RetrogeneDB ID: retro_mmus_134

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:50599219..50600410(+)
• Located in intron of: ENSMUSG00000055409

Retrocopy information

• Ensembl ID: ENSMUSG00000084234
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Idh3g
• Ensembl ID: ENSMUSG00000002010
• Aliases: None
• Description: isocitrate dehydrogenase 3 (NAD+), gamma [Source:MGI Symbol;Acc:MGI:1099463]

Sequence

>retro_mmus_134
ATGTTGGCAGTAACCAGCTGTTCTATGAAAACAGTTCTCCAATATGCTGTGTTTCTTGGCCATTCTAGGGAGGTAGTGTG
TGAGCTTGTGACCTCCTTCAGAAGTTTCTGCTCACATTGCGCAGTGCCTCCTTCACCAAAGTATGGAGGAAGACACACGG
TGGCTATGATTCCTGGAGATGGCATTGGGCCTGAGCTTATGGTTCATGTCAAGAAAATATTCAGATCAAATTGTGTGCCA
GTGGACTTTGAAGAGGTGTGGGTCACCTCGACATCTAATGAAGAGGAGATCAACAATGCTCTCATGGCCATCCGTCGGAA
CCGTGTCGCTCTGAAGGGCAATATTGCAACCAACCACAATCTGCCTGCCCGTTACAAGTCTCACAACACCAAGTTTCGCA
CCATCCTTGACCTCTATGCCAGTGTCGTCCATTTCAAGACTTTTCCTGGTGTTATGACCCGACACAAAGACATAGACATC
TTGGTTGTTCGGGAGAATACAGAGGGGGAGTACACTAACCTAGAGCATGAGAGCGTGAAAGGCGTGGTAGAAAGCCTTAA
GATTGTGACAAAGACCAAGTCTGTGCGCATTGCTGATTATGCCTTCAAGTTGGCCCAAAAGATGGGGCGGAAAAAGGTGA
CAGTTGTTCACAAAGCCAACATCATGAAACTGGGAGATGGGCTCTTCCTTCAGTGCTGTAAGGATGTGGCAGCTCACTAT
CCTCAGATCACCTTAGAGAGTATGATTATAGACAACACCACAATGCAGTTGGTATCGAAGCCCCAACAGTTTGATGTCAT
GGTGATGCCCAATCTTTATGGCAACATTATCAACAGTATCTGCACAGGACTGGTTGGAGGGTCAGGAATTGTCCCTGGAG
CCAATTATGGTGATTCATATGCAATATTTGAGATGGGTTCAAAGGAAATAGGTAAAGATTTGGCTCACAGAAATATTGCC
AATCCTGTCGCCATGCTGCTGACCAGCTGTATCATGCTGGACTACCTTGATCTCCAACCCTATGCCACTCACATCCGCTC
TGCAGTCATGGCGTCCTTACAAAACAAAGCTGTCTGCACTCCAGACATTGGAGGTCAAGGGAACACTGCAAGCACTGTAG
AGTATATCTTACACCACATGAAAGAACAAACTAGTGGTTGTCATCCAAATTTCTTCCTGCAGTTCACTTGA

Alignment

ORF - retro_mmus_134 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.83 %
• Parental protein coverage: 91.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EVLAAHVAPRRSISSQQTIPPSAKYGGRHTVTMIPGDGIGPELMLHVKSVFRHACVPVDFEEVHVSSNAD
          EV....V...RS..S....PPS.KYGGRHTV.MIPGDGIGPELM.HVK..FR..CVPVDFEEV.V.S...
Retrocopy EVVCELVTSFRSFCSHCAVPPSPKYGGRHTVAMIPGDGIGPELMVHVKKIFRSNCVPVDFEEVWVTSTSN

Parental  EEDIRNAIMAIRRNRVALKGNIETNHNLPPSHKSRNNILRTSLDLYANVIHCKSLPGVVTRHKDIDILIV
          EE.I.NA.MAIRRNRVALKGNI.TNHNLP...KS.N...RT.LDLYA.V.H.K..PGV.TRHKDIDIL.V
Retrocopy EEEINNALMAIRRNRVALKGNIATNHNLPARYKSHNTKFRTILDLYASVVHFKTFPGVMTRHKDIDILVV

Parental  RENTEGEYSSLEHESVAGVVESLKIITKAKSLRIAEYAFKLAQESGRKKVTAVHKANIMKLGDGLFLQCC
          RENTEGEY..LEHESV.GVVESLKI.TK.KS.RIA.YAFKLAQ..GRKKVT.VHKANIMKLGDGLFLQCC
Retrocopy RENTEGEYTNLEHESVKGVVESLKIVTKTKSVRIADYAFKLAQKMGRKKVTVVHKANIMKLGDGLFLQCC

Parental  REVAAHYPQITFDSMIVDNTTMQLVSRPQQFDVMVMPNLYGNIVNNVCAGLVGGPGLVAGANYGHVYAVF
          ..VAAHYPQIT..SMI.DNTTMQLVS.PQQFDVMVMPNLYGNI.N..C.GLVGG.G.V.GANYG..YA.F
Retrocopy KDVAAHYPQITLESMIIDNTTMQLVSKPQQFDVMVMPNLYGNIINSICTGLVGGSGIVPGANYGDSYAIF

Parental  ETATRNTGKSIANKNIANPTATLLASCMMLDHLKLHSYATSIRKAVLASMDNENMHTPDIGGQGTTSQAI
          E......GK..A..NIANP.A.LL.SC.MLD.L.L..YAT.IR.AV.AS..N....TPDIGGQG.T....
Retrocopy EMGSKEIGKDLAHRNIANPVAMLLTSCIMLDYLDLQPYATHIRSAVMASLQNKAVCTPDIGGQGNTASTV

Parental  QDIIRHIR
          ..I..H..
Retrocopy EYILHHMK

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	0.21 RPM	124.10 RPM
SRP007412_cerebellum	0.04 RPM	216.80 RPM
SRP007412_heart	0.00 RPM	490.61 RPM
SRP007412_kidney	0.00 RPM	361.80 RPM
SRP007412_liver	0.00 RPM	65.08 RPM
SRP007412_testis	37.92 RPM	16.42 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_134 was not detected

EST

1 EST(s) were mapped to retro_mmus_134 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BB616954	50599189	50599841	99	644	7	636

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_136205	1067 libraries	2 libraries	2 libraries	1 library	0 libraries
TSS #2	TSS_136206	1066 libraries	3 libraries	1 library	0 libraries	2 libraries
TSS #3	TSS_136207	1063 libraries	3 libraries	3 libraries	0 libraries	3 libraries
TSS #4	TSS_136208	1063 libraries	4 libraries	2 libraries	1 library	2 libraries

The graphical summary, for retro_mmus_134 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_134 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_134 has 7 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_759
Pan troglodytes	retro_ptro_534
Oryctolagus cuniculus	retro_ocun_80
Bos taurus	retro_btau_1194
Sus scrofa	retro_sscr_662
Canis familiaris	retro_cfam_1023
Equus caballus	retro_ecab_941

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018466	1 retrocopy	retro_amel_1892,
Bos taurus	ENSBTAG00000001059	1 retrocopy	retro_btau_1194,
Canis familiaris	ENSCAFG00000019286	1 retrocopy	retro_cfam_1023,
Callithrix jacchus	ENSCJAG00000011185	1 retrocopy	retro_cjac_1597,
Equus caballus	ENSECAG00000018509	1 retrocopy	retro_ecab_941,
Homo sapiens	ENSG00000067829	1 retrocopy	retro_hsap_759,
Latimeria chalumnae	ENSLACG00000007365	1 retrocopy	retro_lcha_17,
Loxodonta africana	ENSLAFG00000006904	1 retrocopy	retro_lafr_560,
Macropus eugenii	ENSMEUG00000013934	1 retrocopy	retro_meug_203,
Myotis lucifugus	ENSMLUG00000004457	1 retrocopy	retro_mluc_396,
Mustela putorius furo	ENSMPUG00000008781	1 retrocopy	retro_mputfur_644,
Mus musculus	ENSMUSG00000002010	1 retrocopy	retro_mmus_134 ,
Nomascus leucogenys	ENSNLEG00000013540	1 retrocopy	retro_nleu_394,
Otolemur garnettii	ENSOGAG00000006735	1 retrocopy	retro_ogar_25,
Pteropus vampyrus	ENSPVAG00000013163	1 retrocopy	retro_pvam_373,
Rattus norvegicus	ENSRNOG00000037284	1 retrocopy	retro_rnor_209,
Sus scrofa	ENSSSCG00000012783	1 retrocopy	retro_sscr_662,
Tursiops truncatus	ENSTTRG00000011728	1 retrocopy	retro_ttru_848,