RetrogeneDB ID: retro_mmus_1715

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 18:43171158..43171824(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000048188
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: C330007P06Rik
• Ensembl ID: ENSMUSG00000006423
• Aliases: None
• Description: RIKEN cDNA C330007P06 gene [Source:MGI Symbol;Acc:MGI:1924894]

Sequence

>retro_mmus_1715
ATGCCGAAAGTCGTGTCGCGGTCGGTGGTCTGCTCAGACACCCGGAACCGCGAGGAATATGATGATGGCGAGAAGCCCCT
CCATGTCTACTACTGTTTATGTGGCCAGATGGTCCTGGTGCTGGATTGCCAGTTAGAGAAATTGCCCATGAGGCCCCGGG
ACCGGTCTCGCGTGATCGATGCTGCCAAACATGCTCACAAGTTTTGTAACACAGAAGATGAGGAGACTACTTATCTTCGG
AGGCCTGAGGGCATTGAACGTCAGTACAGGAAGAAGTGTGCAAAGTGTGGACTGCCGCTCTTCTACCAATCCCAGCCGAA
GAATGCTCCTGTGACCTTCATTGTGGATGGAGCAGTAGTGAAATTTGGCCAAGGCTTTGGGAAAACCAATATATATACTC
AGAAACAAGAGCCTCCTAAGAAGGTTATGATGACCAAAAGGACTAAAGACATGGGCAAGTTCAGCTCTGTTACTGTGTCT
ACCATTGATGAAGAAGAAGAGGAGATAGAGGCTAGGGAAGTTGCTGACTCTTACGCGCAGAATGCCAAAGTGATTGAAAA
GCAGCTGGAGCGCAAAGGCCTGAGCAAGAGGAGGCTGCAGGAGTTGGCTGAATTGGAAGCCAAGAAAGCAAAAATGAAGG
GGACCCTGATCGACAATCAGTTCAAA

Alignment

ORF - retro_mmus_1715 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.1 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPKVVSRSVVCSDTRDREEYDDGEKPLHVYYCLCGQMVLVLDCQLEKLPMRPRDRSRVIDAAKHAHKFCN
          MPKVVSRSVVCSDTR.REEYDDGEKPLHVYYCLCGQMVLVLDCQLEKLPMRPRDRSRVIDAAKHAHKFCN
Retrocopy MPKVVSRSVVCSDTRNREEYDDGEKPLHVYYCLCGQMVLVLDCQLEKLPMRPRDRSRVIDAAKHAHKFCN

Parental  TEDEETTYLRRPEGIERQYRKKCAKCGLPLFYQSQPKNAPVTFIVDGAVVKFGQGFGKTNIYTQKQEPPK
          TEDEETTYLRRPEGIERQYRKKCAKCGLPLFYQSQPKNAPVTFIVDGAVVKFGQGFGKTNIYTQKQEPPK
Retrocopy TEDEETTYLRRPEGIERQYRKKCAKCGLPLFYQSQPKNAPVTFIVDGAVVKFGQGFGKTNIYTQKQEPPK

Parental  KVMMTKRTKDMGKFSSVTVSTIDEEEEEIEAREVADSYAQNAKVIEKQLERKGMSKRRLQELAELEAKKA
          KVMMTKRTKDMGKFSSVTVSTIDEEEEEIEAREVADSYAQNAKVIEKQLERKG.SKRRLQELAELEAKKA
Retrocopy KVMMTKRTKDMGKFSSVTVSTIDEEEEEIEAREVADSYAQNAKVIEKQLERKGLSKRRLQELAELEAKKA

Parental  KMKGTLIDNQFK
          KMKGTLIDNQFK
Retrocopy KMKGTLIDNQFK

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	0.12 RPM	28.34 RPM
SRP007412_cerebellum	0.09 RPM	26.79 RPM
SRP007412_heart	0.03 RPM	13.42 RPM
SRP007412_kidney	0.10 RPM	27.51 RPM
SRP007412_liver	0.16 RPM	22.75 RPM
SRP007412_testis	0.82 RPM	5.12 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1715 was not detected

EST

No EST(s) were mapped for retro_mmus_1715 retrocopy.

TSS

No TSS is located nearby retro_mmus_1715 retrocopy 5' end.

Lab

retro_mmus_1715 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1715 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005111	1 retrocopy	retro_cjac_311,
Homo sapiens	ENSG00000018610	1 retrocopy	retro_hsap_4044,
Gorilla gorilla	ENSGGOG00000013324	1 retrocopy	retro_ggor_2711,
Latimeria chalumnae	ENSLACG00000012468	1 retrocopy	retro_lcha_59,
Myotis lucifugus	ENSMLUG00000015751	1 retrocopy	retro_mluc_72,
Macaca mulatta	ENSMMUG00000022665	1 retrocopy	retro_mmul_2333,
Mus musculus	ENSMUSG00000006423	1 retrocopy	retro_mmus_1715 ,
Nomascus leucogenys	ENSNLEG00000014862	1 retrocopy	retro_nleu_2057,
Otolemur garnettii	ENSOGAG00000012474	1 retrocopy	retro_ogar_145,
Pongo abelii	ENSPPYG00000020670	1 retrocopy	retro_pabe_177,
Pan troglodytes	ENSPTRG00000022224	1 retrocopy	retro_ptro_104,
Sorex araneus	ENSSARG00000003163	1 retrocopy	retro_sara_5,
Sarcophilus harrisii	ENSSHAG00000006319	1 retrocopy	retro_shar_16,
Ictidomys tridecemlineatus	ENSSTOG00000011579	1 retrocopy	retro_itri_103,
Tursiops truncatus	ENSTTRG00000013101	2 retrocopies	retro_ttru_231, retro_ttru_77,