RetrogeneDB ID: retro_cjac_858

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 11:59698436..59699045(+)
• Located in intron of: ENSCJAG00000014753

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACBD6
• Ensembl ID: ENSCJAG00000007953
• Aliases: None
• Description: acyl-CoA binding domain containing 6 [Source:HGNC Symbol;Acc:23339]

Sequence

>retro_cjac_858
GTGGCTTCATCATTCCTGCCTGCTAGAGCCACCTCCGGCAACAGCGGTGGAAAGCTAAGCTCAGGGGACAACTCAGGAGG
TGGAGTTCCCCCATAGCCCTAAGATTAAGGAGTCCCGTTGTCTGGCCGAGCTGTTTGAGAAGGCTTTAGAGCACCTGCAA
GCCCTTATTCAGGTGGCCAGCAGGGAGCAGCTCTTGTACCTATATGCCAGGTACAAACAGGTCAAATTGGAAATTGCAGT
ACTCCTAAACCAAGCTTCTTTGATTTTGAAGGAAAGTGAAAATGGGAAGCATGGAAAGCACTTGGTGATTCAAGCCCCAG
CCAAGCAGTGCAGGAATATATCGCAGTAGTTAAAAAACTAGATCCCAGTTGGAATCCTCAGATACCAGAGAAGAAAGGGA
AAGAAGAAAATACTGGTTTTGGTGGGCCAGTTATTAGTTCTCTGTTTCATGAAGAAACCATCAGGGAAGAAGACAAAAAT
ATGTTTGATTACTGCAGGGGAAACAGCATTGACCATATAACCAAAGCCATCAAATCAAAAACTGTGGATATGAATGTGAA
AGATGAAGAGCGTAGGGCTCTACTTTCTTGGGCCTGTGATCAAGGACAT

Alignment

ORF - retro_cjac_858 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.04 %
• Parental protein coverage: 72.34 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MASSFLPAGATTGDSGGELSSRDDSG-EVEFPHSPETEESSCLAELFEKAAAHLQGLIHVASREQLLYLY
          .ASSFLPA.AT.G.SGG.L.S..D...EVEFPHSP...ES.CLAELFEKA..HLQ.LI.VASREQLLYLY
Retrocopy VASSFLPARATSGNSGGKL-SSGDNS>EVEFPHSPKIKESRCLAELFEKALEHLQALIQVASREQLLYLY

Parental  ARYKQVK-VGNCNTPKPSFFDFEGKQKWEAWKALGDSSPSQAMQEYIAVVRKLDPGWNPQVPEKKGKEIN
          ARYKQVK..GNC.TPKPSFFDFEGK.KWEAWKALGDSSPSQA.QEYIAVV.KLDP.WNPQ.PEKKGKE.N
Retrocopy ARYKQVK<IGNCSTPKPSFFDFEGK*KWEAWKALGDSSPSQAVQEYIAVVKKLDPSWNPQIPEKKGKEEN

Parental  TGFGGPVISSLYHEETIREEDKNIFDYCRENNIDHITKAIKSKNVDVNVKDEEGRALLHWACDRGH
          TGFGGPVISSL.HEETIREEDKN.FDYCR.N.IDHITKAIKSK.VD.NVKDEE.RALL.WACD.GH
Retrocopy TGFGGPVISSLFHEETIREEDKNMFDYCRGNSIDHITKAIKSKTVDMNVKDEERRALLSWACDQGH

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	0.78 RPM	4.55 RPM
SRP051959_heart	0.61 RPM	4.96 RPM
SRP051959_kidney	0.53 RPM	5.04 RPM
SRP051959_liver	0.67 RPM	2.53 RPM
SRP051959_lung	0.94 RPM	6.04 RPM
SRP051959_lymph_node	1.51 RPM	11.55 RPM
SRP051959_skeletal_muscle	0.50 RPM	1.99 RPM
SRP051959_spleen	1.64 RPM	7.84 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_858 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_858 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_858 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007953	1 retrocopy	retro_cjac_858 ,
Callithrix jacchus	ENSCJAG00000012808	1 retrocopy	retro_cjac_3249,