RetrogeneDB ID: retro_mmus_1322

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 15:7342126..7342516(+)
• Located in intron of: ENSMUSG00000042961

Retrocopy information

• Ensembl ID: ENSMUSG00000089966
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Fkbp3
• Ensembl ID: ENSMUSG00000020949
• Aliases: Fkbp3, 25kDa, FKBP-3, FKBP25
• Description: FK506 binding protein 3 [Source:MGI Symbol;Acc:MGI:1353460]

Sequence

>retro_mmus_1322
GATGATAAACCCAAAGAAACCAAGTCTGAAGAGACTCTTGATGAGGGTCCACGGAAATATAGAAAATCGGTTCTAAAAAG
GGAGCTAAACCAACACTCCCAAAAAGGACGATGTTGTTCACGGCTGGTATACAGGGACACTCCCAGATGGGACTGGTTTT
GATACTAATATTCACTCAAGCTCAAAGAAGAGAAACGCCAAGCCTTTAAGTTCCAAGGTCACAATAGGGAGGTTGTCAGA
GGAGGGGATGAGGCGCTCCTGACCATGAGCAAAGGAGAATGGGCTCAAGTGGAGACTGAACCAGAATGGGCTTATGGAAA
GCAAGCACAGCCTGATGTCAGAATTCCACCAAATGCCAAACTCATTTCTGAAGTAGAATTAGTAGGTATT

Alignment

ORF - retro_mmus_1322 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.81 %
• Parental protein coverage: 58.93 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DDKPKDSKSEETLDEGPPKYTKSILK-KGDK-TNFPKKGDVVHCWYTGTLPDGTVFDTNIQTSSKKKKNA
          DDKPK..KSEETLDEGP.KY.KS.LK.KG.K.TN.PKK.DVVH.WYTGTLPDGT.FDTNI..SSKK..NA
Retrocopy DDKPKETKSEETLDEGPRKYRKSVLK<KGAK<TNTPKKDDVVHGWYTGTLPDGTGFDTNIHSSSKKR-NA

Parental  KPLSFKVGVGK-VIRGWDEALLTMSKGEKARLEIEPEWAYGKKGQPDAKIPPNTKLIFEVELVDI
          KPLS.KV..G..V.RG.DEALLTMSKGE.A..E.EPEWAYGK..QPD..IPPN.KLI.EVELV.I
Retrocopy KPLSSKVTIGR<VVRGGDEALLTMSKGEWAQVETEPEWAYGKQAQPDVRIPPNAKLISEVELVGI

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	43.85 RPM
SRP007412_cerebellum	0.00 RPM	32.78 RPM
SRP007412_heart	0.03 RPM	75.80 RPM
SRP007412_kidney	0.00 RPM	30.38 RPM
SRP007412_liver	0.00 RPM	9.12 RPM
SRP007412_testis	0.00 RPM	6.40 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1322 was not detected

EST

No EST(s) were mapped for retro_mmus_1322 retrocopy.

TSS

No TSS is located nearby retro_mmus_1322 retrocopy 5' end.

Lab

retro_mmus_1322 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1322 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014018	4 retrocopies	retro_cfam_1788, retro_cfam_440, retro_cfam_616, retro_cfam_798,
Felis catus	ENSFCAG00000027304	1 retrocopy	retro_fcat_1894,
Loxodonta africana	ENSLAFG00000003572	2 retrocopies	retro_lafr_357, retro_lafr_76,
Macropus eugenii	ENSMEUG00000004962	1 retrocopy	retro_meug_679,
Macaca mulatta	ENSMMUG00000016512	2 retrocopies	retro_mmul_2094, retro_mmul_735,
Monodelphis domestica	ENSMODG00000007352	1 retrocopy	retro_mdom_1554,
Mus musculus	ENSMUSG00000020949	1 retrocopy	retro_mmus_1322 ,
Mus musculus	ENSMUSG00000032966	1 retrocopy	retro_mmus_1293,
Otolemur garnettii	ENSOGAG00000003012	2 retrocopies	retro_ogar_2247, retro_ogar_3472,
Rattus norvegicus	ENSRNOG00000004629	1 retrocopy	retro_rnor_1165,
Tupaia belangeri	ENSTBEG00000006017	13 retrocopies	retro_tbel_1032, retro_tbel_1125, retro_tbel_1696, retro_tbel_1783, retro_tbel_2151, retro_tbel_2569, retro_tbel_3297, retro_tbel_3567, retro_tbel_3807, retro_tbel_4222, retro_tbel_4482, retro_tbel_730, retro_tbel_800,
Tursiops truncatus	ENSTTRG00000006664	1 retrocopy	retro_ttru_1041,