retro_ttru_1005, retro_ttru_1051, retro_ttru_1473, retro_ttru_580, retro_ttru_600,