RetrogeneDB ID: retro_cjac_1497

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 16:12116723..12117071(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUDT15
• Ensembl ID: ENSCJAG00000009274
• Aliases: None
• Description: nudix (nucleoside diphosphate linked moiety X)-type motif 15 [Source:HGNC Symbol;Acc:23063]

Sequence

>retro_cjac_1497
GTCGGAGCAGGGAAGACCAGCTGCAGGCATCGCGTTGTGTCCTCCTGGGGAAGAGGAACGGGTCATCTGAAGCTGGCAGT
TTCCAACTTTCTGCGGATCATTTAGAGTTCGGTGAGAGCTGGGAAGAATGCACTCAAAAGGAAACTTGGAAAGAAGCAGC
TCTTCACCTGAAAATGTTTGCTTTGCCTCAGTTGAGAATTATTTCGTTGAGAAAGAGAATTACCATGTTACCATGTTTAC
CAAAGGAGGGCTGGACGCGACACATGATTCAGAACCACAGAATGTAGAGCCTGAAAAATGGACTGTGTTTCTTGGGAAGA
ATTTCCTCTACTAGATCAACTTCTCTGG

Alignment

ORF - retro_cjac_1497 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.55 %
• Parental protein coverage: 73.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VGVVVTSCKH-PGCVLLGKRKGSVGAGSFQLPGGHLEFGESWEECAQRETWEEAALHLK-NVRFASVVNS
          VG...TSC.H...CVLLGKR.GS..AGSFQL...HLEFGESWEEC.Q.ETW.EAALHLK.NV.FASV.N.
Retrocopy VGAGKTSCRH<SRCVLLGKRNGSSEAGSFQLSADHLEFGESWEECTQKETWKEAALHLK<NVCFASVENY

Parental  FIEKENYHYVTILMKGEVDVTHDSEPKNVEPEKNESW-EWVPWEEFPPLDQLFW
          F.EKENYH.VT...KG..D.THDSEP.NVEP...E.W...V.WEEFP.LDQL.W
Retrocopy FVEKENYH-VTMFTKGGLDATHDSEPQNVEP---EKW<DCVSWEEFPLLDQLLW

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	2.33 RPM
SRP051959_heart	0.00 RPM	2.09 RPM
SRP051959_kidney	0.00 RPM	2.55 RPM
SRP051959_liver	0.09 RPM	2.23 RPM
SRP051959_lung	0.00 RPM	1.71 RPM
SRP051959_lymph_node	0.00 RPM	3.17 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.98 RPM
SRP051959_spleen	0.00 RPM	3.09 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1497 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1497 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1497 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019501	1 retrocopy	retro_btau_559,
Callithrix jacchus	ENSCJAG00000009274	1 retrocopy	retro_cjac_1497 ,
Homo sapiens	ENSG00000136159	2 retrocopies	retro_hsap_1822, retro_hsap_4063,
Gorilla gorilla	ENSGGOG00000008232	3 retrocopies	retro_ggor_2171, retro_ggor_2257, retro_ggor_2729,
Microcebus murinus	ENSMICG00000009583	1 retrocopy	retro_mmur_962,
Mus musculus	ENSMUSG00000033405	1 retrocopy	retro_mmus_1923,
Nomascus leucogenys	ENSNLEG00000002957	2 retrocopies	retro_nleu_2878, retro_nleu_563,
Pongo abelii	ENSPPYG00000005353	2 retrocopies	retro_pabe_1490, retro_pabe_3337,
Pan troglodytes	ENSPTRG00000042329	1 retrocopy	retro_ptro_82,
Tarsius syrichta	ENSTSYG00000006960	1 retrocopy	retro_tsyr_146,