RetrogeneDB ID: retro_mmus_3014

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:27949157..27949763(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000074243
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Josd1
• Ensembl ID: ENSMUSG00000022426
• Aliases: Josd1, 1300006C06Rik, mKIAA0063
• Description: Josephin domain containing 1 [Source:MGI Symbol;Acc:MGI:1921408]

Sequence

>retro_mmus_3014
ATGAGTTGCGTGCCATGGAAAGGAGACAAGGCCAAAGCTGAATCCTCGGACCTTCCCCAAGCAGCACCCCCACAAATCTA
CCATGAGAAGCAGCGCAGGGAGCTCTGTGCTCTTCATGCTCTCAACAACGTCTTCCAGGACAGCAACGCCTTCACGCGGG
AAACGCTGCAGGAGATTTTCCAGAGGCTGTCTCCGAACACTATGGTGACGCCCCACAAGAAGAGCATGCTGGGAAATGGG
AACTATGATGTGAATGTCATCATGGCAGCACTTCAAACCAAAGGCTATGAAGCTGTTTGGTGGGACAAGCGAAGGGACGT
GGGTGTCATTGCTCTTACTAATGTCATGGGCTTCATCATGAACCTGCCCTCCAGCCTCTGCTGGGGTCCACTCAAGTTGC
CTCTCAAAAGGCAGCACTGGATCTGTGTTCGTGAGGTGGGAGGGGCCTACTACAACCTTGACTCCAAACTCAAGATGCCA
GAGTGGATTGGAGGCGAGAGTGAGCTCAGGAAATTTCTAAAATACCATTTGCGAGGTAAAAACTGTGAACTCCTACTGGT
TGTACCGGAAGAAGTGGAAGCCCATCAGAGCTGGAGGGCCGACGTG

Alignment

ORF - retro_mmus_3014 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

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

Retrocopy - Parental Gene Alignment:

Parental  MSCVPWKGDKAKAESSDLPQAAPPQIYHEKQRRELCALHALNNVFQDSNAFTRETLQEIFQRLSPNTMVT
          MSCVPWKGDKAKAESSDLPQAAPPQIYHEKQRRELCALHALNNVFQDSNAFTRETLQEIFQRLSPNTMVT
Retrocopy MSCVPWKGDKAKAESSDLPQAAPPQIYHEKQRRELCALHALNNVFQDSNAFTRETLQEIFQRLSPNTMVT

Parental  PHKKSMLGNGNYDVNVIMAALQTKGYEAVWWDKRRDVGVIALTNVMGFIMNLPSSLCWGPLKLPLKRQHW
          PHKKSMLGNGNYDVNVIMAALQTKGYEAVWWDKRRDVGVIALTNVMGFIMNLPSSLCWGPLKLPLKRQHW
Retrocopy PHKKSMLGNGNYDVNVIMAALQTKGYEAVWWDKRRDVGVIALTNVMGFIMNLPSSLCWGPLKLPLKRQHW

Parental  ICVREVGGAYYNLDSKLKMPEWIGGESELRKFLKYHLRGKNCELLLVVPEEVEAHQSWRADV
          ICVREVGGAYYNLDSKLKMPEWIGGESELRKFLKYHLRGKNCELLLVVPEEVEAHQSWRADV
Retrocopy ICVREVGGAYYNLDSKLKMPEWIGGESELRKFLKYHLRGKNCELLLVVPEEVEAHQSWRADV

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	0.14 RPM	58.73 RPM
SRP007412_cerebellum	0.00 RPM	37.17 RPM
SRP007412_heart	0.09 RPM	22.48 RPM
SRP007412_kidney	0.15 RPM	21.31 RPM
SRP007412_liver	0.08 RPM	32.39 RPM
SRP007412_testis	0.00 RPM	33.80 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_3014 was not detected

EST

No EST(s) were mapped for retro_mmus_3014 retrocopy.

TSS

No TSS is located nearby retro_mmus_3014 retrocopy 5' end.

Lab

retro_mmus_3014 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3014 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010171	1 retrocopy	retro_btau_1508,
Canis familiaris	ENSCAFG00000001379	1 retrocopy	retro_cfam_1500,
Choloepus hoffmanni	ENSCHOG00000001723	2 retrocopies	retro_chof_1576, retro_chof_233,
Equus caballus	ENSECAG00000015546	1 retrocopy	retro_ecab_251,
Felis catus	ENSFCAG00000002821	1 retrocopy	retro_fcat_565,
Macropus eugenii	ENSMEUG00000002899	2 retrocopies	retro_meug_1507, retro_meug_531,
Microcebus murinus	ENSMICG00000011798	1 retrocopy	retro_mmur_1202,
Myotis lucifugus	ENSMLUG00000003764	1 retrocopy	retro_mluc_1868,
Mus musculus	ENSMUSG00000022426	1 retrocopy	retro_mmus_3014 ,
Otolemur garnettii	ENSOGAG00000007520	3 retrocopies	retro_ogar_1462, retro_ogar_2911, retro_ogar_3487,
Pteropus vampyrus	ENSPVAG00000010148	1 retrocopy	retro_pvam_181,
Rattus norvegicus	ENSRNOG00000014440	2 retrocopies	retro_rnor_2954, retro_rnor_906,
Sarcophilus harrisii	ENSSHAG00000015931	1 retrocopy	retro_shar_643,
Ictidomys tridecemlineatus	ENSSTOG00000024999	1 retrocopy	retro_itri_193,
Tarsius syrichta	ENSTSYG00000008846	1 retrocopy	retro_tsyr_1076,