RetrogeneDB ID: retro_mmus_1293

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 14:76636540..76636864(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: Fkbp1a
• Ensembl ID: ENSMUSG00000032966
• Aliases: Fkbp1a, 12kDa, FKBP12, FKBP12-T1, FKBP12-T2, Fkbp, Fkbp1, mFKBP1, mFKBP12
• Description: FK506 binding protein 1a [Source:MGI Symbol;Acc:MGI:95541]

Sequence

>retro_mmus_1293
ATGGGAATGCAGGTGGAAACCATCTCTCCTGGAGACCGGTGCACCTTCCCAAAGCACAGCCAGAACTGCATGGTGCATTA
CACGGGGATGCTTGAAGATGGAAAGAAATTTGCCTCCTCTCGGGACAGAAACAATCCTTTTAAGTTTACACTAGGCAAGC
AGGAGGTGATCCGAGGCTGGAAGGAAGGGGTAGCCCAGATGAGTGTGGGTCATAGAGCCAAACTGATAATTTCCTGAGAC
TATGCCTATGGAACCACTGGGCACCCAGGCATCATCCCACCACATGCCACTCTTGTTTTTGATGTGGAGCATCTAAAACT
GGAA

Alignment

ORF - retro_mmus_1293 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.04 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGVQVETISPGDGRTFPKRGQTCVVHYTGMLEDGKKFDSSRDRNKPFKFTLGKQEVIRGWEEGVAQMSVG
          MG.QVETISPGD..TFPK..Q.C.VHYTGMLEDGKKF.SSRDRN.PFKFTLGKQEVIRGW.EGVAQMSVG
Retrocopy MGMQVETISPGDRCTFPKHSQNCMVHYTGMLEDGKKFASSRDRNNPFKFTLGKQEVIRGWKEGVAQMSVG

Parental  QRAKLIISSDYAYGATGHPGIIPPHATLVFDVELLKLE
          .RAKLIIS.DYAYG.TGHPGIIPPHATLVFDVE.LKLE
Retrocopy HRAKLIIS*DYAYGTTGHPGIIPPHATLVFDVEHLKLE

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	377.80 RPM
SRP007412_cerebellum	0.09 RPM	188.27 RPM
SRP007412_heart	0.06 RPM	129.38 RPM
SRP007412_kidney	0.02 RPM	107.95 RPM
SRP007412_liver	0.00 RPM	49.16 RPM
SRP007412_testis	0.05 RPM	231.90 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1293 was not detected

EST

No EST(s) were mapped for retro_mmus_1293 retrocopy.

TSS

No TSS is located nearby retro_mmus_1293 retrocopy 5' end.

Lab

retro_mmus_1293 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1293 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000008303	4 retrocopies	retro_btau_1220, retro_btau_1265, retro_btau_128, retro_btau_1760,
Ciona savignyi	ENSCSAVG00000006859	1 retrocopy	retro_csav_11,
Dasypus novemcinctus	ENSDNOG00000005868	16 retrocopies	retro_dnov_1289, retro_dnov_1577, retro_dnov_1666, retro_dnov_2236, retro_dnov_228, retro_dnov_2404, retro_dnov_2418, retro_dnov_2544, retro_dnov_2589, retro_dnov_263, retro_dnov_584, retro_dnov_621, retro_dnov_670, retro_dnov_684, retro_dnov_707, retro_dnov_937,
Homo sapiens	ENSG00000088832	1 retrocopy	retro_hsap_1198,
Gorilla gorilla	ENSGGOG00000001729	3 retrocopies	retro_ggor_1494, retro_ggor_2344, retro_ggor_933,
Macaca mulatta	ENSMMUG00000015996	1 retrocopy	retro_mmul_10,
Monodelphis domestica	ENSMODG00000019554	2 retrocopies	retro_mdom_151, retro_mdom_733,
Mus musculus	ENSMUSG00000020949	1 retrocopy	retro_mmus_1322,
Mus musculus	ENSMUSG00000032966	1 retrocopy	retro_mmus_1293 ,
Procavia capensis	ENSPCAG00000008816	2 retrocopies	retro_pcap_289, retro_pcap_37,
Rattus norvegicus	ENSRNOG00000008822	1 retrocopy	retro_rnor_453,
Sus scrofa	ENSSSCG00000007188	1 retrocopy	retro_sscr_98,
Tursiops truncatus	ENSTTRG00000003547	3 retrocopies	retro_ttru_1227, retro_ttru_802, retro_ttru_904,
Vicugna pacos	ENSVPAG00000011511	1 retrocopy	retro_vpac_171,