RetrogeneDB ID: retro_mmus_769

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 11:21683304..21683949(-)
• Located in intron of: ENSMUSG00000020319

Retrocopy information

• Ensembl ID: ENSMUSG00000083761
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Pgam1
• Ensembl ID: ENSMUSG00000011752
• Aliases: Pgam1, 2310050F24Rik, Pgam-1
• Description: phosphoglycerate mutase 1 [Source:MGI Symbol;Acc:MGI:97552]

Sequence

>retro_mmus_769
GGGCAGGCGTTGCGAGATACTGGCTATGAATTTGACATCTGCTTCACCTCTGTGCAGAAGAGAGCAATCCGGACCCTCTG
GATAGTCCTGGATGCCATTGACCAGATGTGGTTGCCAGTGGTCAGGACTTGGCGCCTCAATGAGCGACACTATGGCCGTG
TAACAGGTCTCAACAAAGCAGAAACTGCTGGTAAGCATGGTGAGGCCTAGGTAAAGATCTGGAGACGATATTACTATTAC
GATGTCCCACTGCCTCCCATGGAGCCTGATCACCCCTTCTACAGCAACATCAGCAAGGATCGCAGGTACGCAGACCTTAC
TGAGGACCAGCTCCCCTCCTGTGAGAGCCTGAAGGATACTATTGCCAGAGCACTGCCCTTCTGGAATGAAGAAATTGTCC
CCCAGATCAAAGAGGGGAAAAGGGTCTTGATTGCCGCCCATGGCAACAGCCTTCGGGGCATCGTTAAGCATCTGGAGGGT
CTCTCAGAAGAGGCCATCATGGAGCTGAACCTGCCCACGGGCATCCCTATCGTCTATGAACTGGACAAGAACTTGAAGCC
CATCAAGCCCATGCAGTTCCTGGGAGATGAGGAGACCGTGCGCAAAGCCATGGAAGCTGTGGCTGCTCAGGGCAAGGTGA
AGAAG

Alignment

ORF - retro_mmus_769 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.35 %
• Parental protein coverage: 83.86 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GQALRDAGYEFDICFTSVQKRAIRTLWTVLDAIDQMWLPVVRTWRLNERHYGGLTGLNKAETAAKHGEAQ
          GQALRD.GYEFDICFTSVQKRAIRTLW.VLDAIDQMWLPVVRTWRLNERHYG..TGLNKAETA.KHGEA.
Retrocopy GQALRDTGYEFDICFTSVQKRAIRTLWIVLDAIDQMWLPVVRTWRLNERHYGRVTGLNKAETAGKHGEA*

Parental  VKIWRRSY--DVPPPPMEPDHPFYSNISKDRRYADLTEDQLPSCESLKDTIARALPFWNEEIVPQIKEGK
          VKIWRR.Y..DVP.PPMEPDHPFYSNISKDRRYADLTEDQLPSCESLKDTIARALPFWNEEIVPQIKEGK
Retrocopy VKIWRRYYYYDVPLPPMEPDHPFYSNISKDRRYADLTEDQLPSCESLKDTIARALPFWNEEIVPQIKEGK

Parental  RVLIAAHGNSLRGIVKHLEGLSEEAIMELNLPTGIPIVYELDKNLKPIKPMQFLGDEETVRKAMEAVAAQ
          RVLIAAHGNSLRGIVKHLEGLSEEAIMELNLPTGIPIVYELDKNLKPIKPMQFLGDEETVRKAMEAVAAQ
Retrocopy RVLIAAHGNSLRGIVKHLEGLSEEAIMELNLPTGIPIVYELDKNLKPIKPMQFLGDEETVRKAMEAVAAQ

Parental  GKVKK
          GKVKK
Retrocopy GKVKK

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	0.12 RPM	34.88 RPM
SRP007412_cerebellum	0.09 RPM	19.84 RPM
SRP007412_heart	0.03 RPM	5.88 RPM
SRP007412_kidney	0.10 RPM	16.92 RPM
SRP007412_liver	0.11 RPM	10.13 RPM
SRP007412_testis	0.05 RPM	3.52 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_769 was not detected

EST

No EST(s) were mapped for retro_mmus_769 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_11514	536 libraries	465 libraries	71 libraries	0 libraries	0 libraries

The graphical summary, for retro_mmus_769 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_769 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_769 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 15 parental genes, and 64 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012697	2 retrocopies	retro_btau_1611, retro_btau_472,
Canis familiaris	ENSCAFG00000009062	1 retrocopy	retro_cfam_1297,
Callithrix jacchus	ENSCJAG00000016575	1 retrocopy	retro_cjac_370,
Cavia porcellus	ENSCPOG00000006844	4 retrocopies	retro_cpor_158, retro_cpor_539, retro_cpor_605, retro_cpor_660,
Erinaceus europaeus	ENSEEUG00000005630	1 retrocopy	retro_eeur_680,
Echinops telfairi	ENSETEG00000002467	1 retrocopy	retro_etel_1595,
Homo sapiens	ENSG00000171314	12 retrocopies	retro_hsap_1048, retro_hsap_1052, retro_hsap_1142, retro_hsap_2235, retro_hsap_2604, retro_hsap_3083, retro_hsap_3488, retro_hsap_4249, retro_hsap_4686, retro_hsap_4821, retro_hsap_885, retro_hsap_913,
Gorilla gorilla	ENSGGOG00000028602	13 retrocopies	retro_ggor_1220, retro_ggor_1500, retro_ggor_1667, retro_ggor_1824, retro_ggor_2061, retro_ggor_2118, retro_ggor_2353, retro_ggor_2849, retro_ggor_3005, retro_ggor_3034, retro_ggor_716, retro_ggor_738, retro_ggor_827,
Macaca mulatta	ENSMMUG00000020027	1 retrocopy	retro_mmul_119,
Monodelphis domestica	ENSMODG00000004242	4 retrocopies	retro_mdom_1342, retro_mdom_1893, retro_mdom_610, retro_mdom_668,
Mus musculus	ENSMUSG00000011752	6 retrocopies	retro_mmus_1741, retro_mmus_2221, retro_mmus_3012, retro_mmus_411, retro_mmus_729, retro_mmus_769 ,
Pongo abelii	ENSPPYG00000002530	9 retrocopies	retro_pabe_1325, retro_pabe_2309, retro_pabe_2554, retro_pabe_2639, retro_pabe_2881, retro_pabe_3389, retro_pabe_3639, retro_pabe_3749, retro_pabe_671,
Rattus norvegicus	ENSRNOG00000050585	7 retrocopies	retro_rnor_1669, retro_rnor_2241, retro_rnor_2275, retro_rnor_2361, retro_rnor_2568, retro_rnor_691, retro_rnor_703,
Sarcophilus harrisii	ENSSHAG00000018230	1 retrocopy	retro_shar_323,
Drosophila melanogaster	FBgn0014869	1 retrocopy	retro_dmel_57,