RetrogeneDB ID: retro_mmus_405

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:4692598..4693424(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Gpbp1l1
• Ensembl ID: ENSMUSG00000034042
• Aliases: Gpbp1l1, 5330440M15Rik, BC002292
• Description: GC-rich promoter binding protein 1-like 1 [Source:MGI Symbol;Acc:MGI:1924360]

Sequence

>retro_mmus_405
ATGGCGCAGCATGACTTTGTTCCTGCTTGGCTAAATTTCTCAATGCCACAGTCAGCTAAGTCATCTACAACCATCTTTGA
CAAACATGGAGAGTACCTATCCCGTGGAGAAGGTAGATTTTGAATAAGCCGTCGACAACATAATTCCTCTGATGACTTTT
TAAACAATGGACCTCTACGGACTACAGGAGATTCTTGTCACCAACACTCCCTATTCTGCCATGAGTCTGTTGACTCTGGT
GTCTCTAAGGGATCATATGCTGGAACAACAGGGGATCTATCTGGTTGGCATGGCTCTTCCCGAGGTCATGATGGTATGAG
CCAACATAGTGGAGGTAGTACAGGAAACCAACGACACGGGAATGGCAGCTTCCATTCCTGGAAAGGCTGTGCCTTTCAAG
AAAAAACACCAACTGAGATTAGGGAAGAGAAAAAAAAGGGATAAAGTAGAAAAGTTGCAGTTCGAAGAGGAAGATTTCCC
TTCTTTGAATCCAGAAGCTGGCAAACAGAATCAGTCATGCAGACCTGTTGGGACCCCTTCTGGAGTGTGGGAAGCCAAGC
AACCCTCAAAGATGCTAGTCATCAAAAAAATTTCCAAAGAGGATCCTGCTGCTGCCTTTTCTGCTGCATTCACCTCCTCA
GGATCCCCCCATGCAAATGGGAACAAAGTGTCAACAATAGTTTCAAGTGTCTATAAGAACTTGGTTCCTAAGCCTCCACC
ACCACCCTCTAAGCCCAACGCCTGGAAAGCTAACAGAATGGAACACAAACCTGGATCACTTTGCTCTAGCCGGGAGTCTG
CTTTTACCAATCCAATTTCTGTTACT

Alignment

ORF - retro_mmus_405 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.83 %
• Parental protein coverage: 58.35 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAQHDFVPAWLNFSTPQSSKSSTATFDKHGEHLSRGEGRFGISRRRHNSSDGFFNNGPLRTTGDSWHQPS
          MAQHDFVPAWLNFS.PQS.KSST..FDKHGE.LSRGEGRF.ISRR.HNSSD.F.NNGPLRTTGDS.HQ.S
Retrocopy MAQHDFVPAWLNFSMPQSAKSSTTIFDKHGEYLSRGEGRF*ISRRQHNSSDDFLNNGPLRTTGDSCHQHS

Parental  LFRHDSVDSGVSKGAYAGTT----GWHGSSRGHDGMSQRSGGSSTGNHRHWNGSFHSRKGCAFQEKTPTE
          LF.H.SVDSGVSKG.YAGTT....GWHGSSRGHDGMSQ.SGGS.TGN.RH.NGSFHS.KGCAFQEKTPTE
Retrocopy LFCHESVDSGVSKGSYAGTTGDLSGWHGSSRGHDGMSQHSGGS-TGNQRHGNGSFHSWKGCAFQEKTPTE

Parental  IREEKKE-DKVEKLQFEEEDFPSLNPEAGKQNQPCRPVGTPSGVWENPPSAKQPSKMLVIKKISKEDPAA
          IREE....DKVEKLQFEEEDFPSLNPEAGKQNQ.CRPVGTPSGVWE....AKQPSKMLVIKKISKEDPAA
Retrocopy IREEXXX>DKVEKLQFEEEDFPSLNPEAGKQNQSCRPVGTPSGVWE----AKQPSKMLVIKKISKEDPAA

Parental  AFSAAFTSSGSHHANGNKVSTMVPSVYKNLVPKPAPPPSKPNAWKANRTEHKPGSLCSSRESAFTNPISV
          AFSAAFTSSGS.HANGNKVST.V.SVYKNLVPKP.PPPSKPNAWKANR.EHKPGSLCSSRESAFTNPISV
Retrocopy AFSAAFTSSGSPHANGNKVSTIVSSVYKNLVPKPPPPPSKPNAWKANRMEHKPGSLCSSRESAFTNPISV

Parental  T
          T
Retrocopy T

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	22.05 RPM
SRP007412_cerebellum	0.00 RPM	18.76 RPM
SRP007412_heart	0.00 RPM	30.45 RPM
SRP007412_kidney	0.00 RPM	36.81 RPM
SRP007412_liver	0.00 RPM	28.78 RPM
SRP007412_testis	0.00 RPM	36.32 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_405 was not detected

EST

No EST(s) were mapped for retro_mmus_405 retrocopy.

TSS

No TSS is located nearby retro_mmus_405 retrocopy 5' end.

Lab

retro_mmus_405 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_405 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010454	1 retrocopy	retro_chof_53,
Microcebus murinus	ENSMICG00000008449	1 retrocopy	retro_mmur_164,
Myotis lucifugus	ENSMLUG00000012432	2 retrocopies	retro_mluc_211, retro_mluc_834,
Mus musculus	ENSMUSG00000034042	2 retrocopies	retro_mmus_1391, retro_mmus_405 ,
Oryctolagus cuniculus	ENSOCUG00000017939	1 retrocopy	retro_ocun_427,
Otolemur garnettii	ENSOGAG00000004134	1 retrocopy	retro_ogar_1859,
Ochotona princeps	ENSOPRG00000001584	1 retrocopy	retro_opri_928,
Rattus norvegicus	ENSRNOG00000037595	1 retrocopy	retro_rnor_390,
Ictidomys tridecemlineatus	ENSSTOG00000013491	1 retrocopy	retro_itri_243,