RetrogeneDB ID: retro_mmus_1741

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 18:80162786..80163514(+)
• Located in intron of: None

Retrocopy information

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

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_1741
CATGACGAAAGCACATGGAACATGGAAAGCGGCTTCAGCAGCTGGTACGACGCCGCCGCAGACCTGAGCCCGGAGGGCCA
CGAGGAGGCGAAGCGCGATGGACAGACGTTGTAAGATGCTGGCTATGAATTTGACATCTGCTTCATCTCTGCGCAGAAGA
GAACAATCCGGACGCCCTGGACAGTCCTGGATGCCATTGATCAGATGTATTTGCCAATGGTCAGGACTTGGCACCTCAAT
GAGCGACAGTATGGGGGTCTACCGGGTCTCACTAAAGAAAACTGCTGGTAAGCATGGTGAGGCCCGGGTAAAGACCTGAA
GACTATCTTTCGATGTTCCACCGCCTCCCATGGAGCCTGATCACCTCTTCTACAGCAACATCATCAAGGATCGCAGGTAT
GCAGACCTTACTGAGGACCAGCTACCCTCCTGTGAGAGCCTGAAGGACACTATTGCCAGAGCACTGCCCTTCTGGGATGA
AGAAACTGTCCCCCAGATCAAAGAAGGGGAAAAGGGCCCTGATTGCCGCCCATGGCAACAGCCTTCGTGGCATCGTTAAG
CACCTGGAGGGTCTCTCTGAAGACGCCATCACGGAGCTGAACCTGCCCACGGACATTCCCATCGTCTATGAACTGGACAA
GCCCGTCAAGCCCATGCAGTTCCTGGGAGATGAGGAGACCACGCGTAAAGCCATGGAAGATGTGGCTGCTCAGGGCAAGA
TGAAGAAG

Alignment

ORF - retro_mmus_1741 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.32 %
• Parental protein coverage: 96.06 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  HGESAWNLENRFSGWYDA--DLSPAGHEEAKRGGQALRDAGYEFDICFTSVQKRAIRTLWTVLDAIDQMW
          H.ES.WN.E..FS.WYDA..DLSP.GHEEAKR.GQ.L.DAGYEFDICF.S.QKR.IRT.WTVLDAIDQM.
Retrocopy HDESTWNMESGFSSWYDAAADLSPEGHEEAKRDGQTL*DAGYEFDICFISAQKRTIRTPWTVLDAIDQMY

Parental  LPVVRTWRLNERHYGGL-TG-LNKAETAAKHGEAQVKIWRRSYDVPPPPMEPDHPFYSNISKDRRYADLT
          LP.VRTW.LNER.YGGL.TG......TA.KHGEA.VK..R.S.DVPPPPMEPDH.FYSNI.KDRRYADLT
Retrocopy LPMVRTWHLNERQYGGL<TG<VSLKKTAGKHGEARVKT*RLSFDVPPPPMEPDHLFYSNIIKDRRYADLT

Parental  EDQLPSCESLKDTIARALPFWNEEIVPQIKE-GKRVLIAAHGNSLRGIVKHLEGLSEEAIMELNLPTGIP
          EDQLPSCESLKDTIARALPFW.EE.VPQIKE.GKR.LIAAHGNSLRGIVKHLEGLSE.AI.ELNLPT.IP
Retrocopy EDQLPSCESLKDTIARALPFWDEETVPQIKE>GKRALIAAHGNSLRGIVKHLEGLSEDAITELNLPTDIP

Parental  IVYELDKNLKPIKPMQFLGDEETVRKAMEAVAAQGKVKK
          IVYELDK...P.KPMQFLGDEET.RKAME.VAAQGK.KK
Retrocopy IVYELDK---PVKPMQFLGDEETTRKAMEDVAAQGKMKK

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	0.00 RPM	34.88 RPM
SRP007412_cerebellum	0.00 RPM	19.84 RPM
SRP007412_heart	0.00 RPM	5.88 RPM
SRP007412_kidney	0.00 RPM	16.92 RPM
SRP007412_liver	0.00 RPM	10.13 RPM
SRP007412_testis	0.64 RPM	3.52 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1741 was not detected

EST

No EST(s) were mapped for retro_mmus_1741 retrocopy.

TSS

No TSS is located nearby retro_mmus_1741 retrocopy 5' end.

Lab

retro_mmus_1741 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1741 has 0 orthologous retrocopies within eutheria group .

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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,