RetrogeneDB ID: retro_mmus_3260

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 9:31948346..31948937(+)
• 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_3260
ACTGACCTTCAGAGACTTGAGATTAGTACAATGGCGCCTTCCAGGAAGTTCTTCGTTGGGGGCAACTGGAAGATGAACGG
GAGGAAGCAGTGCCTGGAAGAACTCATTTGCACCCCGGACGCAGCCAACCTGCTGGCAGACACCGAAGTAGTTTGTGCAC
GGCCAACCACTTACATCGACTTCGCCAGTCAGAAGTTGGATCCCAAAAGCTCTGTGGCTACACAAAACTGCTACAATGTG
AACAGTGGGGCCTTCCCTGGGGAAATCAGCCCTGGCATTATCAGAGTTAGGAGCCACCTGGGTCGTGCTGGGGCACTCGG
AAAAGAAGACACGTCTTTGGAGAATCAGATGAGTTGATTGGGCACAAAGTGAACCATGCCCTAGCAGAGGGACTCGCGGT
GATCGCCTGCATCGGGAGAAGCTAGGCGAAAGGGAAGATGACATCACTGAGAAGGCTGCTTTCGAGCAAACCAAGGTCAT
CGCAGATAACGTGAAGAACTGGAGCAAGGTGGTCCTGCCTATGATCCTGTGTGGGCCATTGGGACTGCGACCCCTCAACA
GGCCCGGGAAGTACATGAGAAGCTCTGGGGA

Alignment

ORF - retro_mmus_3260 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.59 %
• Parental protein coverage: 67.22 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  TDLQRLEPGTMAPTRKFFVGGNWKMNGRKKCLGELICTLNAANVPAGTEVVCAPPTAYIDFARQKLDPKI
          TDLQRLE..TMAP.RKFFVGGNWKMNGRK.CL.ELICT..AAN..A.TEVVCA.PT.YIDFA.QKLDPK.
Retrocopy TDLQRLEISTMAPSRKFFVGGNWKMNGRKQCLEELICTPDAANLLADTEVVCARPTTYIDFASQKLDPKS

Parental  AVAAQNCYKV-TNGAFTGEISPGMIKDLGATWVVLGHSE-RRHVFGESDELIGQKVSHALAEGLGVIACI
          .VA.QNCY.V.T.G...G..S......LGATWVVLGHSE.RRHVFGESDELIG.KV.HALAEGL.VIACI
Retrocopy SVATQNCYNV>TVGPSLGK-SALALSELGATWVVLGHSE>RRHVFGESDELIGHKVNHALAEGLAVIACI

Parental  G-EKLDEREAGITEKVVFEQTKVIADNVKDWSKVVL-AYEPVWAIGTGKTATPQQAQEVHEKLRG
          G.EKL.ERE..ITEK..FEQTKVIADNVK.WSKVVL.AY.PVWAIGT...ATPQQA.EVHEKL.G
Retrocopy G<EKLGEREDDITEKAAFEQTKVIADNVKNWSKVVL<AYDPVWAIGT---ATPQQAREVHEKLWG

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	0.02 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	0.11 RPM	259.08 RPM
SRP007412_testis	0.46 RPM	293.10 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3260 was not detected

EST

No EST(s) were mapped for retro_mmus_3260 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_149206	306 libraries	285 libraries	378 libraries	90 libraries	13 libraries

The graphical summary, for retro_mmus_3260 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_3260 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3260 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,