RetrogeneDB ID: retro_cjac_2788

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:17437492..17437937(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C6orf106
• Ensembl ID: ENSCJAG00000015304
• Aliases: None
• Description: chromosome 6 open reading frame 106 [Source:HGNC Symbol;Acc:21215]

Sequence

>retro_cjac_2788
CCCGGGCCGGTGCAGAAGTTTGGCTGCCTGGGCACCACGGACAAGGATGTGCTCATCTCTGAGTTCCAGAGGCTGCTCAG
CTTCCAGCTCAACCCTGCCGACAGCACCTCCTTCCTGGACATGACCAATTGGAACCTACCAGCCTCAATTGGCACCTCCT
GTGACTTTGAGAGCCCAAACATCAGTGAGCCCTCTATGTCCTTCGTTGAAGATGTCACAAAAGGAGAAGCAGAGTCAATA
TCTCCTGATACTTAGTTTGTAAAAACATGGTAGATCCAGAAATCTGGGACAGAGGCCTGGCTTCCAGGGGTTTAAGTAAG
TCGGGGGAGACCAATTTGCACAGGTGAACATGGTGACAGTTAGTATACTAGAAGCCCCTCAACATTGCAGAAGTCAGTGT
CCAGATGTGCAGCTCCAGCAAGCAGGAAGGAATCAGGGACAGTGG

Alignment

ORF - retro_cjac_2788 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.28 %
• Parental protein coverage: 50.34 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PELMQKFSCLGTTDKDVLISEFQRLLGFQLNPAGCAFFLDMTNWNLQAAIGAYYDFESPNISVPSMSFVE
          P...QKF.CLGTTDKDVLISEFQRLL.FQLNPA....FLDMTNWNL.A.IG...DFESPNIS.PSMSFVE
Retrocopy PGPVQKFGCLGTTDKDVLISEFQRLLSFQLNPADSTSFLDMTNWNLPASIGTSCDFESPNISEPSMSFVE

Parental  DVTIGEGESIPPDTQFVKTW-RIQNSGAEAWPPGVCLKYVGGDQFGHVNMVMVRSLE-PQEIADVSVQMC
          DVT.GE.ESI.PDT.FVKTW.R..N.G......G...K.VGGDQF..VNMV.V..LE.P..IA.VSVQMC
Retrocopy DVTKGEAESISPDT*FVKTW>RSRNLGQRPGFQG--FK*VGGDQFAQVNMVTVSILE>PLNIAEVSVQMC

Parental  SPSR-AGMYQGQW
          S.S..AG..QGQW
Retrocopy SSSK<AGRNQGQW

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	10.10 RPM
SRP051959_heart	0.00 RPM	10.56 RPM
SRP051959_kidney	0.00 RPM	13.11 RPM
SRP051959_liver	0.00 RPM	22.16 RPM
SRP051959_lung	0.00 RPM	14.30 RPM
SRP051959_lymph_node	0.00 RPM	10.62 RPM
SRP051959_skeletal_muscle	0.00 RPM	13.41 RPM
SRP051959_spleen	0.00 RPM	10.84 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2788 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2788 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2788 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000034493	1 retrocopy	retro_btau_1343,
Callithrix jacchus	ENSCJAG00000015304	1 retrocopy	retro_cjac_2788 ,
Homo sapiens	ENSG00000196821	1 retrocopy	retro_hsap_2137,
Gorilla gorilla	ENSGGOG00000000388	1 retrocopy	retro_ggor_1653,
Microcebus murinus	ENSMICG00000013442	1 retrocopy	retro_mmur_1615,
Macaca mulatta	ENSMMUG00000022824	1 retrocopy	retro_mmul_2155,
Nomascus leucogenys	ENSNLEG00000008387	2 retrocopies	retro_nleu_1933, retro_nleu_2739,
Otolemur garnettii	ENSOGAG00000011264	1 retrocopy	retro_ogar_3245,
Ochotona princeps	ENSOPRG00000009350	1 retrocopy	retro_opri_559,
Pongo abelii	ENSPPYG00000016519	2 retrocopies	retro_pabe_1265, retro_pabe_1928,
Pan troglodytes	ENSPTRG00000018068	1 retrocopy	retro_ptro_1564,