RetrogeneDB ID: retro_mmus_3519

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:122452367..122452775(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000086452
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Fam133b
• Ensembl ID: ENSMUSG00000058503
• Aliases: None
• Description: family with sequence similarity 133, member B [Source:MGI Symbol;Acc:MGI:1915402]

Sequence

>retro_mmus_3519
CTGGGGAAACAGGATACCTGTGTAGCTTATATGACTCCTATAGCAATGGCCAGATGGAGGGGTGCAAGTCAATCTGAAGG
CACAACTATACAGGGTTATCTGAATAGACCAAGGCCTACCTTGGAAGAAGTAAAGAAACAATTACAGAATAAAAAGAAAG
GCTCCAAGGCATTGACTGAATTTGAAGAAAAGATGAATCAAATTTGGACTAAAGAGCTCAAGAATAACAAAGAGAAAGCA
TTAAGTGGAAATGTGAGTTCATACAAAAGAAAGGAAAGAACAAAAAAGAAAAAGAAGAAATCATGTCAATATACATCTGC
TTCATCAAGCTCTGATTCATCAAGCAGTTTTTCAGATTTGGAGGATGAAACCAAGAAACAGGAGAAAAAAATGAAAGAGA
AAGAAGAG

Alignment

ORF - retro_mmus_3519 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.74 %
• Parental protein coverage: 55.51 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGKRDNRVAYMNPIAMARSRGPIQSSGPTIQDYLNRPRPTWEEVKEQLEKKKKGSKALAEFEEKMNENWK
          .GK.D..VAYM.PIAMAR.RG..QS.G.TIQ.YLNRPRPT.EEVK.QL..KKKGSKAL.EFEEKMN..W.
Retrocopy LGKQDTCVAYMTPIAMARWRGASQSEGTTIQGYLNRPRPTLEEVKKQLQNKKKGSKALTEFEEKMNQIWT

Parental  KELEKHREKLLSGNESSSKKRQKKKKEKKKSGRYSSSSSSSSDSSSSSSDSEDEDKKQTKRRKKKK
          KEL....EK.LSGN.SS.............S..Y...........S.S.......K...K...K..
Retrocopy KELKNNKEKALSGNVSSYXXXXXXXXXXXXSCQYTXXXXXXXXXXSFSDLEDETKKQEKKMKEKEE

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	16.40 RPM
SRP007412_cerebellum	0.00 RPM	27.31 RPM
SRP007412_heart	0.00 RPM	6.35 RPM
SRP007412_kidney	0.00 RPM	17.11 RPM
SRP007412_liver	0.00 RPM	6.88 RPM
SRP007412_testis	0.00 RPM	28.63 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_3519 was not detected

EST

No EST(s) were mapped for retro_mmus_3519 retrocopy.

TSS

No TSS is located nearby retro_mmus_3519 retrocopy 5' end.

Lab

retro_mmus_3519 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3519 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007438	1 retrocopy	retro_amel_102,
Callithrix jacchus	ENSCJAG00000013910	3 retrocopies	retro_cjac_1084, retro_cjac_1163, retro_cjac_4095,
Equus caballus	ENSECAG00000026810	1 retrocopy	retro_ecab_95,
Homo sapiens	ENSG00000234545	4 retrocopies	retro_hsap_2336, retro_hsap_3179, retro_hsap_55, retro_hsap_577,
Loxodonta africana	ENSLAFG00000029755	1 retrocopy	retro_lafr_594,
Myotis lucifugus	ENSMLUG00000005933	1 retrocopy	retro_mluc_2301,
Macaca mulatta	ENSMMUG00000019802	4 retrocopies	retro_mmul_1415, retro_mmul_226, retro_mmul_420, retro_mmul_765,
Mus musculus	ENSMUSG00000058503	2 retrocopies	retro_mmus_3481, retro_mmus_3519 ,
Nomascus leucogenys	ENSNLEG00000015333	1 retrocopy	retro_nleu_14,
Pongo abelii	ENSPPYG00000025825	1 retrocopy	retro_pabe_225,
Rattus norvegicus	ENSRNOG00000009163	1 retrocopy	retro_rnor_2891,
Sus scrofa	ENSSSCG00000015317	1 retrocopy	retro_sscr_49,
Ictidomys tridecemlineatus	ENSSTOG00000028195	1 retrocopy	retro_itri_12,
Tupaia belangeri	ENSTBEG00000011674	1 retrocopy	retro_tbel_1,