RetrogeneDB ID: retro_mmus_3061

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:97282475..97282775(-)
• Located in intron of: ENSMUSG00000004508

Retrocopy information

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

Parental gene information

• Parental gene symbol: 1110032A03Rik
• Ensembl ID: ENSMUSG00000037971
• Aliases: 1110032A03Rik, 4930500N06Rik, c11orf1
• Description: RIKEN cDNA 1110032A03 gene [Source:MGI Symbol;Acc:MGI:1915971]

Sequence

>retro_mmus_3061
AACTCATATTCCAACAGTACCCTGATAGGAACTGGAAGCAGGAAAGATACAACCTAAGGAAGACTGCAAAACCTGCACCC
CTACCCTTCCAGCTTTGGACACTACTTCGAAACAACATATAACACAAGCTATACCAGCAGAAAGATTCTTTTAAACCATA
GATTTACAGGAGGGCCTCATTGGTTCTCTAGATATTATCCTGAGCTGGATTCTCTTTACAGATGATCCATAGAAAATCCA
ACTTATATGAATAGTAATTCAAAGCCTCAAATCAGGTATTACTTTGGGTGTGTATATGAT

Alignment

ORF - retro_mmus_3061 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.96 %
• Parental protein coverage: 54.95 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NSYSNRTLVG-NWNQERYDLKNIVKPKPL-PSQFGHAFETTYDANYSRKKPQSTHRFKREPHWFPGHQPE
          NSYSN.TL.G.NW.QERY.L....KP.PL.PS.FGH.FETTY...Y...K....HRF...PHWF....PE
Retrocopy NSYSNSTLIG<NWKQERYNLRKTAKPAPL>PSSFGHYFETTYNTSYTSRKILLNHRFTGGPHWFSRYYPE

Parental  LDPPHYKCTAKSTYMTNYSEPQPTHYSCCVYD
          LD..........TYM...S.PQ...Y..CVYD
Retrocopy LDSLYR*SIENPTYMNSNSKPQIRYYFGCVYD

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	20.16 RPM
SRP007412_cerebellum	0.00 RPM	17.59 RPM
SRP007412_heart	0.00 RPM	7.94 RPM
SRP007412_kidney	0.02 RPM	27.20 RPM
SRP007412_liver	0.00 RPM	23.92 RPM
SRP007412_testis	0.05 RPM	193.16 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3061 was not detected

EST

No EST(s) were mapped for retro_mmus_3061 retrocopy.

TSS

No TSS is located nearby retro_mmus_3061 retrocopy 5' end.

Lab

retro_mmus_3061 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3061 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003039	3 retrocopies	retro_chof_1409, retro_chof_1629, retro_chof_888,
Cavia porcellus	ENSCPOG00000021163	1 retrocopy	retro_cpor_455,
Erinaceus europaeus	ENSEEUG00000009977	1 retrocopy	retro_eeur_658,
Mus musculus	ENSMUSG00000037971	1 retrocopy	retro_mmus_3061 ,