RetrogeneDB ID: retro_cjac_3835

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL284913.1:39901..40605(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SPIC
• Ensembl ID: ENSCJAG00000001906
• Aliases: None
• Description: Spi-C transcription factor (Spi-1/PU.1 related) [Source:HGNC Symbol;Acc:29549]

Sequence

>retro_cjac_3835
ATGACTTGGATTGAAGAAGACAAGCTGGATCAAGCATTTGAAGATGGTTTTGAGGTACCGAGGCAACACACCACTTTACA
TCCTCGGTACTCCCCGATGACAAAAATGTCCTGTCTTTCACAACTGTTGTCTTCATGTCAGAGGAAATTCCAGCTGTTAT
GAGTGCTGCCTACAGAGGAACCTACTTAGATTTGGAGAACTGTAATAGCAGGGCCATGGACTTCTGTTTTAAAGCAAATG
TTCATCAACCGCTGCAGAGCGTAACTGAAAACCAGCCAGTACAACCTGCGGTTCTCCAGCGAGACGACGAAAAGGCAGGA
AGAAGCTCTCTCTGCTTGATCACCTTCACAAATCCCTGTGTGATTCTGAGATAGCATGTTGGATTCAGTGGGAAGATAAA
ACCGAAGATAGCTTTCGGTTTGTAACAAAAAACAAGGAAACTTCCGAACTCTGGGGGAAGAGAAGAGGCAACCTGAGTAC
CCTGACTTTCCAGAAATGGCCGGGGCACTGAGGAGTTATGGAAGAACTGGGAACATCACCAAAACCCAGTGCCGTGTCAG
TGAGGCATTCTCTAGAAATTCTCTCCATCTTATTTCTTGGGGAAAGAGTTCTGCTTACAATATGATCAACCCGATCAAGA
ATATATTGGTTTAAATAACTGTGATGCAAATTATAAGTATACAAATGCCAATTAACAGAAGTTG

Alignment

ORF - retro_cjac_3835 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.0 %
• Parental protein coverage: 97.98 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  MTCVEQDKLGQAFEDAFEVLRQHSIGDLQYSP-DYKNYLALI-NHRAYVKGNSSCYG-VLPTEEPVYNWR
          MT..E.DKL.QAFED.FEV.RQH......YSP.D.KN.L....N....V.GNSSCY..VLPTEEP...WR
Retrocopy MTWIEEDKLDQAFEDGFEVPRQHTTLHPRYSP<DDKNVLSFT<NCCLHVRGNSSCYE<VLPTEEPT*IWR

Parental  TVI-NNAADFYFEGNIHQSLQNITENQLIQPTILQQ-KRGKGRKKLRLFEYLHESLCNPEMASCIQWVDK
          TVI...A.DF.F..N.HQ.LQ..TENQ..QP..LQ...R.KGRKKL.L...LH.SLC..E.A..IQW.DK
Retrocopy TVI<SRAMDFCFKANVHQPLQSVTENQPVQPAVLQR<RRRKGRKKLSLLDHLHKSLCDSEIACWIQWEDK

Parental  TKGIFQFVSKNKEKLAELWGKRKGNRKTMTYQK-MARALRNYGRSGEITKIRRKLTYQFSEA-ILQRLSP
          T...F.FV.KNKE...ELWGKR.GN..T.T.QK.MA.ALR.YGR.G.IT....K.....SEA.IL...SP
Retrocopy TEDSFRFVTKNKET-SELWGKRRGNLSTLTFQK<MAGALRSYGRTGNIT----KTQCRVSEA<IL*KFSP

Parental  SYFLGKEIFYSPCVQPDQEYLSLNNWNANYNYTYANYHEL
          SYFLGKE.F.....QPDQEY..LNN..ANY.YT.AN...L
Retrocopy SYFLGKE-FCLQYDQPDQEYIGLNNCDANYKYTNAN*QKL

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	0.00 RPM	0.11 RPM
SRP051959_heart	0.00 RPM	0.25 RPM
SRP051959_kidney	0.04 RPM	0.02 RPM
SRP051959_liver	0.02 RPM	4.20 RPM
SRP051959_lung	0.02 RPM	1.68 RPM
SRP051959_lymph_node	0.02 RPM	3.56 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.02 RPM
SRP051959_spleen	0.86 RPM	70.34 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3835 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3835 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3835 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009904	2 retrocopies	retro_btau_1281, retro_btau_1837,
Callithrix jacchus	ENSCJAG00000001906	1 retrocopy	retro_cjac_3835 ,
Dasypus novemcinctus	ENSDNOG00000004496	1 retrocopy	retro_dnov_759,
Equus caballus	ENSECAG00000009614	1 retrocopy	retro_ecab_542,
Echinops telfairi	ENSETEG00000004217	6 retrocopies	retro_etel_1675, retro_etel_2007, retro_etel_2008, retro_etel_593, retro_etel_929, retro_etel_933,
Homo sapiens	ENSG00000166211	4 retrocopies	retro_hsap_1748, retro_hsap_1800, retro_hsap_3135, retro_hsap_864,
Gorilla gorilla	ENSGGOG00000024597	4 retrocopies	retro_ggor_1324, retro_ggor_1362, retro_ggor_2255, retro_ggor_703,
Loxodonta africana	ENSLAFG00000015661	1 retrocopy	retro_lafr_912,
Myotis lucifugus	ENSMLUG00000011052	1 retrocopy	retro_mluc_2169,
Macaca mulatta	ENSMMUG00000020873	1 retrocopy	retro_mmul_1245,
Nomascus leucogenys	ENSNLEG00000006232	1 retrocopy	retro_nleu_53,
Oryctolagus cuniculus	ENSOCUG00000008070	1 retrocopy	retro_ocun_161,
Otolemur garnettii	ENSOGAG00000015148	1 retrocopy	retro_ogar_1782,
Pongo abelii	ENSPPYG00000004873	4 retrocopies	retro_pabe_1444, retro_pabe_1445, retro_pabe_2819, retro_pabe_686,
Pan troglodytes	ENSPTRG00000005351	4 retrocopies	retro_ptro_1206, retro_ptro_1218, retro_ptro_3070, retro_ptro_598,
Rattus norvegicus	ENSRNOG00000005720	1 retrocopy	retro_rnor_1519,
Ictidomys tridecemlineatus	ENSSTOG00000015457	3 retrocopies	retro_itri_1785, retro_itri_235, retro_itri_29,
Tursiops truncatus	ENSTTRG00000017205	1 retrocopy	retro_ttru_1708,