RetrogeneDB ID: retro_cjac_4118

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:115991078..115991474(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BTG3
• Ensembl ID: ENSCJAG00000003406
• Aliases: None
• Description: BTG family, member 3 [Source:HGNC Symbol;Acc:1132]

Sequence

>retro_cjac_4118
AAACAGACAGTTGAGAGGTTTGCTGAGAAATTGACTCTAATATTTCCAGAAAAATATAAATATATATATACTTTTTGTCC
TGAAGTCTCTCAAAAGAAGAGGCCTATATGTGCATTCCTGTTAATAAGTGTCAAAGAGTTTATCCAGGTATCCTGAAGGC
CCATCAGAACAGCTTCATTTTGTATAGAAATCTGTGATTGCCTAAAGAGCTAACTTTCTTGGTGGATCCATGATAGGTGT
GCTGTAAGTAGGGAAAGAAAACCAATGCATTAATTGTTGTCAGCTTTGAAAATGTAGTTGAGAATAAGCACTAGATCTGA
AAGAAAATTCCTAGGGCCCTTTGACATGGTTACCTCTGATTATCATTTATCATCCTTTTCTTCACATGAAAAATCA

Alignment

ORF - retro_cjac_4118 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.7 %
• Parental protein coverage: 51.38 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KEAVERFAEKLTLILQE--KYKNHWYPEKP-SKGQAYRCIRVNKFQRVDPDVLKACENSCILYSDLGLPK
          K..VERFAEKLTLI..E..KY.....PE...SK..AY.CI.VNK.QRV.P..LKA..NS.ILY..L.LPK
Retrocopy KQTVERFAEKLTLIFPEKYKYIYTFCPEVS<SKEEAYMCIPVNKCQRVYPGILKAHQNSFILYRNL*LPK

Parental  ELTLWVDPCEVCCRYGEKNNAFIVASFENEDENKDEISRKVTRA-FDKVTSDYHSGSSSSDEET
          ELT..VDP..VCC..G.K.NA.IV.SFEN..ENK..I..K..RA.FD.VTSDYH..S.SS.E..
Retrocopy ELTFLVDP**VCCK*GKKTNALIVVSFENVVENKH*I*KKIPRA>FDMVTSDYHLSSFSSHEKS

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	5.39 RPM
SRP051959_heart	0.00 RPM	9.75 RPM
SRP051959_kidney	0.02 RPM	8.45 RPM
SRP051959_liver	0.02 RPM	3.90 RPM
SRP051959_lung	0.00 RPM	8.30 RPM
SRP051959_lymph_node	0.00 RPM	3.61 RPM
SRP051959_skeletal_muscle	0.00 RPM	2.64 RPM
SRP051959_spleen	0.00 RPM	7.33 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4118 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4118 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4118 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_2534

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003406	1 retrocopy	retro_cjac_4118 ,
Dasypus novemcinctus	ENSDNOG00000012987	2 retrocopies	retro_dnov_1703, retro_dnov_2682,
Macaca mulatta	ENSMMUG00000002116	1 retrocopy	retro_mmul_2534,
Mustela putorius furo	ENSMPUG00000010746	1 retrocopy	retro_mputfur_849,
Mus musculus	ENSMUSG00000022863	1 retrocopy	retro_mmus_225,
Otolemur garnettii	ENSOGAG00000013303	8 retrocopies	retro_ogar_1693, retro_ogar_1755, retro_ogar_2575, retro_ogar_2769, retro_ogar_2795, retro_ogar_3346, retro_ogar_524, retro_ogar_551,
Ochotona princeps	ENSOPRG00000012837	1 retrocopy	retro_opri_381,
Ictidomys tridecemlineatus	ENSSTOG00000010285	1 retrocopy	retro_itri_617,
Tarsius syrichta	ENSTSYG00000006151	5 retrocopies	retro_tsyr_1172, retro_tsyr_1406, retro_tsyr_1753, retro_tsyr_231, retro_tsyr_495,