RetrogeneDB ID: retro_cjac_333

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:8640758..8641310(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000022869
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000014728
• Aliases: None
• Description: None

Sequence

>retro_cjac_333
ATGGAAATCCCCGCTATCCGGAGTTGTTCGTCTCCCTGTCCGGACTGCTCGGGGCTCCCAGTGTCCAGGGAGCTGCTGAC
TGCGGGATGCGACGGCCATGGAGGTATATGGGACAGGTCGTTCATCAATCCCCAACCTAAGTCCAGAAAGACCTCCACTA
TTCAAACAGTCCGGATAGAAAGGAGTCCCTTACTGGGTCAGGTACAGACCTTTGTCCCACAGATGGCACAGGCAAACGAA
AAGCTAAGAAAAGAAATGGCAGCTGCACTACCTGGTCGTTTCAATATTGAAAACATTGATGGGACTCATGGCAAAGTTAT
ACAAACGGATGTGGCTCAGTTTGAGATGAATCAGTCAGATTCAAAAGAAGTAGACAGTTCAGGGGAGAGTTCACAAGACA
GTTCAGAGAACAGTTCAGAATCAGAGGATGAAGATGAGAGCATCCCATCTGAAGTCACCATAGATAACATTAAGCTTCCC
AATTCTGAAGGTGGAAAAGGCAAGATTGAAGTTTTGGACAGTCCAGCAAGTATAAAAAAGAAATACTCAAAT

Alignment

ORF - retro_cjac_333 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.51 %
• Parental protein coverage: 94.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SCSSPSRDCSGVPVSRELLTTGSDGRGGLWDRLLINPQPKSRKTSTLQTVRIERSPLLDQVQTFLPQMAQ
          SCSSP..DCSG.PVSRELLT.G.DG.GG.WDR..INPQPKSRKTST.QTVRIERSPLL.QVQTF.PQMAQ
Retrocopy SCSSPCPDCSGLPVSRELLTAGCDGHGGIWDRSFINPQPKSRKTSTIQTVRIERSPLLGQVQTFVPQMAQ

Parental  ANEKLRKEMAAAPPGRFNIENIDGTHGKVIQMDVALFEMNRSDSKEADSSEESSQDSSENSSESEDEDDS
          ANEKLRKEMAAA.PGRFNIENIDGTHGKVIQ.DVA.FEMN.SDSKE.DSS.ESSQDSSENSSESEDED.S
Retrocopy ANEKLRKEMAAALPGRFNIENIDGTHGKVIQTDVAQFEMNQSDSKEVDSSGESSQDSSENSSESEDEDES

Parental  IPSEVTIDNIKLPNSEGGKGKIEVLDSPASKKKK
          IPSEVTIDNIKLPNSEGGKGKIEVLDSPAS.KKK
Retrocopy IPSEVTIDNIKLPNSEGGKGKIEVLDSPASIKKK

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	0.40 RPM	3.62 RPM
SRP051959_heart	0.39 RPM	4.47 RPM
SRP051959_kidney	0.07 RPM	6.26 RPM
SRP051959_liver	4.33 RPM	5.05 RPM
SRP051959_lung	0.24 RPM	5.43 RPM
SRP051959_lymph_node	0.07 RPM	10.25 RPM
SRP051959_skeletal_muscle	0.00 RPM	3.54 RPM
SRP051959_spleen	0.19 RPM	8.15 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_333 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_333 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_333 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014728	1 retrocopy	retro_cjac_333 ,
Dasypus novemcinctus	ENSDNOG00000017235	1 retrocopy	retro_dnov_2327,
Homo sapiens	ENSG00000151131	1 retrocopy	retro_hsap_292,
Gallus gallus	ENSGALG00000012694	1 retrocopy	retro_ggal_15,
Gorilla gorilla	ENSGGOG00000027272	1 retrocopy	retro_ggor_331,
Macaca mulatta	ENSMMUG00000017133	1 retrocopy	retro_mmul_551,
Nomascus leucogenys	ENSNLEG00000006584	1 retrocopy	retro_nleu_2414,
Pongo abelii	ENSPPYG00000004897	1 retrocopy	retro_pabe_382,
Pan troglodytes	ENSPTRG00000005381	1 retrocopy	retro_ptro_240,
Sus scrofa	ENSSSCG00000027792	2 retrocopies	retro_sscr_105, retro_sscr_153,
Tursiops truncatus	ENSTTRG00000005714	1 retrocopy	retro_ttru_1381,