RetrogeneDB ID: retro_mmus_3123

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 8:36450240..36450663(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ube2e3
• Ensembl ID: ENSMUSG00000027011
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2E 3 [Source:MGI Symbol;Acc:MGI:107412]

Sequence

>retro_mmus_3123
AGCAGTGGCAGTTCAGATACAGAGCAGCGAGACCCTGCCACCCCAGAGCCTGAGGAACAGGAAGAAAGAAAACCTTCTGC
TACCCAGCAGGAGAGAAAACACCAAACTCCCTAGAAAACTAAGTTATCCACTAGTGCTAAAAGAATTCAGAGGGGCTGTC
TGAGATCACCCGTGATCCTCCTCCTAACTGCAATGCTGGGCCTAAAGGAGATAACATTTATGATTAGAGGTCAACTAGAC
TTGGTCTACCAGGTTCTGTATATGAGGGTAGGTTTTTTTCTGGATACCACATTTCCTTCAGATTATCCATTTAAACCACC
AAAGGTTTCTTTCCGTACCAGAATTCATCACTGCAATACCAACAGTCAGGGAGTCATCTGCAGATGTCTAGATGACAACT
GGAGTCCTGCTTTGACTATTTCA

Alignment

ORF - retro_mmus_3123 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.35 %
• Parental protein coverage: 70.05 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SSGSSDADQRDPAAPEPEEQEERKPSATQQKKNTKLSSKTTAKLSTSAKRIQKE-LAEITLDPPPNCSAG
          SSGSSD..QRDPA.PEPEEQEERKPSATQQ........KT..KLSTSAKRIQ...L.EIT.DPPPNC.AG
Retrocopy SSGSSDTEQRDPATPEPEEQEERKPSATQQERKHQTP*KT--KLSTSAKRIQRG<LSEITRDPPPNCNAG

Parental  PKGDNIYEWRSTILGPPGSVYEGG-VFF-LDITFSSDYPFKPPKVTFRTRIYHCNINSQGVICLDILKDN
          PKGDNIY..RST.LG.PGSVYEG..VFF.LD.TF.SDYPFKPPKV.FRTRI.HCN.NSQGVIC...L.DN
Retrocopy PKGDNIYD*RSTRLGLPGSVYEGR<VFF<LDTTFPSDYPFKPPKVSFRTRIHHCNTNSQGVIC-RCLDDN

Parental  WSPALTIS
          WSPALTIS
Retrocopy WSPALTIS

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	0.05 RPM	51.33 RPM
SRP007412_cerebellum	0.00 RPM	43.33 RPM
SRP007412_heart	0.00 RPM	28.61 RPM
SRP007412_kidney	0.00 RPM	26.72 RPM
SRP007412_liver	0.00 RPM	16.85 RPM
SRP007412_testis	0.23 RPM	19.44 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3123 was not detected

EST

No EST(s) were mapped for retro_mmus_3123 retrocopy.

TSS

No TSS is located nearby retro_mmus_3123 retrocopy 5' end.

Lab

retro_mmus_3123 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3123 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_1236

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 86 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014163	3 retrocopies	retro_cfam_2076, retro_cfam_2161, retro_cfam_27,
Choloepus hoffmanni	ENSCHOG00000007325	3 retrocopies	retro_chof_1756, retro_chof_2077, retro_chof_2358,
Ciona intestinalis	ENSCING00000006860	1 retrocopy	retro_cint_33,
Callithrix jacchus	ENSCJAG00000011559	3 retrocopies	retro_cjac_3194, retro_cjac_3911, retro_cjac_3967,
Equus caballus	ENSECAG00000007233	1 retrocopy	retro_ecab_196,
Echinops telfairi	ENSETEG00000019324	2 retrocopies	retro_etel_314, retro_etel_848,
Homo sapiens	ENSG00000170035	1 retrocopy	retro_hsap_4653,
Macaca mulatta	ENSMMUG00000008069	2 retrocopies	retro_mmul_1382, retro_mmul_1834,
Monodelphis domestica	ENSMODG00000010301	2 retrocopies	retro_mdom_1679, retro_mdom_1688,
Mus musculus	ENSMUSG00000019927	22 retrocopies	retro_mmus_3405, retro_mmus_3406, retro_mmus_3407, retro_mmus_3409, retro_mmus_3430, retro_mmus_3432, retro_mmus_3434, retro_mmus_3435, retro_mmus_3436, retro_mmus_3563, retro_mmus_3564, retro_mmus_3565, retro_mmus_3566, retro_mmus_3567, retro_mmus_3587, retro_mmus_3589, retro_mmus_3590, retro_mmus_3591, retro_mmus_3592, retro_mmus_3593, retro_mmus_3594, retro_mmus_3595,
Mus musculus	ENSMUSG00000021774	3 retrocopies	retro_mmus_2493, retro_mmus_2600, retro_mmus_537,
Mus musculus	ENSMUSG00000027011	4 retrocopies	retro_mmus_2814, retro_mmus_3123 , retro_mmus_3416, retro_mmus_3571,
Mus musculus	ENSMUSG00000038965	10 retrocopies	retro_mmus_1619, retro_mmus_1620, retro_mmus_2147, retro_mmus_2212, retro_mmus_2272, retro_mmus_2315, retro_mmus_3205, retro_mmus_3714, retro_mmus_541, retro_mmus_995,
Mus musculus	ENSMUSG00000078578	11 retrocopies	retro_mmus_1818, retro_mmus_1895, retro_mmus_1913, retro_mmus_2293, retro_mmus_2635, retro_mmus_2643, retro_mmus_3119, retro_mmus_3636, retro_mmus_850, retro_mmus_875, retro_mmus_923,
Mus musculus	ENSMUSG00000091896	3 retrocopies	retro_mmus_2267, retro_mmus_27, retro_mmus_629,
Nomascus leucogenys	ENSNLEG00000006290	1 retrocopy	retro_nleu_2068,
Otolemur garnettii	ENSOGAG00000014956	4 retrocopies	retro_ogar_1343, retro_ogar_2512, retro_ogar_2682, retro_ogar_3443,
Pongo abelii	ENSPPYG00000012987	1 retrocopy	retro_pabe_3614,
Rattus norvegicus	ENSRNOG00000004544	1 retrocopy	retro_rnor_1236,
Tupaia belangeri	ENSTBEG00000009932	2 retrocopies	retro_tbel_1986, retro_tbel_3294,
Tarsius syrichta	ENSTSYG00000002281	5 retrocopies	retro_tsyr_1393, retro_tsyr_1809, retro_tsyr_1842, retro_tsyr_1942, retro_tsyr_457,
Tursiops truncatus	ENSTTRG00000001361	1 retrocopy	retro_ttru_1056,