RetrogeneDB ID: retro_cjac_2245

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:79744621..79745094(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MSMO1
• Ensembl ID: ENSCJAG00000009301
• Aliases: None
• Description: methylsterol monooxygenase 1 [Source:HGNC Symbol;Acc:10545]

Sequence

>retro_cjac_2245
ATGGCAACAAATGAAAGTGTCAGCATCTTTAGTTCAGCATCATTGACTGTGGAGTATGTAGATTCACTTTTACTTGAGAA
TCCCCTGCAACAACTATTTAAAAATGCATGGAACTATATGTTGAATAATTACACCAAGTTCCAGATCACAACATGAGGAT
CCCTATAGTTCACGAAGCCCTTTATTTCTTTTTCTTTTTACCTGGATTATTATTTCAATTTATACCTTACATGAAAAAAT
ACAAAATTCAAAAGACAAACCAGAAACATGGGAAACCAATGGAAATGTTTAAAGTAATTTTCTTCAATCACTTCTGTATC
CAGCTGCCTTTGATTGGTGGAATCTATTATTTTACAGGGTATTTCAATATTTTTTATGATTGGGAAAGAATGCTGAGATT
GTATATGGTTTTCACAAGATGCTTTGACTGTGCAGTCATTGGAGATACTTGGCACTATTTTATACATAAACTC

Alignment

ORF - retro_cjac_2245 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.53 %
• Parental protein coverage: 54.27 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MATNESVSIFSSASLAVEYVDSLLPENPLQEPFKNAWNYMLNNYTKFQIATWGSL-IVHEAIYFLFCVPG
          MATNESVSIFSSASL.VEYVDSLL.ENPLQ..FKNAWNYMLNNYTKFQI.T.GSL.IVHEA.YF.F..PG
Retrocopy MATNESVSIFSSASLTVEYVDSLLLENPLQQLFKNAWNYMLNNYTKFQITT*GSL<IVHEALYFFFFLPG

Parental  FLFQFIPYMKKYKIQK-DKPESLES-QWKC-FKVLLFNHFCIQLPLICGTYYFTEYFNIPYDWERMPRWY
          .LFQFIPYMKKYKIQK.DKPE..E..QWKC.FKV..FNHFCIQLPLI.G.YYFT.YFNI.YDWERM.R.Y
Retrocopy LLFQFIPYMKKYKIQK<DKPETWET<QWKC<FKVIFFNHFCIQLPLIGGIYYFTGYFNIFYDWERMLRLY

Parental  LLLARCLGCAVIEDTWHYFLHRL
          ....RC..CAVI.DTWHYF.H.L
Retrocopy MVFTRCFDCAVIGDTWHYFIHKL

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
SRP051959_colon	0.02 RPM	68.09 RPM
SRP051959_heart	0.00 RPM	7.07 RPM
SRP051959_kidney	0.00 RPM	18.68 RPM
SRP051959_liver	0.00 RPM	326.77 RPM
SRP051959_lung	0.00 RPM	13.50 RPM
SRP051959_lymph_node	0.00 RPM	14.95 RPM
SRP051959_skeletal_muscle	0.00 RPM	5.74 RPM
SRP051959_spleen	0.00 RPM	10.13 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2245 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2245 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2245 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005596	1 retrocopy	retro_amel_447,
Choloepus hoffmanni	ENSCHOG00000007550	2 retrocopies	retro_chof_1657, retro_chof_560,
Callithrix jacchus	ENSCJAG00000009301	1 retrocopy	retro_cjac_2245 ,
Felis catus	ENSFCAG00000023004	1 retrocopy	retro_fcat_863,
Homo sapiens	ENSG00000052802	1 retrocopy	retro_hsap_4672,
Gorilla gorilla	ENSGGOG00000015730	1 retrocopy	retro_ggor_2898,
Loxodonta africana	ENSLAFG00000007061	1 retrocopy	retro_lafr_570,
Macaca mulatta	ENSMMUG00000012994	1 retrocopy	retro_mmul_2486,
Nomascus leucogenys	ENSNLEG00000006501	1 retrocopy	retro_nleu_2164,
Oryctolagus cuniculus	ENSOCUG00000003769	1 retrocopy	retro_ocun_1454,
Otolemur garnettii	ENSOGAG00000009281	2 retrocopies	retro_ogar_182, retro_ogar_3404,
Pan troglodytes	ENSPTRG00000016574	1 retrocopy	retro_ptro_3104,
Pteropus vampyrus	ENSPVAG00000013707	4 retrocopies	retro_pvam_1405, retro_pvam_550, retro_pvam_598, retro_pvam_784,
Sorex araneus	ENSSARG00000013546	1 retrocopy	retro_sara_635,
Sarcophilus harrisii	ENSSHAG00000000135	1 retrocopy	retro_shar_530,
Tursiops truncatus	ENSTTRG00000012897	2 retrocopies	retro_ttru_20, retro_ttru_801,