RetrogeneDB ID: retro_mmus_3625

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:60726391..60727448(-)
• Located in intron of: ENSMUSG00000067835

Retrocopy information

• Ensembl ID: ENSMUSG00000084331
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Fdps
• Ensembl ID: ENSMUSG00000059743
• Aliases: Fdps, 6030492I17Rik, AI256750, Fdpsl1, mKIAA1293
• Description: farnesyl diphosphate synthetase [Source:MGI Symbol;Acc:MGI:104888]

Sequence

>retro_mmus_3625
ATGAATGGGAACCAGAAATTGGATGTTTATAACCAAGAAAAGCAGAATTTCATCCAGCACTTCTCCCAGATCGTCAAGGT
GCTGACTGAGAAGGTGCTGGTACACCCAGACATAGGGGATGCTATTGCCCGGCTCAAGGAGGTCCTAGAGTACAATGCCT
TAGGAGGCAAGTACAACCGGGGTTTGGCCATGGTACAAGCCTTCCAGGAGCTGGTGGAGCCGAAGAAACAGGATACTGAG
AGTCTTCAGCGGGCCCTGACAGTGGGCTGGTGTGTAGAAATGCTCCAGGCTTTCTTCTTCGTGTCAGATGATATCATGGA
CTCTTCCCTCACTCGCGGGGCCAGATCTGCTGGTATCAGAAGCCAGGCATTGGCTTGGATGCCATCAACAACACTCTGCT
TTTGGAAGCCTCCATCTATCGTTTGCTGAAGTTCTACTGCAGGGAGCAGCCCTACTACCTGAACCTGCTGGAGCTCTTTC
TGCAGAGTTCCTATCAGACTGAGATCGGCAGACTCTAGACCTCATGACAGCACCCCGGGGCCATGTGGATCTTGGTAAAT
ACACTGAAAAGTGGTACAAATCGATTGTCAAGTACAAGACGGCTTTCTACTCTTTCTACCTGCCTATCGCGACCACCATG
TACATGGCAGGCATTGATGGGGAGAAGGAACATGCCAATGCCCTGAAGATCCTGCTGGAGATGGGCGAGTTCTTTCAGGT
CCAGGACTACTACCTTGATCTCTTTGGAGACCCCAGTGTGACGGGAAAGATTGGCACTGACATCCAGGACAACAAATGCA
GCTGGCTGGTGGTTCAGTGTCTGCTACGAGCCTGTCCTCAACAGCGCCAGATCTTAGAGGAGAATTATAGGCAGAAGGAC
CCATAAAAAGTGGCTCGGGTGAAAGCACTGTATGAGGCGCTGGATCTGCAGTCTGTTTTCTTCAAGTAGGAGGAAGACAA
TTACAACCGCCTCAAGAGTCTCATAGAGCAGTGCTCTGTGCCCCTGCCCCCATCCATCTTCATGGAACTTGCAAACAAGA
TCTATAAGAGGAGAAAG

Alignment

ORF - retro_mmus_3625 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.11 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MNGNQKLDAYNQEKQNFIQHFSQIVKVLTEKELGHPEIGDAIARLKEVLEYNALGGKYNRGLTVVQAFQE
          MNGNQKLD.YNQEKQNFIQHFSQIVKVLTEK.L.HP.IGDAIARLKEVLEYNALGGKYNRGL..VQAFQE
Retrocopy MNGNQKLDVYNQEKQNFIQHFSQIVKVLTEKVLVHPDIGDAIARLKEVLEYNALGGKYNRGLAMVQAFQE

Parental  LVEPKKQDAESLQRALTVGWCVELLQAFFLVSDDIMDSSLTR-RGQICWYQKPGIGLDAINDALLLEASI
          LVEPKKQD.ESLQRALTVGWCVE.LQAFF.VSDDIMDSSLTR.RGQICWYQKPGIGLDAIN..LLLEASI
Retrocopy LVEPKKQDTESLQRALTVGWCVEMLQAFFFVSDDIMDSSLTR<RGQICWYQKPGIGLDAINNTLLLEASI

Parental  YRLLKFYCREQPYYLNLLELFLQSSYQTEIG-QTLDLMTAPQGHVDLGRYTEKRYKSIVKYKTAFYSFYL
          YRLLKFYCREQPYYLNLLELFLQSSYQTEIG.QTLDLMTAP.GHVDLG.YTEK.YKSIVKYKTAFYSFYL
Retrocopy YRLLKFYCREQPYYLNLLELFLQSSYQTEIG<QTLDLMTAPRGHVDLGKYTEKWYKSIVKYKTAFYSFYL

Parental  PIAAAMYMAGIDGEKEHANALKILMEMGEFFQVQDDYLDLFGDPSVTGKVGTDIQDNKCSWLVVQCLLRA
          PIA..MYMAGIDGEKEHANALKIL.EMGEFFQVQD.YLDLFGDPSVTGK.GTDIQDNKCSWLVVQCLLRA
Retrocopy PIATTMYMAGIDGEKEHANALKILLEMGEFFQVQDYYLDLFGDPSVTGKIGTDIQDNKCSWLVVQCLLRA

Parental  SPQQRQILEENYGQKDPEKVARVKALYEALDLQSAFFKYEEDSYNRLKSLIEQCSAPLPPSIFMELANKI
          .PQQRQILEENY.QKDP.KVARVKALYEALDLQS.FFK.EED.YNRLKSLIEQCS.PLPPSIFMELANKI
Retrocopy CPQQRQILEENYRQKDP*KVARVKALYEALDLQSVFFK*EEDNYNRLKSLIEQCSVPLPPSIFMELANKI

Parental  YKRRK
          YKRRK
Retrocopy YKRRK

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	21.52 RPM
SRP007412_cerebellum	0.00 RPM	12.42 RPM
SRP007412_heart	0.00 RPM	7.13 RPM
SRP007412_kidney	0.00 RPM	9.76 RPM
SRP007412_liver	0.03 RPM	155.82 RPM
SRP007412_testis	0.05 RPM	39.84 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3625 was not detected

EST

No EST(s) were mapped for retro_mmus_3625 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_157469	244 libraries	355 libraries	382 libraries	81 libraries	10 libraries

The graphical summary, for retro_mmus_3625 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_3625 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3625 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000030749	2 retrocopies	retro_cfam_1822, retro_cfam_1888,
Callithrix jacchus	ENSCJAG00000008364	11 retrocopies	retro_cjac_1066, retro_cjac_1217, retro_cjac_1395, retro_cjac_157, retro_cjac_2011, retro_cjac_2081, retro_cjac_2161, retro_cjac_299, retro_cjac_4154, retro_cjac_44, retro_cjac_70,
Echinops telfairi	ENSETEG00000001154	6 retrocopies	retro_etel_1770, retro_etel_1818, retro_etel_2179, retro_etel_730, retro_etel_743, retro_etel_990,
Macaca mulatta	ENSMMUG00000023144	3 retrocopies	retro_mmul_1190, retro_mmul_2152, retro_mmul_565,
Mus musculus	ENSMUSG00000059743	5 retrocopies	retro_mmus_1028, retro_mmus_1552, retro_mmus_2802, retro_mmus_3625 , retro_mmus_590,
Pongo abelii	ENSPPYG00000000747	3 retrocopies	retro_pabe_1290, retro_pabe_1329, retro_pabe_235,
Rattus norvegicus	ENSRNOG00000043377	3 retrocopies	retro_rnor_1175, retro_rnor_153, retro_rnor_2897,
Ictidomys tridecemlineatus	ENSSTOG00000004475	1 retrocopy	retro_itri_488,
Tursiops truncatus	ENSTTRG00000013326	1 retrocopy	retro_ttru_689,