RetrogeneDB ID: retro_mmus_649

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 10:65771557..65772204(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Tmed10
• Ensembl ID: ENSMUSG00000021248
• Aliases: Tmed10, 1110014C03Rik, Tmp21, p23, p24delta1
• Description: transmembrane emp24-like trafficking protein 10 (yeast) [Source:MGI Symbol;Acc:MGI:1915831]

Sequence

>retro_mmus_649
ATATCCGGTTTGTCTGGCCAACTATCCTGGCTTGGCCCTGCCCATTGGCATTGCTCTTTACATTACTGCTTGGCCCCATC
TCAGTTCTCACGATCTTTGTCCATCTGTTCATGAGCTCTTGCAAATCTCTCCATGAGGAGATATGGAATGACCTTCTAAT
GATGTGCACGTGTGAGATCACTGACCAGCCTGGGCAATGTCAGCGATCAGCACTCCAAATTCAAATGACAGACTCTGCTA
GCCATATTCTGTATACCAAGAAGGACACAAGTAAGTGGAATTTTGCCTTTACCATGGAAGATTATGACAAGATGGAAGTG
TGTTTTGAGAGCGAGGGAGATGGGCGGATACCTGACCTACTTGTAATTCTACACAAGAAGCATGGATTGAGGGTGAAGAA
TTAGGACGAGATTGCAAAAGTTGAGGAACCTAAATATTTGGAGCTGGCGTTCTGATGCCTAAAGGACATTTGAAAGACAA
TTTTTAATGGTTTGGCATACATGAAGAAGCGGGAAGTTGAGATGTGCGGTACCAATAATTCCATATGCACCAGAGTCCTG
TATTTCAGCATCTTTTCAATAATCTGTCTAGCTGCATGGCAGCTCTTCTGCCCGTGTCCCTTTTGCAAGTGCAAGAACTT
GATACAG

Alignment

ORF - retro_mmus_649 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.36 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSGLFGPLSRPGPL-PSAWLFLLLLGPSSVLGISFHLPVNSRKCLREEIHKDLLVTGAYEITDQSGGAGG
          .SGL.G.LS..GP..P.A.LF.LLLGP.SVL.I..HL...S.K.L.EEI..DLL.....EITDQ.G....
Retrocopy ISGLSGQLSWLGPA<PLALLFTLLLGPISVLTIFVHLFMSSCKSLHEEIWNDLLMMCTCEITDQPGQCQR

Parental  LRTHLKITDSAGHILYAKEDATKGKFAFTTEDYDMFEVCFESKGTGRIPDQLVILDMKHGVEAKNYEEIA
          .......TDSA.HILY.K.D..K..FAFT.EDYD..EVCFES.G.GRIPD.LVIL..KHG...KN..EIA
Retrocopy SALQIQMTDSASHILYTKKDTSKWNFAFTMEDYDKMEVCFESEGDGRIPDLLVILHKKHGLRVKN*DEIA

Parental  KVEKLKPLEVELRRLEDLSESIVNDFAYMKKREEEMRDTNESTNTRVLYFSIFSMFCLIGLATWQVFYLR
          KVE..K.LE.....L.D....I.N..AYMKKRE.EM..TN.S..TRVLYFSIFS..CL...A.WQ.F...
Retrocopy KVEEPKYLELAF*CLKDI*KTIFNGLAYMKKREVEMCGTNNSICTRVLYFSIFSIICL---AAWQLFCPC

Parental  RFFKAKKLIE
          .F.K.K.LI.
Retrocopy PFCKCKNLIQ

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	94.50 RPM
SRP007412_cerebellum	0.00 RPM	76.29 RPM
SRP007412_heart	0.00 RPM	89.47 RPM
SRP007412_kidney	0.00 RPM	83.31 RPM
SRP007412_liver	0.00 RPM	76.55 RPM
SRP007412_testis	0.00 RPM	49.35 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_649 was not detected

EST

No EST(s) were mapped for retro_mmus_649 retrocopy.

TSS

No TSS is located nearby retro_mmus_649 retrocopy 5' end.

Lab

retro_mmus_649 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_649 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_1729

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000016899	1 retrocopy	retro_acar_187,
Callithrix jacchus	ENSCJAG00000020627	2 retrocopies	retro_cjac_1409, retro_cjac_4223,
Dasypus novemcinctus	ENSDNOG00000019851	1 retrocopy	retro_dnov_1225,
Echinops telfairi	ENSETEG00000010607	1 retrocopy	retro_etel_1798,
Homo sapiens	ENSG00000170348	2 retrocopies	retro_hsap_2701, retro_hsap_4014,
Gorilla gorilla	ENSGGOG00000007453	1 retrocopy	retro_ggor_2696,
Myotis lucifugus	ENSMLUG00000017125	2 retrocopies	retro_mluc_2079, retro_mluc_2093,
Macaca mulatta	ENSMMUG00000015168	2 retrocopies	retro_mmul_2316, retro_mmul_885,
Mus musculus	ENSMUSG00000021248	2 retrocopies	retro_mmus_1093, retro_mmus_649 ,
Nomascus leucogenys	ENSNLEG00000016453	2 retrocopies	retro_nleu_2897, retro_nleu_2963,
Oryctolagus cuniculus	ENSOCUG00000004669	1 retrocopy	retro_ocun_875,
Pongo abelii	ENSPPYG00000029389	1 retrocopy	retro_pabe_3296,
Pan troglodytes	ENSPTRG00000006552	2 retrocopies	retro_ptro_1823, retro_ptro_2724,
Rattus norvegicus	ENSRNOG00000007901	2 retrocopies	retro_rnor_1729, retro_rnor_2031,
Ictidomys tridecemlineatus	ENSSTOG00000007392	1 retrocopy	retro_itri_362,
Vicugna pacos	ENSVPAG00000003089	1 retrocopy	retro_vpac_573,