RetrogeneDB ID: retro_cjac_969

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 12:32958310..32958682(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000022551
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TAF13
• Ensembl ID: ENSCJAG00000002701
• Aliases: None
• Description: TAF13 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 18kDa [Source:HGNC Symbol;Acc:11546]

Sequence

>retro_cjac_969
ATGGCAGATGAGGAAGAGGACCCTACCTTTGAGGAAGAAAATGAAGAAATTGGAGGAGGTGCAGAAAGTGGACAGGGTAA
AAGAAAGAGACTTTTATCTAAAGAATTGCGATGTATGATGTATGGCTTTGGGGATGACCAGAATCCTTATACTGAGTCAG
TGGATATTCTTGAAGATCTTGTCATAGAGTTTATCACTAAAATGACTCACAAGGCAATGTCCGTTGGAAGACAAGGTCGG
GTACAAGATGAAGATATCGTCTTCTTGATTCAAAAGGACCCAAGGAAGTTTGCCAGGGTTAAAGACTTGCTTACTATGAA
TGAAGAATTGAAACAAGCTAGAAAAGCATTTGATGAAGCAAACTATGAATCC

Alignment

ORF - retro_cjac_969 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.55 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MADEEEDPTFEEENEEIGGGAEGGQGKRKRLFSKELRCMMYGFGDDQNPYTESVDILEDLVIEFITEMTH
          MADEEEDPTFEEENEEIGGGAE.GQGKRKRL.SKELRCMMYGFGDDQNPYTESVDILEDLVIEFIT.MTH
Retrocopy MADEEEDPTFEEENEEIGGGAESGQGKRKRLLSKELRCMMYGFGDDQNPYTESVDILEDLVIEFITKMTH

Parental  KAMSIGRQGRVQVEDIVFLIRKDPRKFARVKDLLTMNEELKRARKAFDEANYGS
          KAMS.GRQGRVQ.EDIVFLI.KDPRKFARVKDLLTMNEELK.ARKAFDEANY.S
Retrocopy KAMSVGRQGRVQDEDIVFLIQKDPRKFARVKDLLTMNEELKQARKAFDEANYES

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	0.11 RPM	2.75 RPM
SRP051959_heart	0.26 RPM	3.00 RPM
SRP051959_kidney	0.09 RPM	2.66 RPM
SRP051959_liver	0.82 RPM	3.73 RPM
SRP051959_lung	0.11 RPM	3.01 RPM
SRP051959_lymph_node	0.02 RPM	1.83 RPM
SRP051959_skeletal_muscle	0.26 RPM	3.89 RPM
SRP051959_spleen	0.08 RPM	3.03 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_969 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_969 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_969 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 52 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004542	1 retrocopy	retro_amel_1015,
Canis familiaris	ENSCAFG00000019855	1 retrocopy	retro_cfam_1084,
Choloepus hoffmanni	ENSCHOG00000003347	2 retrocopies	retro_chof_1739, retro_chof_296,
Callithrix jacchus	ENSCJAG00000002701	3 retrocopies	retro_cjac_1241, retro_cjac_1268, retro_cjac_969 ,
Cavia porcellus	ENSCPOG00000001081	1 retrocopy	retro_cpor_1042,
Dasypus novemcinctus	ENSDNOG00000018227	16 retrocopies	retro_dnov_1126, retro_dnov_1140, retro_dnov_1237, retro_dnov_1308, retro_dnov_1539, retro_dnov_1899, retro_dnov_214, retro_dnov_222, retro_dnov_234, retro_dnov_314, retro_dnov_577, retro_dnov_599, retro_dnov_630, retro_dnov_703, retro_dnov_893, retro_dnov_925,
Loxodonta africana	ENSLAFG00000011432	2 retrocopies	retro_lafr_781, retro_lafr_799,
Microcebus murinus	ENSMICG00000008725	5 retrocopies	retro_mmur_1061, retro_mmur_128, retro_mmur_1376, retro_mmur_53, retro_mmur_576,
Mus musculus	ENSMUSG00000048100	2 retrocopies	retro_mmus_1272, retro_mmus_710,
Nomascus leucogenys	ENSNLEG00000002350	1 retrocopy	retro_nleu_27,
Otolemur garnettii	ENSOGAG00000013494	6 retrocopies	retro_ogar_192, retro_ogar_2232, retro_ogar_23, retro_ogar_2399, retro_ogar_2659, retro_ogar_2931,
Procavia capensis	ENSPCAG00000005773	1 retrocopy	retro_pcap_80,
Sorex araneus	ENSSARG00000008033	1 retrocopy	retro_sara_531,
Sus scrofa	ENSSSCG00000006839	1 retrocopy	retro_sscr_87,
Ictidomys tridecemlineatus	ENSSTOG00000011144	8 retrocopies	retro_itri_1094, retro_itri_1650, retro_itri_1717, retro_itri_1728, retro_itri_214, retro_itri_70, retro_itri_812, retro_itri_969,
Tursiops truncatus	ENSTTRG00000003167	1 retrocopy	retro_ttru_730,