RetrogeneDB ID: retro_mmus_2032

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:53696123..53696858(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000083287
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Idi1
• Ensembl ID: ENSMUSG00000058258
• Aliases: Idi1, 4832416K17Rik
• Description: isopentenyl-diphosphate delta isomerase [Source:MGI Symbol;Acc:MGI:2442264]

Sequence

>retro_mmus_2032
AGCACCTGCAGCCGGAATCTCTGTGTTCTAGGTCAGATCAGACATTCTGTCACAATGCCTGAAATAAATACCAGCCATCT
TGATGAAAAACAGGTTCAGCTTCTAGCGGAGATGTGTATTCTTATTGATGAAAATGACAATAAAATTGGGGCTGACACCA
AGAAAAACTGTCACCTTAATGAAAACATCGACAAAGGATTATTACATCGAGCTTTTAGTGTCTTCTTGTTTAATACTGAA
AATAAGCTCCTGTTACAGCAGAGATCAGATGCTAAAATTACCTTTCCAGGTTGTTTCACCAATAGTTGCTGTAGTCATCC
ATTAAGTAACCCAGGCGAGCTGGAAGAGAACAACGCCATTGGTGTGAAGCGAGCAGCAAAGCGGCGCTTGAAAGCCGAGT
TGGGAATACCCTTGGAAGAGGTTGATCTAAATGAAATGGATTATCTAACAAGAATTTACTACAAGGCCCAATCTGATGGT
ATCTGGGGTGAACATGAAGTTGATTACATTCTGTTTCTGAGGAAGAATGTAACCTTGAATCCAGATCCCAACGAGATTAA
AAGCTATTGCTATGTATCAAAGGAAGAAGTCAGAGAAATTTTGAAGAAGGCAGCCAGTGGTGAAATTAAGTTAACTCCGT
GGTTTAAGATAATTGCAGATACTTTCCTCTTCAAATGGTGGGATAACTTAAACCATTTGAGTCCATTTGTTGACCATGAG
AAAATACATAGATTG

Alignment

ORF - retro_mmus_2032 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100. %
• Parental protein coverage: 86.57 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  STCSRNLCVLGQIRHSVTMPEINTSHLDEKQVQLLAEMCILIDENDNKIGADTKKNCHLNENIDKGLLHR
          STCSRNLCVLGQIRHSVTMPEINTSHLDEKQVQLLAEMCILIDENDNKIGADTKKNCHLNENIDKGLLHR
Retrocopy STCSRNLCVLGQIRHSVTMPEINTSHLDEKQVQLLAEMCILIDENDNKIGADTKKNCHLNENIDKGLLHR

Parental  AFSVFLFNTENKLLLQQRSDAKITFPGCFTNSCCSHPLSNPGELEENNAIGVKRAAKRRLKAELGIPLEE
          AFSVFLFNTENKLLLQQRSDAKITFPGCFTNSCCSHPLSNPGELEENNAIGVKRAAKRRLKAELGIPLEE
Retrocopy AFSVFLFNTENKLLLQQRSDAKITFPGCFTNSCCSHPLSNPGELEENNAIGVKRAAKRRLKAELGIPLEE

Parental  VDLNEMDYLTRIYYKAQSDGIWGEHEVDYILFLRKNVTLNPDPNEIKSYCYVSKEEVREILKKAASGEIK
          VDLNEMDYLTRIYYKAQSDGIWGEHEVDYILFLRKNVTLNPDPNEIKSYCYVSKEEVREILKKAASGEIK
Retrocopy VDLNEMDYLTRIYYKAQSDGIWGEHEVDYILFLRKNVTLNPDPNEIKSYCYVSKEEVREILKKAASGEIK

Parental  LTPWFKIIADTFLFKWWDNLNHLSPFVDHEKIHRL
          LTPWFKIIADTFLFKWWDNLNHLSPFVDHEKIHRL
Retrocopy LTPWFKIIADTFLFKWWDNLNHLSPFVDHEKIHRL

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	3.64 RPM
SRP007412_cerebellum	0.00 RPM	1.69 RPM
SRP007412_heart	0.00 RPM	0.72 RPM
SRP007412_kidney	0.10 RPM	3.58 RPM
SRP007412_liver	0.22 RPM	20.04 RPM
SRP007412_testis	0.00 RPM	6.72 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2032 was not detected

EST

No EST(s) were mapped for retro_mmus_2032 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_87599	708 libraries	350 libraries	14 libraries	0 libraries	0 libraries

The graphical summary, for retro_mmus_2032 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_2032 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2032 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008483	3 retrocopies	retro_cjac_2083, retro_cjac_2591, retro_cjac_2820,
Erinaceus europaeus	ENSEEUG00000012555	3 retrocopies	retro_eeur_188, retro_eeur_198, retro_eeur_61,
Homo sapiens	ENSG00000067064	3 retrocopies	retro_hsap_2161, retro_hsap_2444, retro_hsap_4053,
Gorilla gorilla	ENSGGOG00000000934	3 retrocopies	retro_ggor_1521, retro_ggor_1717, retro_ggor_2722,
Macaca mulatta	ENSMMUG00000017115	3 retrocopies	retro_mmul_2340, retro_mmul_632, retro_mmul_899,
Monodelphis domestica	ENSMODG00000005998	5 retrocopies	retro_mdom_1107, retro_mdom_1692, retro_mdom_1697, retro_mdom_1724, retro_mdom_547,
Mus musculus	ENSMUSG00000058258	4 retrocopies	retro_mmus_2032 , retro_mmus_2660, retro_mmus_417, retro_mmus_552,
Nomascus leucogenys	ENSNLEG00000013594	3 retrocopies	retro_nleu_1810, retro_nleu_2777, retro_nleu_2804,
Oryctolagus cuniculus	ENSOCUG00000007493	1 retrocopy	retro_ocun_267,
Ochotona princeps	ENSOPRG00000008692	2 retrocopies	retro_opri_694, retro_opri_755,
Pongo abelii	ENSPPYG00000002039	2 retrocopies	retro_pabe_1783, retro_pabe_3327,
Pan troglodytes	ENSPTRG00000002239	3 retrocopies	retro_ptro_1412, retro_ptro_1647, retro_ptro_2747,
Ictidomys tridecemlineatus	ENSSTOG00000023260	1 retrocopy	retro_itri_118,
Tursiops truncatus	ENSTTRG00000011174	1 retrocopy	retro_ttru_255,