RetrogeneDB ID: retro_mmus_338

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:77065966..77067101(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Tfdp1
• Ensembl ID: ENSMUSG00000038482
• Aliases: Tfdp1, Dp1, Drtf1
• Description: transcription factor Dp 1 [Source:MGI Symbol;Acc:MGI:101934]

Sequence

>retro_mmus_338
GTGGCGTCCCTTGTCACCATCCACCGTTCCACAGTGAACACACTTGGAAAGCAGCTTTTGCCAAAAACCTTCGGACAGTC
CAATGTCAATGTCACACAGCAAGTGGTGATTGGCACGCCTCACAGTCCTGCAGCATCCAACACTATTGTGGTAGGGAGCC
CACACTCTCCCAACACTCACTTTGTGTCCCAGAATCAGACGTCTGACTCCTCACCTTGGTCTGCTGGGAGGTGGAACAGG
AAAGGCGAGAAGAATAGCAAGGGCCTGTGGCATTTCTCCATGAAGGTGTGTGAGAAGGTGCAGAGGAAAGGAACTACCTC
CTACAGTGAGGTGGCTGACGAGCTGGTGGCAGAGTTCAGTACTGCCGACAACCACATCCTACCAAACCAATCAGCTTATG
ACCAGAAGAACATCTGGAGGAGTGTCTATGATGCCTTAAATGTGCTAATAACCATGAACATCATCTTCAAGGAGAAGAAG
GAGAGCAAATGGATCGGCCTGCCCACCAACTCAGCTCAGGAGTGCCAGAACTTAGAGGTAGAGAGGCAGCGGAGGCTGGA
GAGGATCAAACAGAAGCAGTCACAGCTCCAGGAGCTCATCTGCAGCAAATTGCCTTCAAGAACTTGGTGCAGAGAAATCA
CCAAGCTGAGCAGCAGGCCTGCAGGCTGTCTCCTCCCACCTCTGTCATCCACTTGCCCTTCATCATTGTCAACACCAGCA
GGAAGACAGTCATTGACTGCAGCATCTCCAATGACAAATTTGAGTATCTGTTTAACTTTGACAACACGTTTGAAATCCAT
GATGACATTGAGGTGCTCAAGTGCATGGGCACTGCGTGTGGGCTGGAGTGTGGCAACTGCTCTGCTGAAGACCTCAAGGT
GGTGAGAAGTTTGGTACTAAAAGCTCTAGAACCATAAGTGACAGAAATGGCTCAGGGATCCATTGGTGGAGTATTCCTCA
CGACAACAGGTTCTACATCCAATGGCACAAGGCTTTCTGCCAGTGATTTGAGCAATGGTGCAGATGGAATGCTGGCCATA
AGCTCCATGGGTCTCAGTACAGAGGCTCCAGGGTTGAGAGCCCTGTGTCCTACATTGGGGAGGATGATGACAACAATGAC
TATGACTTTAATGAG

Alignment

ORF - retro_mmus_338 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.71 %
• Parental protein coverage: 92.2 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VVSLVAVHPSTVNTLGKQLLPKTFGQSNVNITQQVVIGTPQRPAASNTIVVGSPHTPNTHFVSQNQTSDS
          V.SLV..H.STVNTLGKQLLPKTFGQSNVN.TQQVVIGTP..PAASNTIVVGSPH.PNTHFVSQNQTSDS
Retrocopy VASLVTIHRSTVNTLGKQLLPKTFGQSNVNVTQQVVIGTPHSPAASNTIVVGSPHSPNTHFVSQNQTSDS

Parental  SPWSAGKRNRKGEKNGKGLRHFSMKVCEKVQRKGTTSYNEVADELVAEFSAADNHILPNESAYDQKNIRR
          SPWSAG..NRKGEKN.KGL.HFSMKVCEKVQRKGTTSY.EVADELVAEFS.ADNHILPN.SAYDQKNI.R
Retrocopy SPWSAGRWNRKGEKNSKGLWHFSMKVCEKVQRKGTTSYSEVADELVAEFSTADNHILPNQSAYDQKNIWR

Parental  RVYDALNVLMAMNIISKEKKEIKWIGLPTNSAQECQNLEVERQRRLERIKQKQSQLQELI-LQQIAFKNL
          .VYDALNVL..MNII.KEKKE.KWIGLPTNSAQECQNLEVERQRRLERIKQKQSQLQELI.LQQIAFKNL
Retrocopy SVYDALNVLITMNIIFKEKKESKWIGLPTNSAQECQNLEVERQRRLERIKQKQSQLQELI<LQQIAFKNL

Parental  VQRNRQAEQQARRPPPPNSVIHLPFIIVNTSRKTVIDCSISNDKFEYLFNFDNTFEIHDDIEVLKRMGMA
          VQRN.QAEQQA.R..PP.SVIHLPFIIVNTSRKTVIDCSISNDKFEYLFNFDNTFEIHDDIEVLK.MG.A
Retrocopy VQRNHQAEQQACRLSPPTSVIHLPFIIVNTSRKTVIDCSISNDKFEYLFNFDNTFEIHDDIEVLKCMGTA

Parental  CGLESGNCSAEDLKVARSLVPKALEPYVTEMAQGSIGGVFVTTTGSTSNGTRLSASDLSNGADGMLATSS
          CGLE.GNCSAEDLKV.RSLV.KALEP.VTEMAQGSIGGVF.TTTGSTSNGTRLSASDLSNGADGMLA.SS
Retrocopy CGLECGNCSAEDLKVVRSLVLKALEP*VTEMAQGSIGGVFLTTTGSTSNGTRLSASDLSNGADGMLAISS

Parental  -NGSQYSGSRVETPVSYVGEDDDDDD-DFNE
          ..GSQY.GSRVE.PVSY.GEDDD..D.DFNE
Retrocopy <HGSQYRGSRVESPVSYIGEDDDNNDYDFNE

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	0.02 RPM	24.74 RPM
SRP007412_cerebellum	0.00 RPM	24.45 RPM
SRP007412_heart	0.12 RPM	14.88 RPM
SRP007412_kidney	0.04 RPM	15.13 RPM
SRP007412_liver	0.00 RPM	12.32 RPM
SRP007412_testis	0.05 RPM	27.49 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_338 was not detected

EST

No EST(s) were mapped for retro_mmus_338 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_76595	189 libraries	327 libraries	551 libraries	5 libraries	0 libraries

The graphical summary, for retro_mmus_338 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_338 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_338 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004467	8 retrocopies	retro_chof_2187, retro_chof_2229, retro_chof_2621, retro_chof_506, retro_chof_529, retro_chof_837, retro_chof_854, retro_chof_895,
Callithrix jacchus	ENSCJAG00000006950	2 retrocopies	retro_cjac_179, retro_cjac_4094,
Homo sapiens	ENSG00000198176	4 retrocopies	retro_hsap_1601, retro_hsap_299, retro_hsap_4803, retro_hsap_61,
Gorilla gorilla	ENSGGOG00000004908	2 retrocopies	retro_ggor_17, retro_ggor_335,
Loxodonta africana	ENSLAFG00000007927	1 retrocopy	retro_lafr_914,
Myotis lucifugus	ENSMLUG00000012165	1 retrocopy	retro_mluc_896,
Macaca mulatta	ENSMMUG00000007423	1 retrocopy	retro_mmul_177,
Mus musculus	ENSMUSG00000038482	2 retrocopies	retro_mmus_3243, retro_mmus_338 ,
Nomascus leucogenys	ENSNLEG00000000849	3 retrocopies	retro_nleu_2177, retro_nleu_2598, retro_nleu_49,
Otolemur garnettii	ENSOGAG00000003532	1 retrocopy	retro_ogar_3334,
Pongo abelii	ENSPPYG00000025889	3 retrocopies	retro_pabe_1314, retro_pabe_132, retro_pabe_378,