RetrogeneDB ID: retro_cjac_1127

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 13:28982704..28983318(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LPGAT1
• Ensembl ID: ENSCJAG00000015870
• Aliases: None
• Description: None

Sequence

>retro_cjac_1127
GTTGCTCAGGGAAACTTCTTTATAAGACAAGGAAGATCTTATCGTGACCAACAGCTGCTGCTTCTCAAGAAGCACTTAGA
AAATAATTACAGGAGCAGAGATCGAAAATGAATTGTTTTGTTTCCAGAAGGGGGCTTCCTCAGGAAGAGCAAGAAACAAG
TCAGGCATTTGCCAAGAAAAATAACTTGCCATTTCTTACACATGTTACTCTGCCTAGGTCTGAGGCAATAAAATGGTTTC
AAATGCGCTTGTAGCACAACAAGAAAATGGAAGTCCAGCAGGAGGAGATGCTAAAGAATTAGACAACAAATCAAAATTAT
CCAGTGGATGATAGATAAAACGATAGCTTATCCCAAAGCTGAACCCATAGATATTCAAACCTGGATCCTTGGATACAGGA
AATCAATGGTCATACATGTACATTATAGGATCTTTCCAATTAAATATGTACCCCTGGAGACTGATGACCTTACCAATTGG
CTCAATTCACGGTTTATGGAAAAAGAGGACCTCTTATCACATTTTATGAAACAGGAGCTTTTCCACCTTCCAAGGGCCAT
AAGGAAGCTATTTCCAAGGAGATGACCCTCAGCAACATGTGGATATTCCTCATA

Alignment

ORF - retro_cjac_1127 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.29 %
• Parental protein coverage: 55.68 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LVHGDFFIRQGRSYRDQQLLLLKKHLENNYRSRDRKWIVLFPEGGFLRKRR-ETSQAFAKKNNLPFLTHV
          ...G.FFIRQGRSYRDQQLLLLKKHLENNYRSRDRK.IVLFPEGGFLRK...ETSQAFAKKNNLPFLTHV
Retrocopy VAQGNFFIRQGRSYRDQQLLLLKKHLENNYRSRDRK*IVLFPEGGFLRKSK<ETSQAFAKKNNLPFLTHV

Parental  TLPRSGA-TKIILNALVAQQENGSPAGGDAKELDSNSKG-LQWIIDATIAYPKAEPIDIQTWILGYRKPT
          TLPRS.A..K...NALVAQQENGSPAGGDAKELD..SK...QW.ID.TIAYPKAEPIDIQTWILGYRK..
Retrocopy TLPRSEA<NKMVSNALVAQQENGSPAGGDAKELDNKSKL<IQWMIDKTIAYPKAEPIDIQTWILGYRKSM

Parental  VTHVHYRIFPIKDVPLETDDLNNWLYQRFIEKEDLLSH-FYETGAFPPSKGHKEAVSREMSLSNMWIFLI
          V.HVHYRIFPIK.VPLETDDL.NWL..RF.EKEDLLSH.FYETGAFPPSKGHKEA.S.EM.LSNMWIFLI
Retrocopy VIHVHYRIFPIKYVPLETDDLTNWLNSRFMEKEDLLSH<FYETGAFPPSKGHKEAISKEMTLSNMWIFLI

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	14.22 RPM
SRP051959_heart	0.00 RPM	20.08 RPM
SRP051959_kidney	0.00 RPM	10.94 RPM
SRP051959_liver	0.00 RPM	22.74 RPM
SRP051959_lung	0.03 RPM	15.18 RPM
SRP051959_lymph_node	0.00 RPM	22.74 RPM
SRP051959_skeletal_muscle	0.00 RPM	9.30 RPM
SRP051959_spleen	0.02 RPM	17.10 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1127 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1127 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1127 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015870	1 retrocopy	retro_cjac_1127 ,