RetrogeneDB ID: retro_mmus_2256

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 3:58666075..58666566(-)
• 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_2256
ATGGGTGGCACGCGGGACGTGGGCTGGGTGGCAGCAGGGCTGGGCGCTGCGCCTGTTACTGTATTTACCGGCTGACTCGG
GGACCACGCGGTCACCGACTGCGCCCTTCGCCCTTCGCGGTCTGCAGAAGAGAGCTTGAGAAACTTCTGTAGTTGCTGGA
GTCAACCAACGATCCTATAATTACTAAAAAAGCCTTGGTCACCTTAGGAAATAATGCAGCCTTTTCTACTAACCAGGCCA
TTATTCGTGAGTTGGGTGGTATGCCAATCGTTGGAAACAAAATCAACTCCCTGAACCAAAGTATTAGAGAGAAAGCTTTA
AATGTACTGAATAACCTGAGTGTGAATGTTGAAAATCAAACTAAGATAAAGATATACATCCCTCAAGTGTGTGGGGACGT
CTTTGCTGATCCCCTGAACTCTGCGGTGCAGCTGGCGGGACTGAGGCTGCTGACAAACATGACAGTCACCAACGACTACC
AGCACCTGCTC

Alignment

ORF - retro_mmus_2256 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.21 %
• Parental protein coverage: 56.51 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGGARDVGWVAAGLVLGAG-ACYCIYRLTRGPRRGGRRLRPSRSA---EQLKKLLYLLESTDDPVITEKA
          MGG.RDVGWVAAG..LGA..ACYCIYRLTRGPR..G.RLRPS..A.....L.KLL.LLEST.DP.IT.KA
Retrocopy MGGTRDVGWVAAG--LGAA<ACYCIYRLTRGPR--GHRLRPSPFAVCRRELEKLL*LLESTNDPIITKKA

Parental  LVTLGNNAAFSTNQAIIRELGGIPIVGNKINSLNQSIKEKALNALNNLSVNVENQTKIKIYVPQVCEDVF
          LVTLGNNAAFSTNQAIIRELGG.PIVGNKINSLNQSI.EKALN.LNNLSVNVENQTKIKIY.PQVC.DVF
Retrocopy LVTLGNNAAFSTNQAIIRELGGMPIVGNKINSLNQSIREKALNVLNNLSVNVENQTKIKIYIPQVCGDVF

Parental  ADPLNSAVQLAGLRLLTNMTVTNDYQHLL
          ADPLNSAVQLAGLRLLTNMTVTNDYQHLL
Retrocopy ADPLNSAVQLAGLRLLTNMTVTNDYQHLL

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	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	1.19 RPM	6.95 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2256 was not detected

EST

No EST(s) were mapped for retro_mmus_2256 retrocopy.

TSS

No TSS is located nearby retro_mmus_2256 retrocopy 5' end.

Lab

retro_mmus_2256 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2256 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,