RetrogeneDB ID: retro_cjac_3208

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:36695114..36695634(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: WRB
• Ensembl ID: ENSCJAG00000005714
• Aliases: None
• Description: None

Sequence

>retro_cjac_3208
ATGAGCTCAGCCCGGGCCCACCACTGGGCCTGGTTGCTGGTGATCAGCTTCGTGTTTGGGTGCAGTATTCTTAGGATCCT
CTTCCCGTCCTTCTCGTCTTTCATGTCCAGGGTGCTGCACAAGGATGCGGAGGAGTCACAGATGAGAACGGCGATCAAGG
ACATGAAGCAGGAGCTGTCCATGGTCAACATGATGGATGAGTTTGCCAGATATGCCAGGCTGGAAAGAAAGAACAACAAG
ATGACAGATAAGCTCAAAACTCACATGAAAGCTTGGACAGCTCTATTAGGCAAGATAAAATAGGTGATAAGTGTTGCTTT
TTACATTTTGCAGGCTGCCCTGATGATCTCACTCATTTGGAGGTATTATTTTGTCCCTGTGGCTGTGGTGCCGAGTAAAT
GGATAACCCAGCTAGACTGCCTGGGTAGTCTTTCCTACTAGAGTAGCAGGTGGTGTTGGAATTGCCTGCTGGATTTTAGT
CTGTAACAAAGTTGTGGCTGTTGTGCTTCATCCATTCAGC

Alignment

ORF - retro_cjac_3208 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.0 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSSAAADHWAWLLVLSFVFGCNVLRILLPSFSSFMSRMLQKDAEQESQMRAEIQDMKQELSTVNMMDEFA
          MSSA.A.HWAWLLV.SFVFGC..LRIL.PSFSSFMSR.L.KDAE.ESQMR..I.DMKQELS.VNMMDEFA
Retrocopy MSSARAHHWAWLLVISFVFGCSILRILFPSFSSFMSRVLHKDAE-ESQMRTAIKDMKQELSMVNMMDEFA

Parental  RYARLERKINKMTDKLKTHVKARTAQLAKIKWVISVAFYVLQAALMISLIWKYYSVPVAVVPSKWITPLD
          RYARLERK.NKMTDKLKTH.KA.TA.L.KIK.VISVAFY.LQAALMISLIW.YY.VPVAVVPSKWIT.LD
Retrocopy RYARLERKNNKMTDKLKTHMKAWTALLGKIK*VISVAFYILQAALMISLIWRYYFVPVAVVPSKWITQLD

Parental  RL-VAFPTRVAGGVGITCWILVCNKVVAIVLHPFS
          .L.V.FPTRVAGGVGI.CWILVCNKVVA.VLHPFS
Retrocopy CL>VVFPTRVAGGVGIACWILVCNKVVAVVLHPFS

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	4.77 RPM
SRP051959_heart	0.00 RPM	10.91 RPM
SRP051959_kidney	0.00 RPM	23.78 RPM
SRP051959_liver	0.00 RPM	16.07 RPM
SRP051959_lung	0.00 RPM	8.49 RPM
SRP051959_lymph_node	0.00 RPM	5.11 RPM
SRP051959_skeletal_muscle	0.00 RPM	6.75 RPM
SRP051959_spleen	0.00 RPM	6.20 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3208 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3208 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3208 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_853

---

Parental genes homology:

Parental genes homology involve 13 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005714	2 retrocopies	retro_cjac_2153, retro_cjac_3208 ,
Dasypus novemcinctus	ENSDNOG00000024987	1 retrocopy	retro_dnov_1496,
Homo sapiens	ENSG00000182093	1 retrocopy	retro_hsap_3080,
Gorilla gorilla	ENSGGOG00000013144	1 retrocopy	retro_ggor_2116,
Microcebus murinus	ENSMICG00000015808	1 retrocopy	retro_mmur_1275,
Macaca mulatta	ENSMMUG00000020654	2 retrocopies	retro_mmul_1966, retro_mmul_853,
Mus musculus	ENSMUSG00000023147	1 retrocopy	retro_mmus_1452,
Nomascus leucogenys	ENSNLEG00000013146	1 retrocopy	retro_nleu_2014,
Otolemur garnettii	ENSOGAG00000026761	1 retrocopy	retro_ogar_2691,
Pongo abelii	ENSPPYG00000011427	1 retrocopy	retro_pabe_2552,
Pan troglodytes	ENSPTRG00000013915	1 retrocopy	retro_ptro_2078,
Ictidomys tridecemlineatus	ENSSTOG00000012736	1 retrocopy	retro_itri_1744,
Tursiops truncatus	ENSTTRG00000015373	1 retrocopy	retro_ttru_1711,