RetrogeneDB ID: retro_mmus_956

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 12:84334383..84334618(-)
• Located in intron of: ENSMUSG00000042472

Retrocopy information

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

Parental gene information

• Parental gene symbol: Lsm6
• Ensembl ID: ENSMUSG00000031683
• Aliases: Lsm6, 1500031N17Rik, 2410088K19Rik, AI747288
• Description: LSM6 homolog, U6 small nuclear RNA associated (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:1925901]

Sequence

>retro_mmus_956
AGCCTTCCGAAGCAAACCCCTAGTGACTTCTTAAAGCAGATCATCGGGCAGCCAGTTGTGGTGAAATTAAATTCTGGAGT
GAACTGTTGAGGGCTGCTGGCCTGCCTGGATGGCTACATGAATATAGCCCTGGAACAGACAGGGGAGTATGTAAACGGAC
AGCTGGAGATAAGTATGGAGATGCGTTCATCTGAGGAACAATGTGCTGTACATAAGTACACAGAAGAGGCGGATG

Alignment

ORF - retro_mmus_956 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.19 %
• Parental protein coverage: 98.75 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SLRKQTPSDFLKQIIGRPVVVKLNSGVDYRGVLACLDGYMNIALEQTEEYVNGQLK-NKYGDAFIRG-NN
          SL.KQTPSDFLKQIIG.PVVVKLNSGV...G.LACLDGYMNIALEQT.EYVNGQL...KYGDAFI.G.NN
Retrocopy SLPKQTPSDFLKQIIGQPVVVKLNSGVNC*GLLACLDGYMNIALEQTGEYVNGQLE<DKYGDAFI*G<NN

Parental  VLYISTQKRRM
          VLYISTQKRRM
Retrocopy VLYISTQKRRM

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	26.73 RPM
SRP007412_cerebellum	0.17 RPM	42.99 RPM
SRP007412_heart	0.06 RPM	16.25 RPM
SRP007412_kidney	0.15 RPM	19.58 RPM
SRP007412_liver	0.14 RPM	22.07 RPM
SRP007412_testis	0.09 RPM	10.57 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_956 was not detected

EST

No EST(s) were mapped for retro_mmus_956 retrocopy.

TSS

No TSS is located nearby retro_mmus_956 retrocopy 5' end.

Lab

retro_mmus_956 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_956 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002482	4 retrocopies	retro_cjac_1173, retro_cjac_1278, retro_cjac_3176, retro_cjac_3248,
Dasypus novemcinctus	ENSDNOG00000009322	5 retrocopies	retro_dnov_1118, retro_dnov_176, retro_dnov_2092, retro_dnov_301, retro_dnov_664,
Microcebus murinus	ENSMICG00000000571	1 retrocopy	retro_mmur_1563,
Macaca mulatta	ENSMMUG00000005524	2 retrocopies	retro_mmul_668, retro_mmul_991,
Mus musculus	ENSMUSG00000020018	4 retrocopies	retro_mmus_1060, retro_mmus_1197, retro_mmus_2537, retro_mmus_3210,
Mus musculus	ENSMUSG00000031683	2 retrocopies	retro_mmus_820, retro_mmus_956 ,
Otolemur garnettii	ENSOGAG00000026665	1 retrocopy	retro_ogar_233,
Pongo abelii	ENSPPYG00000015105	1 retrocopy	retro_pabe_1994,
Pan troglodytes	ENSPTRG00000016488	1 retrocopy	retro_ptro_1545,
Tarsius syrichta	ENSTSYG00000012759	4 retrocopies	retro_tsyr_1332, retro_tsyr_1727, retro_tsyr_340, retro_tsyr_653,