RetrogeneDB ID: retro_mmus_558

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 10:44589926..44590552(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Tpi1
• Ensembl ID: ENSMUSG00000023456
• Aliases: Tpi1, AI255506, Tpi, Tpi-1
• Description: triosephosphate isomerase 1 [Source:MGI Symbol;Acc:MGI:98797]

Sequence

>retro_mmus_558
ACTGACTTTCAGAGACTTGAGCTTAGTATGATGGTGCCTTCCAGGAAGCTCTTCGTGGGGGGCAACTGGAAGATGAACGG
GAGGAAGCAGTGCCTGGGAGAACTCAGCTGCACCCCGAAGGCAGCCAGTGTGCTGGCAGACACTGAGGTGGGTTGTGCAC
TGACAACCTCTTACATCGACTTCGCTAGGCAGAAGCTGGATCCCAAGATTGCTGTGGCTGCACAGAACTGCTACAAAGTG
ACCAATGGGGCCTTCACTGGAGAAATCAGCCCTGACATGATCAGAGACTTAGGAGCCACCAGAGTGGTGCTGGGGCACTC
GGGAAAGAAGGTGTGTCTTTGGGAATCAGATGAGTTGATTGGGCAGAAAGTAAACCATGCCCTAGCAGAGGGACTTGCAG
TGATCCCCTGCATTGGGGAGAAGCTAGACGAAAGGGAAGCTGGCATCACGGAGGAAGTTGTTTTTGAGCAAACCAAGGTC
ATCGCAGATAATGTGAAGGACAGAAGCAAGGTGGTCCTGGCCCATGAACCTGTATGGGCCATTGGGACTAGCAAGACTGC
AACCCCTCAACCGGAAGTACATGAGAAGCTCCAGGTTGGCTGAAATCCAATGTCTCTGATGGGGTG

Alignment

ORF - retro_mmus_558 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.71 %
• Parental protein coverage: 70.57 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TDLQRLEPGTMAPTRKFFVGGNWKMNGRKKCLGELICTLNAANVPAGTEVVCAPPTAYIDFARQKLDPKI
          TD.QRLE...M.P.RK.FVGGNWKMNGRK.CLGEL.CT..AA.V.A.TEV.CA..T.YIDFARQKLDPKI
Retrocopy TDFQRLELSMMVPSRKLFVGGNWKMNGRKQCLGELSCTPKAASVLADTEVGCALTTSYIDFARQKLDPKI

Parental  AVAAQNCYKVTNGAFTGEISPGMIKDLGATWVVLGHS-ERRHVFG-ESDELIGQKVSHALAEGLGVIACI
          AVAAQNCYKVTNGAFTGEISP.MI.DLGAT.VVLGHS.ERR.VFG.ESDELIGQKV.HALAEGL.VI.CI
Retrocopy AVAAQNCYKVTNGAFTGEISPDMIRDLGATRVVLGHS>ERRCVFG<ESDELIGQKVNHALAEGLAVIPCI

Parental  GEKLDEREAGITEKVVFEQTKVIADNVKDWSKVVLAYEPVWAIGTGKTATPQQAQEVHEKLR-GWLKSNV
          GEKLDEREAGITE.VVFEQTKVIADNVKD.SKVVLA.EPVWAIGT.KTATPQ...EVHEKL..GWLKSNV
Retrocopy GEKLDEREAGITEEVVFEQTKVIADNVKDRSKVVLAHEPVWAIGTSKTATPQ--PEVHEKLQ<GWLKSNV

Parental  NDGV
          .DGV
Retrocopy SDGV

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	308.62 RPM
SRP007412_cerebellum	0.00 RPM	340.64 RPM
SRP007412_heart	0.00 RPM	409.52 RPM
SRP007412_kidney	0.00 RPM	450.52 RPM
SRP007412_liver	0.00 RPM	259.08 RPM
SRP007412_testis	0.00 RPM	293.10 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_558 was not detected

EST

No EST(s) were mapped for retro_mmus_558 retrocopy.

TSS

No TSS is located nearby retro_mmus_558 retrocopy 5' end.

Lab

retro_mmus_558 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_558 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007348	2 retrocopies	retro_cjac_2190, retro_cjac_2370,
Homo sapiens	ENSG00000111669	3 retrocopies	retro_hsap_3038, retro_hsap_3510, retro_hsap_3784,
Gorilla gorilla	ENSGGOG00000002623	1 retrocopy	retro_ggor_151,
Macropus eugenii	ENSMEUG00000006977	5 retrocopies	retro_meug_1348, retro_meug_1520, retro_meug_1934, retro_meug_267, retro_meug_512,
Myotis lucifugus	ENSMLUG00000024989	4 retrocopies	retro_mluc_1090, retro_mluc_1311, retro_mluc_1777, retro_mluc_1807,
Macaca mulatta	ENSMMUG00000005194	2 retrocopies	retro_mmul_1864, retro_mmul_250,
Mustela putorius furo	ENSMPUG00000016774	1 retrocopy	retro_mputfur_136,
Mus musculus	ENSMUSG00000023456	4 retrocopies	retro_mmus_1180, retro_mmus_3260, retro_mmus_532, retro_mmus_558 ,
Nomascus leucogenys	ENSNLEG00000004821	2 retrocopies	retro_nleu_1120, retro_nleu_847,
Otolemur garnettii	ENSOGAG00000031254	1 retrocopy	retro_ogar_109,
Pongo abelii	ENSPPYG00000004207	1 retrocopy	retro_pabe_2902,
Pan troglodytes	ENSPTRG00000004595	4 retrocopies	retro_ptro_160, retro_ptro_1999, retro_ptro_2382, retro_ptro_2565,
Rattus norvegicus	ENSRNOG00000015290	1 retrocopy	retro_rnor_1304,
Rattus norvegicus	ENSRNOG00000050669	2 retrocopies	retro_rnor_2615, retro_rnor_787,