RetrogeneDB ID: retro_cjac_4080

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:66127065..66127806(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUP50
• Ensembl ID: ENSCJAG00000016242
• Aliases: None
• Description: None

Sequence

>retro_cjac_4080
CAGTCTCTTTCCCTTTTTGGCTCAACAAAATTACAGCAAGAGTCAACGTTTTTGTTTCATGGCAACAAAACTGAAGATAC
ACCTGGAAAGAAGGTGGAGGTTGCAACTGAAAAGCAAACAGACCTATCACTAGGAGCAACAAGTGCCTCATTGAACTTCG
GCAAGAAAGTTGATAGCTCTGTTGTGGGCTAATTAAGCTCTGACCCCCTGACTGGATTTTCATTTTCCCCTGGAAATTCC
AGTTTATTTGGCAAAGATATTACCCAGAGTAAACCAGTCTCTTCACCATTTCCTGCTAAACCATTGGAGGGCCAAATAGA
AGGTGACAGTACTGAATGCAAAGGTGGAGATGACAAAGAGAGTGATGAGCCACCCAAAGTAGTAGTTACTGAAGTAAAAG
AAGACGATGCTTTTTACTTCCAAAAGTGTAAACTATTTTACAAGAAAGACAATGAGTTCAAAGAGAAAGGCATAGGTACC
CTGCATTTAAAACCTACAGTGAATCAGAAGACACAGCTTTTGGTGCGGGCAGACACCCATTTAGGCAACATATTGTTGAA
TGTTCTGATTCCGCCCAATATGCCATGTACCCAAACAGGGAAAAATAATGTTCTTATCATCTGTGTTCCAAATCCACCAA
CTGATGAGAAGAATGCCACCATCCCAGTTATCACGTTGATTTGGGTAAAAACCAGCGAGGATGCAGATGAGTTGCACAAA
ATTTTACTGGAGAAAAAGGAT

Alignment

ORF - retro_cjac_4080 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.88 %
• Parental protein coverage: 52.78 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QSLSLFGSTKLQQESVFLFHGNKTEDTPEKKVEVAAEKKTDPSLGATSASFNFGKKVDSSVVGSLSSVPL
          QSLSLFGSTKLQQES.FLFHGNKTEDTP.KKVEVA.EK.TD.SLGATSAS.NFGKKVDSSVVG.LSS.PL
Retrocopy QSLSLFGSTKLQQESTFLFHGNKTEDTPGKKVEVATEKQTDLSLGATSASLNFGKKVDSSVVG*LSSDPL

Parental  TGFSFSPGNSSLLGKDITQSKPVSSPFPAKPLEGQVEGDSSECKGGDEEESDEPPKVVVTEVKEDDAFYS
          TGFSFSPGNSSL.GKDITQSKPVSSPFPAKPLEGQ.EGDS.ECKGGD..ESDEPPKVVVTEVKEDDAFY.
Retrocopy TGFSFSPGNSSLFGKDITQSKPVSSPFPAKPLEGQIEGDSTECKGGDDKESDEPPKVVVTEVKEDDAFYF

Parental  KKCKLFYKKDNEFKEKGIGTLHLKPTVNQKTQLLVRADTNLGNILLNVLIPPNMPCTRTGKNNVLIVCVP
          .KCKLFYKKDNEFKEKGIGTLHLKPTVNQKTQLLVRADT.LGNILLNVLIPPNMPCT.TGKNNVLI.CVP
Retrocopy QKCKLFYKKDNEFKEKGIGTLHLKPTVNQKTQLLVRADTHLGNILLNVLIPPNMPCTQTGKNNVLIICVP

Parental  NPPIDEKNATVPVTMLIRVKTSEDAEELHKILLEKRD
          NPP.DEKNAT.PV..LI.VKTSEDA.ELHKILLEK.D
Retrocopy NPPTDEKNATIPVITLIWVKTSEDADELHKILLEKKD

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	20.81 RPM
SRP051959_heart	0.16 RPM	13.98 RPM
SRP051959_kidney	0.18 RPM	15.13 RPM
SRP051959_liver	0.04 RPM	19.73 RPM
SRP051959_lung	0.33 RPM	27.28 RPM
SRP051959_lymph_node	0.05 RPM	39.27 RPM
SRP051959_skeletal_muscle	0.02 RPM	9.59 RPM
SRP051959_spleen	0.08 RPM	30.27 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4080 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4080 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4080 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016242	1 retrocopy	retro_cjac_4080 ,
Homo sapiens	ENSG00000093000	3 retrocopies	retro_hsap_1429, retro_hsap_3301, retro_hsap_3434,
Microcebus murinus	ENSMICG00000006840	1 retrocopy	retro_mmur_534,
Mus musculus	ENSMUSG00000016619	1 retrocopy	retro_mmus_1905,
Nomascus leucogenys	ENSNLEG00000013154	2 retrocopies	retro_nleu_1359, retro_nleu_1844,
Otolemur garnettii	ENSOGAG00000002320	1 retrocopy	retro_ogar_942,
Pongo abelii	ENSPPYG00000011928	1 retrocopy	retro_pabe_2723,