RetrogeneDB ID: retro_cjac_1687

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 18:37965542..37965989(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DCTN5
• Ensembl ID: ENSCJAG00000020623
• Aliases: None
• Description: dynactin 5 (p25) [Source:HGNC Symbol;Acc:24594]

Sequence

>retro_cjac_1687
GTGGAGTTGGGTGAGCTGCTCTACAACAAGTCTGAGTACATCGAGGCAGCGTCTGGGAACAAAGTCAGTTGCCGGTCAGT
GTTGTGTGGAATCTAGACCATCGTTCTCAATGGCAAGACTGTTGTGACGAATGACTGTATTATCCTAGCGGATCTGGCAA
ACGTAAGAGTTGGACGCCATGGTGTTGTGAAAAGTTGTAGTGTCATAAGGCCACCATTCAAGACATTCAGCAAAGGTGTT
GCATTCTTTCCTTTACATATTGGGGACCATGTCTTTATTGAGGAAGATTATATGGTCAACGCAGCTCAGATTGGTTCCTA
TGTTGGCAAGAGCTGGGTGACTGGGTGCTGGTGTGTGTTGAAAGACTGCTGCAGAATTCTTGATGACGCAGTATTATCTC
CAGAAACTGTGGCCCCACTGGTCACTGTCTTCTCAGGCTGCCCAGGA

Alignment

ORF - retro_cjac_1687 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.13 %
• Parental protein coverage: 82.97 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MELGELLYNKSEYIETASGNKVSRQSVLCGSQNIVLNGKTIVMNDCIIRGDLANVRVGRHCVVKSRSVIR
          .ELGELLYNKSEYIE.ASGNKVS..SVLCG...IVLNGKT.V.NDCII..DLANVRVGRH.VVKS.SVIR
Retrocopy VELGELLYNKSEYIEAASGNKVSCRSVLCGI*TIVLNGKTVVTNDCIILADLANVRVGRHGVVKSCSVIR

Parental  PPFKKFSKGVAFFPLHIGDHVFIEEDCVVNAAQIGSYVHVGKNCVIGRRCVLKDCCKILDNTVLPPETVV
          PPFK.FSKGVAFFPLHIGDHVFIEED..VNAAQIGSY..VGK..V.G..CVLKDCC.ILD..VL.PETV.
Retrocopy PPFKTFSKGVAFFPLHIGDHVFIEEDYMVNAAQIGSY--VGKSWVTGCWCVLKDCCRILDDAVLSPETVA

Parental  PPFTVFSGCPG
          P..TVFSGCPG
Retrocopy PLVTVFSGCPG

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	11.54 RPM
SRP051959_heart	0.02 RPM	9.16 RPM
SRP051959_kidney	0.00 RPM	10.94 RPM
SRP051959_liver	0.00 RPM	7.06 RPM
SRP051959_lung	0.00 RPM	13.01 RPM
SRP051959_lymph_node	0.00 RPM	11.92 RPM
SRP051959_skeletal_muscle	0.00 RPM	6.75 RPM
SRP051959_spleen	0.00 RPM	13.13 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1687 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1687 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1687 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006410	1 retrocopy	retro_btau_1203,
Callithrix jacchus	ENSCJAG00000020623	1 retrocopy	retro_cjac_1687 ,
Homo sapiens	ENSG00000166847	1 retrocopy	retro_hsap_260,
Gorilla gorilla	ENSGGOG00000012834	1 retrocopy	retro_ggor_309,
Microcebus murinus	ENSMICG00000007806	1 retrocopy	retro_mmur_1082,
Myotis lucifugus	ENSMLUG00000012148	1 retrocopy	retro_mluc_140,
Mus musculus	ENSMUSG00000030868	2 retrocopies	retro_mmus_2733, retro_mmus_625,
Nomascus leucogenys	ENSNLEG00000012015	1 retrocopy	retro_nleu_863,
Pongo abelii	ENSPPYG00000007194	2 retrocopies	retro_pabe_1729, retro_pabe_405,
Pan troglodytes	ENSPTRG00000007891	1 retrocopy	retro_ptro_220,
Rattus norvegicus	ENSRNOG00000018048	2 retrocopies	retro_rnor_1351, retro_rnor_1847,