RetrogeneDB ID: retro_cjac_4168

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:57293565..57294135(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C9ORF21
• Ensembl ID: ENSCJAG00000005509
• Aliases: None
• Description: None

Sequence

>retro_cjac_4168
GAGCTGCTGGTGCTGGACACTCACAGGCAGAGGGTGCTGTTCCACCCACTGTTCCGGAGTGCTGAGCCATGGTGGTGGTA
GTGCGGCATTTCCTCTGTTACATCTGCAAGGAATATGTAGAGGATTTGGCCAAAATCCCCAAGAGTTTTTTACAAAAAGC
AAATGTCACCCTCATAGTGATTAGACAGTCATCTTATCATCATATAGAGCCTTTTTTGCAAATTGACTGGATATTCTCAT
AAAATGTATGTCGATTTTAAGAGGGAAATTTATATAAGATTGGGAATGAAAAGAAGTGGAGAAATTGCTTTTTCAGGACA
GAGTCCCCACATAAATTCAAATCTACTCTCAGAAGCCTTCAGAACCTGTAATAGGCAGTAACTGGAACTCTTTGATTTTC
AAGGAGACCCATTTCAGCAAGGTGGAACTCTCATTTTAGGTCCATGTAACAACATTCATTTTATACACTGTTATAGGAAT
AGGTTGGATCACAAACCTATCAACTCTGTTTTACAGCTTGTAGGAATTCAGCATTTGAACTTTACAAACACACCTTCAGT
TACCCATGTA

Alignment

ORF - retro_cjac_4168 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.61 %
• Parental protein coverage: 89.67 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ELPVLDARGQRVPFGALFRERR-AVVVFVRHFLCYICKEYVEDLARIPKSFLQEANVTLIVIGQSSYHHI
          EL.VLD...QRV.F..LFR....A.VV.VRHFLCYICKEYVEDLA.IPKSFLQ.ANVTLIVI.QSSYHHI
Retrocopy ELLVLDTHRQRVLFHPLFRSAE<AMVVVVRHFLCYICKEYVEDLAKIPKSFLQKANVTLIVIRQSSYHHI

Parental  ESF-CKLTGYSHEIYVDPEREIYKRLGMKRGEEIASSGQSPHVKSNLLSGSLQSLWRAVTGPLFDFQGDP
          E.F.CKLTGYSH..YVD..REIY.RLGMKR..EIA.SGQSPH..SNLLS.......R.....LFDFQGDP
Retrocopy EPF>CKLTGYSHKMYVDFKREIYIRLGMKRSGEIAFSGQSPHINSNLLSEAFRTCNRQ*L-ELFDFQGDP

Parental  AQQGGTLILGPGNNIHFIHRDKNRLDHKPINSVLQLVGVQHVNFTNRPSVIHV
          .QQGGTLILGP.NNIHFIH...NRLDHKPINSVLQLVG.QH.NFTN.PSV.HV
Retrocopy FQQGGTLILGPCNNIHFIHCYRNRLDHKPINSVLQLVGIQHLNFTNTPSVTHV

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	9.07 RPM
SRP051959_heart	0.07 RPM	14.26 RPM
SRP051959_kidney	0.04 RPM	18.92 RPM
SRP051959_liver	0.00 RPM	19.21 RPM
SRP051959_lung	0.00 RPM	10.07 RPM
SRP051959_lymph_node	0.00 RPM	9.50 RPM
SRP051959_skeletal_muscle	0.00 RPM	7.64 RPM
SRP051959_spleen	0.02 RPM	13.21 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4168 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4168 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4168 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006422	1 retrocopy	retro_chof_1792,
Choloepus hoffmanni	ENSCHOG00000007723	7 retrocopies	retro_chof_1026, retro_chof_1037, retro_chof_1808, retro_chof_2079, retro_chof_2149, retro_chof_2642, retro_chof_811,
Callithrix jacchus	ENSCJAG00000005509	1 retrocopy	retro_cjac_4168 ,
Dasypus novemcinctus	ENSDNOG00000024562	4 retrocopies	retro_dnov_1226, retro_dnov_1419, retro_dnov_1519, retro_dnov_1871,
Homo sapiens	ENSG00000158122	1 retrocopy	retro_hsap_4843,
Macaca mulatta	ENSMMUG00000008295	1 retrocopy	retro_mmul_2586,
Otolemur garnettii	ENSOGAG00000017058	1 retrocopy	retro_ogar_1866,
Procavia capensis	ENSPCAG00000003177	1 retrocopy	retro_pcap_269,
Pongo abelii	ENSPPYG00000019418	1 retrocopy	retro_pabe_3765,
Pan troglodytes	ENSPTRG00000021156	1 retrocopy	retro_ptro_3227,