RetrogeneDB ID: retro_mmus_27

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 5:107830484..107830928(+)
• Located in intron of: ENSMUSG00000011831

Retrocopy information

• Ensembl ID: ENSMUSG00000063447
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Ube2d2a
• Ensembl ID: ENSMUSG00000091896
• Aliases: Ube2d2a, 1500034D03Rik, Ubc2e, Ube2d2, ubc4
• Description: ubiquitin-conjugating enzyme E2D 2A [Source:MGI Symbol;Acc:MGI:1930715]

Sequence

>retro_mmus_27
ATGGCTCTGAAGAGAATCCACAAGGAACTGAACGACCTGGCCCAGGATCCCCCAGCACAGTGTTCAGCAGGTCCTGTCGG
GGAAGATATGTTTCACTGGCAAGCTACAATCATGGGGCCAAATGATAGTCCCTATCAGGGCGGAGCATTTTTCTTGACAA
TTGATTTCCCAACAGAGTACCCCTTCAAACCACCTAAGGTTGAATTTACAACAAGAATTTATCATCCAAATGTTAACAGT
AACGGCAGTATTTGTCTTGATATTCTTCGGTCACAGTGGTCTCCAGCACTAACTATTTCCAAAGTACTTTTGTCCATCAG
TTCTCTGTTGTGTGACCCCAATCCAGATGATCCCTTAGTGCCTGAGATTGCTCAGATCTACAAAACAGATAGAGACAAGT
ACAACAGAACAGCTCGGGAATGGACTCAGAAATATGCGATGTGA

Alignment

ORF - retro_mmus_27 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.52 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MALKRIHKELNDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFT
          MALKRIHKELNDLA.DPPAQCSAGPVG.DMFHWQATIMGPNDSPYQGG.FFLTI.FPT.YPFKPPKV.FT
Retrocopy MALKRIHKELNDLAQDPPAQCSAGPVGEDMFHWQATIMGPNDSPYQGGAFFLTIDFPTEYPFKPPKVEFT

Parental  TRIYHPNINSNGSICLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVPEIARIYKTDREKYNRIARE
          TRIYHPN.NSNGSICLDILRSQWSPALTISKVLLSI.SLLCDPNPDDPLVPEIA.IYKTDR.KYNR.ARE
Retrocopy TRIYHPNVNSNGSICLDILRSQWSPALTISKVLLSISSLLCDPNPDDPLVPEIAQIYKTDRDKYNRTARE

Parental  WTQKYAM
          WTQKYAM
Retrocopy WTQKYAM

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	0.09 RPM	38.27 RPM
SRP007412_cerebellum	0.13 RPM	22.06 RPM
SRP007412_heart	0.00 RPM	16.09 RPM
SRP007412_kidney	0.15 RPM	21.16 RPM
SRP007412_liver	0.36 RPM	13.82 RPM
SRP007412_testis	90.97 RPM	22.55 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_27 was not detected

EST

No EST(s) were mapped for retro_mmus_27 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_107863	1064 libraries	2 libraries	2 libraries	0 libraries	4 libraries
TSS #2	TSS_107864	1064 libraries	4 libraries	0 libraries	1 library	3 libraries
TSS #3	TSS_107865	1062 libraries	4 libraries	2 libraries	0 libraries	4 libraries
TSS #4	TSS_107866	1057 libraries	9 libraries	0 libraries	0 libraries	6 libraries

The graphical summary, for retro_mmus_27 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_27 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_27 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_342

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Parental genes homology:

Parental genes homology involve 27 parental genes, and 127 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000002183	1 retrocopy	retro_acar_182,
Ailuropoda melanoleuca	ENSAMEG00000011216	6 retrocopies	retro_amel_1295, retro_amel_1427, retro_amel_1648, retro_amel_1750, retro_amel_620, retro_amel_995,
Bos taurus	ENSBTAG00000004161	6 retrocopies	retro_btau_1421, retro_btau_1602, retro_btau_1739, retro_btau_1775, retro_btau_1851, retro_btau_1852,
Canis familiaris	ENSCAFG00000031041	5 retrocopies	retro_cfam_1191, retro_cfam_1439, retro_cfam_1602, retro_cfam_2034, retro_cfam_785,
Ciona intestinalis	ENSCING00000018711	2 retrocopies	retro_cint_19, retro_cint_29,
Ciona savignyi	ENSCSAVG00000006136	1 retrocopy	retro_csav_18,
Erinaceus europaeus	ENSEEUG00000014658	3 retrocopies	retro_eeur_263, retro_eeur_566, retro_eeur_591,
Echinops telfairi	ENSETEG00000001291	3 retrocopies	retro_etel_1218, retro_etel_1998, retro_etel_36,
Gorilla gorilla	ENSGGOG00000001368	2 retrocopies	retro_ggor_1156, retro_ggor_2321,
Loxodonta africana	ENSLAFG00000006878	2 retrocopies	retro_lafr_288, retro_lafr_290,
Macaca mulatta	ENSMMUG00000020666	3 retrocopies	retro_mmul_1298, retro_mmul_2143, retro_mmul_2246,
Monodelphis domestica	ENSMODG00000011783	2 retrocopies	retro_mdom_17, retro_mdom_884,
Mustela putorius furo	ENSMPUG00000009110	5 retrocopies	retro_mputfur_1263, retro_mputfur_1637, retro_mputfur_263, retro_mputfur_682, retro_mputfur_703,
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,
Ornithorhynchus anatinus	ENSOANG00000005415	1 retrocopy	retro_oana_51,
Oryctolagus cuniculus	ENSOCUG00000029448	10 retrocopies	retro_ocun_1220, retro_ocun_1426, retro_ocun_1536, retro_ocun_1660, retro_ocun_1856, retro_ocun_1941, retro_ocun_261, retro_ocun_467, retro_ocun_887, retro_ocun_988,
Pongo abelii	ENSPPYG00000015844	6 retrocopies	retro_pabe_1016, retro_pabe_1164, retro_pabe_1257, retro_pabe_2330, retro_pabe_30, retro_pabe_3670,
Pan troglodytes	ENSPTRG00000017303	3 retrocopies	retro_ptro_26, retro_ptro_3141, retro_ptro_341,
Pteropus vampyrus	ENSPVAG00000015438	1 retrocopy	retro_pvam_234,
Ictidomys tridecemlineatus	ENSSTOG00000013481	6 retrocopies	retro_itri_1222, retro_itri_1474, retro_itri_1628, retro_itri_463, retro_itri_672, retro_itri_998,
Tupaia belangeri	ENSTBEG00000000270	5 retrocopies	retro_tbel_1336, retro_tbel_145, retro_tbel_1837, retro_tbel_262, retro_tbel_3134,
Tarsius syrichta	ENSTSYG00000005459	1 retrocopy	retro_tsyr_1421,