RetrogeneDB ID: retro_mmus_2802

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 6:6735476..6736492(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000093651
• 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_2802
ATGAATGGGAACCAGAAATTAGATGTTTATAACCAAGAAAAGCAGAACTTCATCCAGCACTCCTCCCAGATCGTCAAGGT
GCTGACTGAGAAGGAGCTGGGACACCCAGAGATAGGGGATGCTATTGCCTGGCTCAAGGAGGTCCTAGAGTACAATGACT
TAGGAGGCAAGTACAACCGGGGTTTGACCGTAGTACAAGCCTTCCAGGAGCTGGTGGAGCGGAAGAAACAGGATGCTGAG
AGTCTTCAGCGGGCCCTGACAGTGGGCTGGTGTGTAGAACTGCTCCAGGCTTTCTTCCTTGTGTCAGATGACATCATGGA
CTCTTCCCTTACTCGCCCGGGACAGATCTGCTGGTATCAGAAGCCAGGCATAGGCTTGGATGCCATCAACGACGCTCTGC
TTCTGGAAGCCTCCATCTATCGTTTGCTGAAGTTCTACTGCAGGGAGCAGCCCTACTACCTGAACCTGCTGGAGCTCTTT
CTGCAGAGTTCCTATCAGACTGAGATCGGGCATACTCTAGACCTCATGACAGCACCCCAGGCCCATGTGGATCTTGGTAG
ATACACTGAAAAGAGGTACAAATCGATTGTCAAGTACAAGACAGCTTTCTACTCTTTTCTACCTGCCTATCGCGGCCGCC
ATGTACATGGCAGGCATTGATGGGGAGAAGGAACACGCCAATGCCCTGAAGATACTGATGGAGATGGGCGAGTTCTTCCA
GGTCCAGGACGACTACCTTGATCTCTTTGGAGACCCCAAGTGTGACGGGAAAGGTCGGCACTGACATCCAGGACAACAAA
TACAGCTGACTGGTGGTTCAGTGTCTGCTACTAGCCTCTCCTCAACAGTGCCGGGTCTTAGAGGAGAATTATGGGCAGAA
GGACTCAGAAAAAGTGGCTCGGGTGAAAGCACTGTATGAGGCGCTGGATCTGCAGTCTGTTTTCTTCAAGTATGTGAAAG
ACAGTTACAACCGCCTCAAGAGTCTCATAGAGCAGTGCTCTGCGCCCCTGCCCCCC

Alignment

ORF - retro_mmus_2802 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.12 %
• Parental protein coverage: 95.75 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MNGNQKLDAYNQEKQNFIQHFSQIVKVLTEKELGHPEIGDAIARLKEVLEYNALGGKYNRGLTVVQAFQE
          MNGNQKLD.YNQEKQNFIQH.SQIVKVLTEKELGHPEIGDAIA.LKEVLEYN.LGGKYNRGLTVVQAFQE
Retrocopy MNGNQKLDVYNQEKQNFIQHSSQIVKVLTEKELGHPEIGDAIAWLKEVLEYNDLGGKYNRGLTVVQAFQE

Parental  LVEPKKQDAESLQRALTVGWCVELLQAFFLVSDDIMDSSLTRRGQICWYQKPGIGLDAINDALLLEASIY
          LVE.KKQDAESLQRALTVGWCVELLQAFFLVSDDIMDSSLTR.GQICWYQKPGIGLDAINDALLLEASIY
Retrocopy LVERKKQDAESLQRALTVGWCVELLQAFFLVSDDIMDSSLTRPGQICWYQKPGIGLDAINDALLLEASIY

Parental  RLLKFYCREQPYYLNLLELFLQSSYQTEIGQTLDLMTAPQGHVDLGRYTEKRYKSIVKYKTAFYS-FYLP
          RLLKFYCREQPYYLNLLELFLQSSYQTEIG.TLDLMTAPQ.HVDLGRYTEKRYKSIVKYKTAFYS.FYLP
Retrocopy RLLKFYCREQPYYLNLLELFLQSSYQTEIGHTLDLMTAPQAHVDLGRYTEKRYKSIVKYKTAFYS>FYLP

Parental  IAAAMYMAGIDGEKEHANALKILMEMGEFFQVQDDYLDLFGD-PSVTGKVGTDIQDNKCSWLVVQCLLRA
          IAAAMYMAGIDGEKEHANALKILMEMGEFFQVQDDYLDLFGD.PSVTGKVGTDIQDNK.S.LVVQCLL.A
Retrocopy IAAAMYMAGIDGEKEHANALKILMEMGEFFQVQDDYLDLFGD>PSVTGKVGTDIQDNKYS*LVVQCLLLA

Parental  SPQQRQILEENYGQKDPEKVARVKALYEALDLQSAFFKYEEDSYNRLKSLIEQCSAPLPP
          SPQQ...LEENYGQKD.EKVARVKALYEALDLQS.FFKY..DSYNRLKSLIEQCSAPLPP
Retrocopy SPQQCRVLEENYGQKDSEKVARVKALYEALDLQSVFFKYVKDSYNRLKSLIEQCSAPLPP

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	0.05 RPM	21.52 RPM
SRP007412_cerebellum	0.00 RPM	12.42 RPM
SRP007412_heart	0.00 RPM	7.13 RPM
SRP007412_kidney	0.04 RPM	9.76 RPM
SRP007412_liver	0.11 RPM	155.82 RPM
SRP007412_testis	0.09 RPM	39.84 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2802 was not detected

EST

No EST(s) were mapped for retro_mmus_2802 retrocopy.

TSS

No TSS is located nearby retro_mmus_2802 retrocopy 5' end.

Lab

retro_mmus_2802 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2802 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,