RetrogeneDB ID: retro_mmus_1292

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 14:75930541..75931459(-)
• Located in intron of: ENSMUSG00000067995

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_1292
ATGGGTGGCGCGCGGGACTTGGGCTGGGTGGCAGCAGGGCTGGTTCTGGGCGCCGGCGCCTGCTACTGTATCTACCGGCT
GACTCGGGGACCGCGGCGAGGCGGTCGCTGACTGCGCCCTTCGCGATCCGCAGAAGACCTAACCGATGGCTCCTATGACG
ATATCTTAAATGCAGAGCAGCTTAAGAAACTTCTGTATCTGCTGGAGTCAACCGACGATCCTATCATTACTGAAAAGGCC
TTGGTCACCTTGGGAAATAATGCAGCCTTTTCCACTAAGCAGGCCATTATTCGTGAGTTGGGTGGTATCCCAATTGTTGG
AAACAAAATCAACTCCCTGAACCAAAGTATTAAAGAGAAAGCTTTAAATGCACTGAATAACCTGAGTGTGAATGTTGAAA
ATCAAACTAAGATAAAGATATACGTCCCTCAAGTCTGTGAGGACGTCTTTGCTGATCCCCTGAACTCTGCGGTGCAGCTG
GTGGGACTGAGGCTGCTGACAAACAGGACAGTCACCAACGACTACCAGCACCTGCTCAGCGGCTCCGTCGCTGGCCTGTT
CCACCTGCTGCTGCTGGGAAACGGAAGCACCAAGGTCCAGGTTTTGAAGCTGCTTTTGAATTTGTCTGAGAATCCAGCCA
TGACAGAAGGACTACTGAGTGTCCAAGTGGATTCTTCATTCCTTTCCCTTTATGACAGCCAAGTAGCAAATGAGATTCTT
CTTCGGGCTCTTACACTGTTTCAGAATATAAACAATTGCCTCAAAGTGGAAGGCCGGTTAGCTAATCAGATTCCTTTTGC
TAAAGGGTCATTGTTTTTCCTGTTATACGGAGAAGAATGTGCCCAGAAAATGAGAGCTTTAGCCTGTCATCATGATGCGG
ATGTGAAAGAGAAGGCTTTAGCAATAAAGCCGAAATTC

Alignment

ORF - retro_mmus_1292 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.39 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGGARDVGWVAAGLVLGAGACYCIYRLTRGPRRGGRRLRPSRSAEDLTDGSYDDILNAEQLKKLLYLLES
          MGGARD.GWVAAGLVLGAGACYCIYRLTRGPRRGGR.LRPSRSAEDLTDGSYDDILNAEQLKKLLYLLES
Retrocopy MGGARDLGWVAAGLVLGAGACYCIYRLTRGPRRGGR*LRPSRSAEDLTDGSYDDILNAEQLKKLLYLLES

Parental  TDDPVITEKALVTLGNNAAFSTNQAIIRELGGIPIVGNKINSLNQSIKEKALNALNNLSVNVENQTKIKI
          TDDP.ITEKALVTLGNNAAFST.QAIIRELGGIPIVGNKINSLNQSIKEKALNALNNLSVNVENQTKIKI
Retrocopy TDDPIITEKALVTLGNNAAFSTKQAIIRELGGIPIVGNKINSLNQSIKEKALNALNNLSVNVENQTKIKI

Parental  YVPQVCEDVFADPLNSAVQLAGLRLLTNMTVTNDYQHLLSGSVAGLFHLLLLGNGSTKVQVLKLLLNLSE
          YVPQVCEDVFADPLNSAVQL.GLRLLTN.TVTNDYQHLLSGSVAGLFHLLLLGNGSTKVQVLKLLLNLSE
Retrocopy YVPQVCEDVFADPLNSAVQLVGLRLLTNRTVTNDYQHLLSGSVAGLFHLLLLGNGSTKVQVLKLLLNLSE

Parental  NPAMTEGLLSVQVDSSFLSLYDGQVANEILLRALTLFQNINNCLKVEGRLANQIPFAKGSLFFLLYGEEC
          NPAMTEGLLSVQVDSSFLSLYD.QVANEILLRALTLFQNINNCLKVEGRLANQIPFAKGSLFFLLYGEEC
Retrocopy NPAMTEGLLSVQVDSSFLSLYDSQVANEILLRALTLFQNINNCLKVEGRLANQIPFAKGSLFFLLYGEEC

Parental  AQKMRALACHHDVDVKEKALAIKPKF
          AQKMRALACHHD.DVKEKALAIKPKF
Retrocopy AQKMRALACHHDADVKEKALAIKPKF

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	0.19 RPM	13.11 RPM
SRP007412_cerebellum	0.26 RPM	6.73 RPM
SRP007412_heart	0.03 RPM	7.04 RPM
SRP007412_kidney	0.10 RPM	12.47 RPM
SRP007412_liver	0.03 RPM	4.72 RPM
SRP007412_testis	0.05 RPM	6.95 RPM

ChIP-Seq

RNA Polymerase II actvity may be related with retro_mmus_1292 in 1 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF001YKA	POLR2A	14:75931306..75931679

EST

No EST(s) were mapped for retro_mmus_1292 retrocopy.

TSS

No TSS is located nearby retro_mmus_1292 retrocopy 5' end.

Lab

retro_mmus_1292 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1292 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,