RetrogeneDB ID: retro_mmus_2679

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 5:104988979..104989329(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Sec61b
• Ensembl ID: ENSMUSG00000053317
• Aliases: Sec61b, 1190006C12Rik, AI326121, AW122942
• Description: Sec61 beta subunit [Source:MGI Symbol;Acc:MGI:1913462]

Sequence

>retro_mmus_2679
GCCGGGTCCAAAGCCCAGTGGCACCAACGTGGGTTCCTCTGGCCACTCTCCCAGCAAAGCGGTGGCCACAAGGGCTGCAG
GATCCACTGTCTGGCAGAGAAAAAATGCCAGCTGTGGGACCCGGAGCGCAGGCCGCACCACCTCTGCAGGGACTGGGGGG
ATGTGGCGATTCTACACGGAAGATTCCTCAGGGCTCAAAGTGGGCCTTGTCCCAGTGCTGGTGATGAGTCTTCTGTTCAT
CGCTTCTGTATTTATGCTGAACATTTGGGGCAAGTACACGTGATCTTAGATTGGGCTACATCCATCTGTCATCTGAAGAA
GAAGAAGGAAAAAACCCAACATATCTTGGA

Alignment

ORF - retro_mmus_2679 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.08 %
• Parental protein coverage: 84.29 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AGSNAQWHQRGLLWPLSQQSGGRTGCGIHCSAEKKCQLWDPERRPHHLCRDWGDVAILHGRFPRAQSGPC
          AGS.AQWHQRG.LWPLSQQSGG..GC.IHC.AEKKCQLWDPERRPHHLCRDWGDVAILHGRF.RAQSGPC
Retrocopy AGSKAQWHQRGFLWPLSQQSGGHKGCRIHCLAEKKCQLWDPERRPHHLCRDWGDVAILHGRFLRAQSGPC

Parental  PSAGDESSVHRCCIYAAHLGQVHAIIDWATSICHLKKKKKEK-NPTYLG
          PSAGDESSVHR.CIYA.HLGQVH.I.DWATSICHL.KKKKEK.NPTYLG
Retrocopy PSAGDESSVHRFCIYAEHLGQVHVILDWATSICHL-KKKKEK<NPTYLG

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	6.59 RPM
SRP007412_cerebellum	0.00 RPM	4.69 RPM
SRP007412_heart	0.00 RPM	4.51 RPM
SRP007412_kidney	0.02 RPM	10.78 RPM
SRP007412_liver	0.00 RPM	25.67 RPM
SRP007412_testis	0.00 RPM	6.22 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2679 was not detected

EST

No EST(s) were mapped for retro_mmus_2679 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_107586	26 libraries	36 libraries	208 libraries	249 libraries	553 libraries

The graphical summary, for retro_mmus_2679 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_2679 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2679 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002457	3 retrocopies	retro_btau_1053, retro_btau_360, retro_btau_791,
Callithrix jacchus	ENSCJAG00000011279	1 retrocopy	retro_cjac_503,
Equus caballus	ENSECAG00000026930	1 retrocopy	retro_ecab_711,
Echinops telfairi	ENSETEG00000005293	4 retrocopies	retro_etel_1777, retro_etel_1889, retro_etel_483, retro_etel_695,
Homo sapiens	ENSG00000106803	1 retrocopy	retro_hsap_871,
Gorilla gorilla	ENSGGOG00000004205	1 retrocopy	retro_ggor_708,
Macropus eugenii	ENSMEUG00000000321	1 retrocopy	retro_meug_1921,
Microcebus murinus	ENSMICG00000011121	4 retrocopies	retro_mmur_1037, retro_mmur_1631, retro_mmur_435, retro_mmur_543,
Myotis lucifugus	ENSMLUG00000001097	1 retrocopy	retro_mluc_2170,
Macaca mulatta	ENSMMUG00000010661	1 retrocopy	retro_mmul_86,
Mus musculus	ENSMUSG00000053317	2 retrocopies	retro_mmus_1377, retro_mmus_2679 ,
Nomascus leucogenys	ENSNLEG00000017055	1 retrocopy	retro_nleu_2844,
Otolemur garnettii	ENSOGAG00000004168	3 retrocopies	retro_ogar_1132, retro_ogar_2671, retro_ogar_823,
Pongo abelii	ENSPPYG00000019441	1 retrocopy	retro_pabe_680,
Pan troglodytes	ENSPTRG00000021184	1 retrocopy	retro_ptro_606,
Rattus norvegicus	ENSRNOG00000006345	1 retrocopy	retro_rnor_1589,