RetrogeneDB ID: retro_mmus_1675

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 17:88608003..88608542(-)
• Located in intron of: ENSMUSG00000033855

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ube2s
• Ensembl ID: ENSMUSG00000060860
• Aliases: Ube2s, 0910001J09Rik, 6720465F12Rik, AA409170, E2-EPF
• Description: ubiquitin-conjugating enzyme E2S [Source:MGI Symbol;Acc:MGI:1925141]

Sequence

>retro_mmus_1675
ATGAACTCCGACATAAAGTATCTGCCTCCCCACGTCATCTACCTAGCGTACAAGGAGGGGACAGCACGGGCAGAGGACCC
ACTTGATGACAATAAAGTCTCCCCATTGCGAAGGAGCTCACCAACCTGCAGGTCACTATGGAGGGCCCCACGGGGATCCC
CTATGTCTGGGGTCCGTTCCGCACTTAGTTCCTACTGGGCAAGGACTTCCCTGCCTCTCCACCCACCCAAGAGGTATCTC
CTGACTAAGATCTACCAAATGAGGGTGCCAACGGCCAGCTCTGTGCCAAGGTGCTCACAAGGGACTGAACGATTGTGTTG
GGCACGCAGCAGCCCATGACGGTGAGCATCAAGGGCGTGCTAATCCACCCTAACCCAGAGTCTGCACTCAACCAGGAAGC
TGCCCGCCTCATTTTAGAAAACTATGAAGGAGGATGCTGCTGGCCCAGTCTGCTTACAAAGATCCATGGACGCGTGCATG
CAGGTGGAACCAGAAGTCAGGGGGCTGAGGCTACAGGGAACCTGGCCTGGAGCTGCAGC

Alignment

ORF - retro_mmus_1675 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.04 %
• Parental protein coverage: 79.37 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MNSNVENLPPHIIRLVYKEVTTLTADPPDGIKV-FPNEEDLTDLQVTIEGPEGTPYAGGLFRMKLLLGKD
          MNS....LPPH.I.L.YKE.T....DP.D..KV..P....LT.LQVT.EGP.G.PY..G.FR...LLGKD
Retrocopy MNSDIKYLPPHVIYLAYKEGTARAEDPLDDNKV<LPIAKELTNLQVTMEGPTGIPYVWGPFRT*FLLGKD

Parental  FPASPPKGYFLTKIFHPNVGPNGEICVNVLKRDWTAELGIRH-VLLTIKCLLIHPNPESALNEEAGRLLL
          FPASPP..........PN.G.NG..C..VL.RD.T..LG........IK..LIHPNPESALN.EA.RL.L
Retrocopy FPASPPTQEVSPD*DLPNEGANGQLCAKVLTRD*TIVLGTQQPMTVSIKGVLIHPNPESALNQEAARLIL

Parental  ENYEEYAARARLLTEIHG--GACSTSSGRAEATQDLASGAS
          ENYE.......LLT.IHG...A..T.S..AEAT..LA...S
Retrocopy ENYEGGCCWPSLLTKIHGRVHAGGTRSQGAEATGNLAWSCS

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	0.02 RPM	7.45 RPM
SRP007412_cerebellum	0.09 RPM	5.47 RPM
SRP007412_heart	0.06 RPM	8.81 RPM
SRP007412_kidney	0.04 RPM	7.49 RPM
SRP007412_liver	0.00 RPM	4.29 RPM
SRP007412_testis	0.50 RPM	62.53 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1675 was not detected

EST

No EST(s) were mapped for retro_mmus_1675 retrocopy.

TSS

No TSS is located nearby retro_mmus_1675 retrocopy 5' end.

Lab

retro_mmus_1675 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1675 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000874	3 retrocopies	retro_cjac_1995, retro_cjac_3689, retro_cjac_406,
Homo sapiens	ENSG00000108106	1 retrocopy	retro_hsap_1808,
Mus musculus	ENSMUSG00000020390	1 retrocopy	retro_mmus_736,
Mus musculus	ENSMUSG00000060860	2 retrocopies	retro_mmus_1675 , retro_mmus_3278,
Pan troglodytes	ENSPTRG00000011507	2 retrocopies	retro_ptro_3055, retro_ptro_3059,
Rattus norvegicus	ENSRNOG00000016930	2 retrocopies	retro_rnor_1730, retro_rnor_912,