RetrogeneDB ID: retro_cjac_2986

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:69563668..69564382(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBA3
• Ensembl ID: ENSCJAG00000013395
• Aliases: None
• Description: None

Sequence

>retro_cjac_2986
CTGGAACTTTATCCATCACTGGTTAATTTTCCCCTGTTCACCACTGCATCTATGCCCAGGCGACCAGAACACTGTATTGA
GTATGTAAGGATGTTGCAGTGTCCTAAGGAGCAGCCATTTGGAGAAGGGGTTCTACTAGATGGAGATGATCCTGAGCATA
TACAGTGGATTTTCCAAAAATCGCTAGAGAGAGCATCACAATATAATATTAGGACTGTTACATATAGACTCACTCAAGGG
GTAGTAAAAAGAATCATTCCTGCAGTAGCTTCCACAACTGCAGTCATTGCAGCTGTGTGTGCCACTGAGGTTTTTAAAAT
AGCCACAAGTGCATTCATTCCCTTGAATAATTACTTGGTATTCAATGATGTAGATGGGCTCTATACATACACATTTGAAG
CGGAGAGAAAGGAAAGCTGCCCAGCCTGTATCCAGCTTCCTCAAAATATTCAGTTTTCTCCATCAGCTAAATTACAGGAG
ATTTTGGATTATCTAACCAATAGTGCTTCTCTGCAAATGAAATCTCCAGCCATCACAGCCACCCTAGAGGGAAAAAATAG
AACACTTTACTTCTAGTTGGTAACCTCTATTGAAGAAGGAACAAGGCCAAATCTCTCCAAAACGTTGAAAGGATTGGGGC
TTGTTGATGGACAACTGGTGGTTGCTGATGTCACCACACCGCAGACAGTACTATTCAAACTTCATTTTACTTCT

Alignment

ORF - retro_cjac_2986 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.21 %
• Parental protein coverage: 83.57 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LELYPPQVNFPMCTIASMPRLPEHCIEYVRMLQWPKEQPFGEGVPLDGDDPEHIQWIFQKSLERASQYNI
          LELYP..VNFP..T.ASMPR.PEHCIEYVRMLQ.PKEQPFGEGV.LDGDDPEHIQWIFQKSLERASQYNI
Retrocopy LELYPSLVNFPLFTTASMPRRPEHCIEYVRMLQCPKEQPFGEGVLLDGDDPEHIQWIFQKSLERASQYNI

Parental  RGVTYRLTQGVVKRIIPAVASTNAVIAAVCATEVFKIATSAYIPLNNYLVFNDVDGLYTYTFEAERKENC
          R.VTYRLTQGVVKRIIPAVAST.AVIAAVCATEVFKIATSA.IPLNNYLVFNDVDGLYTYTFEAERKE.C
Retrocopy RTVTYRLTQGVVKRIIPAVASTTAVIAAVCATEVFKIATSAFIPLNNYLVFNDVDGLYTYTFEAERKESC

Parental  PACSQLPQNIQFSPSAKLQEVLDYLTNSASLQMKSPAITATLEGKNRTLYLQSVTSIEERTRPNLSKTLK
          PAC.QLPQNIQFSPSAKLQE.LDYLTNSASLQMKSPAITATLEGKNRTLY...VTSIEE.TRPNLSKTLK
Retrocopy PACIQLPQNIQFSPSAKLQEILDYLTNSASLQMKSPAITATLEGKNRTLYF*LVTSIEEGTRPNLSKTLK

Parental  ELGLVDGQELAVADVTTPQTVLFKLHFTS
          .LGLVDGQ.L.VADVTTPQTVLFKLHFTS
Retrocopy GLGLVDGQ-LVVADVTTPQTVLFKLHFTS

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	17.42 RPM
SRP051959_heart	0.00 RPM	23.75 RPM
SRP051959_kidney	0.02 RPM	25.78 RPM
SRP051959_liver	0.02 RPM	15.79 RPM
SRP051959_lung	0.03 RPM	27.74 RPM
SRP051959_lymph_node	0.02 RPM	41.39 RPM
SRP051959_skeletal_muscle	0.00 RPM	25.59 RPM
SRP051959_spleen	0.02 RPM	25.92 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2986 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2986 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2986 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010117	1 retrocopy	retro_amel_204,
Choloepus hoffmanni	ENSCHOG00000013626	2 retrocopies	retro_chof_1740, retro_chof_553,
Callithrix jacchus	ENSCJAG00000013395	2 retrocopies	retro_cjac_2827, retro_cjac_2986 ,
Erinaceus europaeus	ENSEEUG00000005430	2 retrocopies	retro_eeur_374, retro_eeur_663,
Otolemur garnettii	ENSOGAG00000007771	2 retrocopies	retro_ogar_1868, retro_ogar_2776,
Rattus norvegicus	ENSRNOG00000006221	1 retrocopy	retro_rnor_852,
Sus scrofa	ENSSSCG00000011506	1 retrocopy	retro_sscr_192,