RetrogeneDB ID: retro_mmus_3099

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 8:4391725..4392130(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Rpl32
• Ensembl ID: ENSMUSG00000057841
• Aliases: Rpl32, AU020185, rpL32-3A
• Description: ribosomal protein L32 [Source:MGI Symbol;Acc:MGI:98038]

Sequence

>retro_mmus_3099
GTGGCTGCCCTCCGGCCTCTGGTGAAGCCCAAGATCGTCAAAAAGAGAACCAAGAAGTTCATCAGACACCAGTCAGACCG
ATATGTGAAAATTAAGTGAAACTGGCGGAAACCCAGAGACATCTACAACAGGGTGTGGAGAAGGTTCAAGGGCCAGATCC
TGATGCCCAACATCGGTTACGGGAGCAACAAGAAAACCAAGCACATACTGCTCAGCGGCTTCCGCAAGCTCCTGGTCCAC
AGAGTCAAGGAGCTGGAGGTGCTGCTGATGTGCAACAAATCTTACTGTGCTGAGATTGCACATAATGTGTCCTCTAAGAA
CCGAAAAGCCATTGTAGAAAGAGCAGCACAGCTGGCCATCAGAGTCACCAATCCCAGCGCCAGGCTACGCAGAGAAGAAA
ATGAA

Alignment

ORF - retro_mmus_3099 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.85 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAALRPLVKPKIVKKRTKKFIRHQSDRYVKIKRNWRKPRGIDNRVRRRFKGQILMPNIGYGSNKKTKHML
          .AALRPLVKPKIVKKRTKKFIRHQSDRYVKIK.NWRKPR.I.NRV.RRFKGQILMPNIGYGSNKKTKH.L
Retrocopy VAALRPLVKPKIVKKRTKKFIRHQSDRYVKIK*NWRKPRDIYNRVWRRFKGQILMPNIGYGSNKKTKHIL

Parental  PSGFRKFLVHNVKELEVLLMCNKSYCAEIAHNVSSKNRKAIVERAAQLAIRVTNPNARLRSEENE
          .SGFRK.LVH.VKELEVLLMCNKSYCAEIAHNVSSKNRKAIVERAAQLAIRVTNP.ARLR.EENE
Retrocopy LSGFRKLLVHRVKELEVLLMCNKSYCAEIAHNVSSKNRKAIVERAAQLAIRVTNPSARLRREENE

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	0.07 RPM	66.84 RPM
SRP007412_cerebellum	0.17 RPM	42.08 RPM
SRP007412_heart	0.00 RPM	82.62 RPM
SRP007412_kidney	0.06 RPM	85.24 RPM
SRP007412_liver	0.03 RPM	93.26 RPM
SRP007412_testis	0.05 RPM	100.40 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_3099 was not detected

EST

No EST(s) were mapped for retro_mmus_3099 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_142267	156 libraries	248 libraries	545 libraries	111 libraries	12 libraries

The graphical summary, for retro_mmus_3099 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_3099 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3099 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 129 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000014763	3 retrocopies	retro_acar_104, retro_acar_125, retro_acar_67,
Ailuropoda melanoleuca	ENSAMEG00000004583	26 retrocopies	retro_amel_1004, retro_amel_1041, retro_amel_1059, retro_amel_112, retro_amel_1274, retro_amel_1284, retro_amel_13, retro_amel_1394, retro_amel_1450, retro_amel_150, retro_amel_1651, retro_amel_168, retro_amel_1766, retro_amel_1827, retro_amel_1897, retro_amel_274, retro_amel_275, retro_amel_44, retro_amel_573, retro_amel_658, retro_amel_71, retro_amel_776, retro_amel_781, retro_amel_871, retro_amel_892, retro_amel_923,
Bos taurus	ENSBTAG00000015283	10 retrocopies	retro_btau_1102, retro_btau_1391, retro_btau_1568, retro_btau_1645, retro_btau_1728, retro_btau_1764, retro_btau_377, retro_btau_623, retro_btau_631, retro_btau_654,
Choloepus hoffmanni	ENSCHOG00000013534	27 retrocopies	retro_chof_1131, retro_chof_1164, retro_chof_1181, retro_chof_1234, retro_chof_1461, retro_chof_152, retro_chof_1821, retro_chof_1957, retro_chof_2022, retro_chof_205, retro_chof_2090, retro_chof_2146, retro_chof_2242, retro_chof_2265, retro_chof_2301, retro_chof_2410, retro_chof_2509, retro_chof_2527, retro_chof_2606, retro_chof_276, retro_chof_286, retro_chof_313, retro_chof_554, retro_chof_585, retro_chof_607, retro_chof_758, retro_chof_913,
Dipodomys ordii	ENSDORG00000008426	6 retrocopies	retro_dord_175, retro_dord_251, retro_dord_371, retro_dord_458, retro_dord_522, retro_dord_664,
Equus caballus	ENSECAG00000007201	4 retrocopies	retro_ecab_1115, retro_ecab_26, retro_ecab_369, retro_ecab_698,
Erinaceus europaeus	ENSEEUG00000011609	5 retrocopies	retro_eeur_161, retro_eeur_247, retro_eeur_300, retro_eeur_39, retro_eeur_576,
Homo sapiens	ENSG00000144713	20 retrocopies	retro_hsap_1013, retro_hsap_1115, retro_hsap_1547, retro_hsap_1789, retro_hsap_1956, retro_hsap_2618, retro_hsap_2821, retro_hsap_2891, retro_hsap_3024, retro_hsap_3450, retro_hsap_3536, retro_hsap_3582, retro_hsap_3726, retro_hsap_3805, retro_hsap_3936, retro_hsap_3982, retro_hsap_4008, retro_hsap_4155, retro_hsap_4677, retro_hsap_814,
Loxodonta africana	ENSLAFG00000032737	1 retrocopy	retro_lafr_14,
Myotis lucifugus	ENSMLUG00000022528	6 retrocopies	retro_mluc_100, retro_mluc_1283, retro_mluc_173, retro_mluc_2224, retro_mluc_2256, retro_mluc_48,
Mus musculus	ENSMUSG00000057841	16 retrocopies	retro_mmus_1132, retro_mmus_1142, retro_mmus_1746, retro_mmus_2010, retro_mmus_2263, retro_mmus_2316, retro_mmus_2341, retro_mmus_2699, retro_mmus_3099 , retro_mmus_3378, retro_mmus_3605, retro_mmus_385, retro_mmus_442, retro_mmus_496, retro_mmus_533, retro_mmus_985,
Rattus norvegicus	ENSRNOG00000010746	4 retrocopies	retro_rnor_179, retro_rnor_27, retro_rnor_278, retro_rnor_327,
Sarcophilus harrisii	ENSSHAG00000012782	1 retrocopy	retro_shar_580,