RetrogeneDB ID: retro_cjac_1526

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 16:90882908..90883578(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TARBP2
• Ensembl ID: ENSCJAG00000018668
• Aliases: None
• Description: TAR (HIV-1) RNA binding protein 2 [Source:HGNC Symbol;Acc:11569]

Sequence

>retro_cjac_1526
CCAGGGGCACCCCTCTGGAAAAGCAGCACCCCCGTCTCCCTAACCCCCATTTCCCTTCAGCAGTCTAAGTGCATCCCCGT
TGGTGCTCTGCAGGAGCTGGTGGTGCAAAAAGGCTGGTGGTTGTTGCCAGAGTACACAGTGACCCAGGAATGTGGGCCAG
ACCACCGCAAATAATTCATCATGACCTGCCGAGTGGAGCATTTCATTGATATTGGCAGTGGCATTTCCAAAAAATTGGCA
AAGTGTAATGCGGTGGCCAAAATGCTGCTTCAAGTGCACACAGTGTCTCTGAATGCCCCGAATGGCAATGAGGCGGAGCC
TGAGGATGACCACTTCTTCATTGCTGTGGTCTCCCACCTGGATGGTCTTTGGAACCTGGACCCAGGATGCACCGGGAATT
CTCTACAAAATTCAGTGGAGGGAAGATCCTGTCTTCCTTCAGTTGCTCCTGGGCTCCCTAGGTGCCCTGGGCCCTGCCTG
CTGCCGTGTTCTCAGTGAGCTCTCTGAAGAGTGGGTCTTCCACGTCAGCTACCTGGATATTAAAGAGCTGAGCCTGAGTG
GACTCTGCCAGTGTCTGGTGGAACTGTCCACCTAGCCAGCCACTGTGTGTCATGGCTCTGCAACCACCAGGGAGACAGCC
CATGGTGAGGCTGCTCGCTGTGTCCTGCAG

Alignment

ORF - retro_cjac_1526 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.78 %
• Parental protein coverage: 60.93 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PSVVLTRSPPMEMQPPVSPQQSECNPVGALQELVVQKGW-RLPEYTVTQESGPAHRKEFTMTCRVERFIE
          P...L..S.......P.S.QQS.C.PVGALQELVVQKGW..LPEYTVTQE.GP.HRK.F.MTCRVE.FI.
Retrocopy PGAPLWKSSTPVSLTPISLQQSKCIPVGALQELVVQKGWWLLPEYTVTQECGPDHRK*FIMTCRVEHFID

Parental  IGSGTSKKLAKRNAAAKMLLRVHTVPLDARDGNEVEPDDDHFSIGVGSRLDGLRNRGPGCTWDSLRNSV-
          IGSG.SKKLAK.NA.AKMLL.VHTV.L.A..GNE.EP.DDHF.I.V.S.LDGL.N..PGCT..SL.NSV.
Retrocopy IGSGISKKLAKCNAVAKMLLQVHTVSLNAPNGNEAEPEDDHFFIAVVSHLDGLWNLDPGCTGNSLQNSV<

Parental  GEKILSLRSCS-LGSLGALGPACCRVLSELSEEQAFHVSYLDIEELSLSGLCQCLVELSTQPATVCHGSA
          G.KILS..SCS.LGSLGALGPACCRVLSELSEE..FHVSYLDI.ELSLSGLCQCLVELST.PATVCHGSA
Retrocopy GGKILSSFSCS<LGSLGALGPACCRVLSELSEEWVFHVSYLDIKELSLSGLCQCLVELST*PATVCHGSA

Parental  TTREAARGEAARRALQ
          TTRE.A.GEAAR..LQ
Retrocopy TTRETAHGEAARCVLQ

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	0.04 RPM	6.35 RPM
SRP051959_heart	0.02 RPM	5.37 RPM
SRP051959_kidney	0.02 RPM	9.03 RPM
SRP051959_liver	0.09 RPM	9.96 RPM
SRP051959_lung	0.00 RPM	6.56 RPM
SRP051959_lymph_node	0.00 RPM	6.44 RPM
SRP051959_skeletal_muscle	0.00 RPM	7.45 RPM
SRP051959_spleen	0.02 RPM	6.01 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1526 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1526 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1526 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018668	1 retrocopy	retro_cjac_1526 ,
Homo sapiens	ENSG00000139546	1 retrocopy	retro_hsap_3995,
Gorilla gorilla	ENSGGOG00000012637	1 retrocopy	retro_ggor_2682,
Mus musculus	ENSMUSG00000023051	1 retrocopy	retro_mmus_2820,
Nomascus leucogenys	ENSNLEG00000017690	1 retrocopy	retro_nleu_545,
Pongo abelii	ENSPPYG00000004583	1 retrocopy	retro_pabe_3281,
Pan troglodytes	ENSPTRG00000005020	1 retrocopy	retro_ptro_2712,