RetrogeneDB ID: retro_mmus_969

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 12:97564256..97565068(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Armc10
• Ensembl ID: ENSMUSG00000038525
• Aliases: Armc10, 2810037C14Rik, Svh
• Description: armadillo repeat containing 10 [Source:MGI Symbol;Acc:MGI:1914461]

Sequence

>retro_mmus_969
ATGGGTGGCACACGGGTCATGGGCTGGGTGGCGACAGGGCTGGTCCTGGGCGCCGGCGTCTGCTACTATATCTACCAGCT
GACTCGGGGACCGCACCGAAGCATAGGCCGATTGTTCCCTTCGCGGTCCGCAGAAGACCTAACCGATGGCTCCTATGATG
ATATCTTAAATGTGGAACAGCTTGAGAAACTTCTGTACCTGCTGGAGTCAACCGACAATCCTATAGTTACTGAAAAAGCC
TTGGTCACCTTGGGAAATAATGCAGCCTTTTCCACTACCAGGCCATTATTCGTGAGTTGGGGAGTATCCTAATTGTTGGA
AACAAAATCAGCTCCCTGAACCAAAGTATTAAAGAGAAAGCTTTAAAAGCACTAAATAACCCGAGTGTGAATGTTGAAAA
TCAAACTAAGATAAAGATATACGTTCCTTATATCTGTGAGGACCTCTTTGCTGATGTCGTGAACTCTGCAGTGCAGCTGG
CTAGACTGAGGCTGCCGACAAACATGACGGTCACCAATGACTATCAACACCTGCTCAGCAGCTCCATCGCTGGCCTGTTC
CACCTGCTGCTTATGCGAAATTGAAGCACCACAGTTCAGGTTTGGAAGCTGATTTTGAATTTGTCTGAGAATCCAGCCAG
GACAGAAGGACTACTGAGTGTCCAAGTGGATTCATCATTCCTTTCCTTTTATGACGGCCAAGTAGCAAACGGGATTCTTC
TTCCAGCTCTTACACTGTTTCAGAATAGAAACAATTGCCTCAAAGTGAAAGGCCGGTTAGCTAATCAGCTTCCTTTTACT
AAACGGTCATTG

Alignment

ORF - retro_mmus_969 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.35 %
• Parental protein coverage: 88.56 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGGARDVGWVAAGLVLGAGACYCIYRLTRGPRRGGRRLRPSRSAEDLTDGSYDDILNAEQLKKLLYLLES
          MGG.R..GWVA.GLVLGAG.CY.IY.LTRGP.R...RL.PSRSAEDLTDGSYDDILN.EQL.KLLYLLES
Retrocopy MGGTRVMGWVATGLVLGAGVCYYIYQLTRGPHRSIGRLFPSRSAEDLTDGSYDDILNVEQLEKLLYLLES

Parental  TDDPVITEKALVTLGNNAAFSTN-QAIIRELGGIPIVGNKINSLNQSIKEKALNALNNLSVNVENQTKIK
          TD.P..TEKALVTLGNNAAFST..QAIIRELG.I.IVGNKI.SLNQSIKEKAL.ALNN.SVNVENQTKIK
Retrocopy TDNPIVTEKALVTLGNNAAFSTT<QAIIRELGSILIVGNKISSLNQSIKEKALKALNNPSVNVENQTKIK

Parental  IYVPQVCEDVFADPLNSAVQLAGLRLLTNMTVTNDYQHLLSGSVAGLFHLLLLGNGSTKVQVLKLLLNLS
          IYVP..CED.FAD..NSAVQLA.LRL.TNMTVTNDYQHLLS.S.AGLFHLLL..N.ST.VQV.KL.LNLS
Retrocopy IYVPYICEDLFADVVNSAVQLARLRLPTNMTVTNDYQHLLSSSIAGLFHLLLMRN*STTVQVWKLILNLS

Parental  ENPAMTEGLLSVQVDSSFLSLYDGQVANEILLRALTLFQNINNCLKVEGRLANQIPFAKGSL
          ENPA.TEGLLSVQVDSSFLS.YDGQVAN.ILL.ALTLFQN.NNCLKV.GRLANQ.PF.K.SL
Retrocopy ENPARTEGLLSVQVDSSFLSFYDGQVANGILLPALTLFQNRNNCLKVKGRLANQLPFTKRSL

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	13.11 RPM
SRP007412_cerebellum	0.00 RPM	6.73 RPM
SRP007412_heart	0.00 RPM	7.04 RPM
SRP007412_kidney	0.00 RPM	12.47 RPM
SRP007412_liver	0.00 RPM	4.72 RPM
SRP007412_testis	0.00 RPM	6.95 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_969 was not detected

EST

No EST(s) were mapped for retro_mmus_969 retrocopy.

TSS

No TSS is located nearby retro_mmus_969 retrocopy 5' end.

Lab

retro_mmus_969 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_969 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000004247	1 retrocopy	retro_cfam_1264,
Choloepus hoffmanni	ENSCHOG00000002095	1 retrocopy	retro_chof_2665,
Callithrix jacchus	ENSCJAG00000021208	2 retrocopies	retro_cjac_1758, retro_cjac_2104,
Cavia porcellus	ENSCPOG00000019936	1 retrocopy	retro_cpor_1022,
Homo sapiens	ENSG00000170632	1 retrocopy	retro_hsap_2815,
Microcebus murinus	ENSMICG00000010160	1 retrocopy	retro_mmur_638,
Myotis lucifugus	ENSMLUG00000006088	3 retrocopies	retro_mluc_1587, retro_mluc_1825, retro_mluc_624,
Mus musculus	ENSMUSG00000038525	3 retrocopies	retro_mmus_1292, retro_mmus_2256, retro_mmus_969 ,
Vicugna pacos	ENSVPAG00000008914	1 retrocopy	retro_vpac_19,