RetrogeneDB ID: retro_rnor_1729

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 20:26355349..26355998(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Tmed10
• Ensembl ID: ENSRNOG00000007901
• Aliases: Tmed10, Tmp21
• Description: Transmembrane emp24 domain-containing protein 10 [Source:UniProtKB/Swiss-Prot;Acc:Q63584]

Sequence

>retro_rnor_1729
ATGTCCGGATTTTCTGGCCCACTATTCTGGCTTGGCTCCGACCTTTGCTATTACTCTTTAGATTATTGTTTGGCCCCATC
TCAGTTCTCACCATTTTTTCTCCATCTGTTCGTAAGCTCTTGCAAGTATCTCTGAGAGGAGATCTGGAAGGACCTTCTAA
TGCTGGGCATGTGTGAGATCACTGACAAGTCTGGGGGTGTCAACGACATGTGCAACTGACTCAAATTACAGACTGCTAGA
TAGATCCTGTGCACCAATGAGGACACAACTACGTGGACTTTTGCCTTCAACCATGGAACATTATGAGAAGTTTGAAGTGT
GTTTTGGGAGCAAGGGAAATGGGCGGATACCTGACCAACTCATGATTATACACAAGAAGCATTGATCGGAGGCAAAGACT
TCTGGAGCAAAAGCTGAGATACCCAAACTATTGGAGTTGGCGTTATGATGCCTAAAAGACCTTTGAAAAACAATTGTTAG
TGTTTTGGCATAAATGAAGAAGAGGGAAGTGGAGACGTGCGGTACACATGATTCCATGACCGCCAGAGTACGGTACTTCA
GCGTCTTTTCAGTGACCTGTCTCATTGAACTAGCTACATGGCTGGTCTTCTACCTCCATCCCTTCTTCAAGTTCAAGAAT
TCGATAGAG

Alignment

ORF - retro_rnor_1729 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.05 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 7
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSGLSGPLSWPGPLLS-ALLFLFLLGPSSVLGIS-FHLPVNSRKCLREEIHKDLLVTGAYEITDQSGGAG
          MSG.SGPL.W.G..L...LLF..L.GP.SVL.I...HL.V.S.K.L.EEI.KDLL..G..EITD.SGG..
Retrocopy MSGFSGPLFWLGSDLC<LLLFRLLFGPISVLTIF>LHLFVSSCKYL*EEIWKDLLMLGMCEITDKSGGVN

Parental  GLRTHLKITDSAGHILYAKEDATKGKFAF-TTEDYDMFEVCFESKGTGRIPDQLVILDMKHGVEAKNYEE
          .....LK....A..IL...ED.T...FAF.T.E.Y..FEVCF.SKG.GRIPDQL.I...KH..EAK....
Retrocopy DMCN*LKL-QTAR*ILCTNEDTTTWTFAF>TMEHYEKFEVCFGSKGNGRIPDQLMIIHKKH*SEAKTSGA

Parental  IAKVEKLKPLEVELRRLEDLSESIVNDFAYMKKREEEMRDTNESTNTRVLYFSIFSMFCLIGLATWQVFY
          .A...KL..LE..L..L.DL...IV...A.MKKRE.E...T..S...RV.YFS.FS..CLI.LATW.VFY
Retrocopy KAEIPKL--LELAL*CLKDL*KTIVSVLA*MKKREVETCGTHDSMTARVRYFSVFSVTCLIELATWLVFY

Parental  LRRFFKAKKLIE
          L..FFK.K..IE
Retrocopy LHPFFKFKNSIE

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
SRP017611_brain	0.00 RPM	52.05 RPM
SRP017611_kidney	0.00 RPM	89.39 RPM
SRP017611_liver	0.00 RPM	76.45 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1729 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1729 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1729 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Mus musculus	retro_mmus_649

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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,