RetrogeneDB ID: retro_mmus_532

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 10:19101544..19102314(+)
• 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_532
TCTGACCTTCAGAGACTTGAGCTTAGTGCAATGGCGCCTTCCCGGAAGTTCTTCGTGGGGGGCAACTGGAAGATGAACGG
GAGGAAGCAGTGTCTGGGAGAACTCCTCTGCACCCTGAACACAGCCAGCATGCCAGCAGGCACCGAGGTGGTTTGTGCAC
CGCCAATCGATTACATCAACTTCGCCAGGAAGAAGCTGGATCCCAAAATTGCTATGGCTGCACAGAACTGCTACAAAGTG
ACCAGTGGGGCCTTCACTGGGGAAATCAGCACTGGCATAATTAAAGGCTTAGGAGTTACCTGGGTCGTGCTGGGACACTC
AGAAAGAAGACATGTCTTTGGGAATCAGACGAGTTGATTGGGCAGAAAGAGAACCATGCCCTAGCAGAGGAACTCTGAGT
GATCGCCTACACTGGGTAGAAGCTAGACAAAAGAGAAGTTGGCATCACCGAGAAGGCTGTTTTTGAGCAAACCAAGGTCA
TCGCAGATAATGTGAAGGACCGGAGCAAGGTGGACCTGGCCTGCGAACCTGTATGGGCCATTGGGACTGGCAAGACTGCA
ACCCCTCAACCGGAAGTACATGAGAAGCTCCAGGGATGGCTGAAATCCAATGTCTCTGATGGGGTGGCTCAGTGCACCCA
GATCATTTATGGAGGTGCTATCACTGGAGCAACCTGCAAAGAGCTGGCAAGTCAGCCTGACATGGATGGCTTCCTTGTGG
GTGGTGCATCTCTCAAGCCTGAATCTGTGGACATCATCAATGCCAAACAA

Alignment

ORF - retro_mmus_532 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.69 %
• Parental protein coverage: 86.62 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TDLQRLEPGTMAPTRKFFVGGNWKMNGRKKCLGELICTLNAANVPAGTEVVCAPPTAYIDFARQKLDPKI
          .DLQRLE...MAP.RKFFVGGNWKMNGRK.CLGEL.CTLN.A..PAGTEVVCAPP..YI.FAR.KLDPKI
Retrocopy SDLQRLELSAMAPSRKFFVGGNWKMNGRKQCLGELLCTLNTASMPAGTEVVCAPPIDYINFARKKLDPKI

Parental  AVAAQNCYKVTNGAFTGEISPGMIKDLGATWVVLGHSERRHVFG-ESDELIGQKVSHALAEGLGVIACIG
          A.AAQNCYKVT.GAFTGEIS.G.IK.LG.TWVVLGHSERRHVFG.ESDELIGQK..HALAE.L.VIA..G
Retrocopy AMAAQNCYKVTSGAFTGEISTGIIKGLGVTWVVLGHSERRHVFG<ESDELIGQKENHALAEEL*VIAYTG

Parental  EKLDEREAGITEKVVFEQTKVIADNVKDWSKVVLAYEPVWAIGTGKTATPQQAQEVHEKLRGWLKSNVND
          .KLD.RE.GITEK.VFEQTKVIADNVKD.SKV.LA.EPVWAIGTGKTATPQ...EVHEKL.GWLKSNV.D
Retrocopy *KLDKREVGITEKAVFEQTKVIADNVKDRSKVDLACEPVWAIGTGKTATPQ--PEVHEKLQGWLKSNVSD

Parental  GVAQSTRIIYGGSVTGATCKELASQPDVDGFLVGGASLKPEFVDIINAKQ
          GVAQ.T.IIYGG..TGATCKELASQPD.DGFLVGGASLKPE.VDIINAKQ
Retrocopy GVAQCTQIIYGGAITGATCKELASQPDMDGFLVGGASLKPESVDIINAKQ

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	0.04 RPM	340.64 RPM
SRP007412_heart	0.00 RPM	409.52 RPM
SRP007412_kidney	0.02 RPM	450.52 RPM
SRP007412_liver	0.00 RPM	259.08 RPM
SRP007412_testis	0.32 RPM	293.10 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_532 was not detected

EST

No EST(s) were mapped for retro_mmus_532 retrocopy.

TSS

No TSS is located nearby retro_mmus_532 retrocopy 5' end.

Lab

retro_mmus_532 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_532 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,