RetrogeneDB ID: retro_mmus_2600

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 5:117058811..117059392(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ube2e1
• Ensembl ID: ENSMUSG00000021774
• Aliases: Ube2e1, UbcM3, Ubce5, ubcM2
• Description: ubiquitin-conjugating enzyme E2E 1 [Source:MGI Symbol;Acc:MGI:107411]

Sequence

>retro_mmus_2600
ATATCGGATGAGGATTCGAGGGCCAGCACCAGCTCCTCGCCATCTTTGTCCTCCAACCAGCAGACCGAGAAAGAAGGCAG
CACCCCCAAGAAGAAGGAGAGTAAAGTCAGCATGAGCAAAAATTCGAAGCTCCTCTCCACCAGCACCAAGAGGATCCAGA
AGAGCTGGCAGACATCACTTTAGACCCTCCGCCAAACTGCAGTGCTGGTCCCAAGGGTGACAACATCTACATCTATGAGT
GGAGATCAACCATTCTGGGTCCTCCAGGGTCAGTGTGTGAAAGTGGATTCTTTCCTTGACGTTACTTTTACCCCAGAGTA
TCCCTTCAAGCCTCCAAAGGTTACATCTCGTACAAGAATGTATCACTGTAATATTAATAGCCAAGGAGTTATTTGCTTGG
ACATATTGAGAGACAACTGGAGCCCAGCACTAACATCTCGAAAGTCCTCCTTTCTATCTGCTCACTCCTTATAGACTGCA
ATCCAGCTGACCCTTTGGTGGGAAGTGTTGCCACTCAGTACATGACCAACAGAGCAGAACACGACAGAATGGCCAGACAG
TGGACCCAGAGATATGCTACA

Alignment

ORF - retro_mmus_2600 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.34 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSDDDSRASTSSSSSSSSNQQTEKEGSTPKKKESKVSMSKNSKLLSTSAKRIQK-ELADITLDPPPNCSA
          .SD.DSRASTSSS.S.SSNQQTEKEGSTPKKKESKVSMSKNSKLLSTS.KRIQK.ELADITLDPPPNCSA
Retrocopy ISDEDSRASTSSSPSLSSNQQTEKEGSTPKKKESKVSMSKNSKLLSTSTKRIQK<ELADITLDPPPNCSA

Parental  GPKGDN--IYEWRSTILGPPGSVYEGGVFFLDITFTPEYPFKPPK-VTFRTRIYHCNINSQGVICLDILK
          GPKGDN..IYEWRSTILGPPGSV.E.G.FF....F.P.......K.VT.RTR.YHCNINSQGVICLDIL.
Retrocopy GPKGDNIYIYEWRSTILGPPGSVCESG-FFP*RYFYPRVSLQASK>VTSRTRMYHCNINSQGVICLDILR

Parental  DNWSPALT-ISKVLLSICSLLTDCNPADPLVGSIATQYMTNRAEHDRMARQWTKRYAT
          DNWSPALT.ISKVLLSICSLL.DCNPADPLVGS.ATQYMTNRAEHDRMARQWT.RYAT
Retrocopy DNWSPALT<ISKVLLSICSLLIDCNPADPLVGSVATQYMTNRAEHDRMARQWTQRYAT

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	25.37 RPM
SRP007412_cerebellum	0.00 RPM	30.70 RPM
SRP007412_heart	0.03 RPM	12.20 RPM
SRP007412_kidney	0.02 RPM	26.53 RPM
SRP007412_liver	0.03 RPM	16.60 RPM
SRP007412_testis	0.00 RPM	11.75 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2600 was not detected

EST

No EST(s) were mapped for retro_mmus_2600 retrocopy.

TSS

No TSS is located nearby retro_mmus_2600 retrocopy 5' end.

Lab

retro_mmus_2600 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2600 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 21 parental genes, and 76 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003515	2 retrocopies	retro_amel_1117, retro_amel_483,
Ciona intestinalis	ENSCING00000006860	1 retrocopy	retro_cint_33,
Cavia porcellus	ENSCPOG00000002251	2 retrocopies	retro_cpor_1036, retro_cpor_52,
Dipodomys ordii	ENSDORG00000015441	1 retrocopy	retro_dord_785,
Felis catus	ENSFCAG00000024719	1 retrocopy	retro_fcat_623,
Gorilla gorilla	ENSGGOG00000008393	1 retrocopy	retro_ggor_76,
Loxodonta africana	ENSLAFG00000004150	1 retrocopy	retro_lafr_320,
Macropus eugenii	ENSMEUG00000014517	1 retrocopy	retro_meug_2089,
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,
Oryctolagus cuniculus	ENSOCUG00000006026	2 retrocopies	retro_ocun_134, retro_ocun_243,
Otolemur garnettii	ENSOGAG00000007527	3 retrocopies	retro_ogar_2029, retro_ogar_2566, retro_ogar_626,
Pan troglodytes	ENSPTRG00000014693	1 retrocopy	retro_ptro_68,
Pteropus vampyrus	ENSPVAG00000001773	1 retrocopy	retro_pvam_1451,
Rattus norvegicus	ENSRNOG00000008794	3 retrocopies	retro_rnor_1632, retro_rnor_2291, retro_rnor_2343,
Sarcophilus harrisii	ENSSHAG00000001416	1 retrocopy	retro_shar_712,
Ictidomys tridecemlineatus	ENSSTOG00000025799	2 retrocopies	retro_itri_1371, retro_itri_645,