RetrogeneDB ID: retro_cjac_2348

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:71563621..71564696(+)
• Located in intron of: ENSCJAG00000009942

Retrocopy information

• Ensembl ID: ENSCJAG00000017330
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SCD
• Ensembl ID: ENSCJAG00000017338
• Aliases: None
• Description: None

Sequence

>retro_cjac_2348
CCAGCCCACTTGCTGCAGGAGGAGATCTCTAGCTCCTATACCACCACCACCACCACCATCACAGCGCCTCCCTCCAGGGT
CCCGCAGAATGGAGGATATAAGTTGGAGAAGACGCCCCTCTATTTGGAAGAAGACATTCGTCCTGATATAAAAGATGATA
TATATGACCCCACCTACAAGGATAAGGAAGGCCCAAGGCCCAAGGTTGAATATGTCTGGAGAAACATCATCCTGATGTCT
CTGCAACACTTGGGCGCCCTGTATGGGATCATTTTGATTCCTATCTGCAAGTTCTACACCTGGCTTTGGGGATTATTCTA
CTATTTTGTCAGTGCCCTGGGCATAACAGCAGGAGTTCATCGCCTGTGGAGCCACCGAACTTAAAAAGCTCGGCCGCCCC
TTCGGGTCTTTCTGATCGTTGCCAACACAATGGCATTCCAGAATGATGTCTTTTGAATGGGCTTGTGACCACCATGCCCA
CCACAAGTTTTCAGAAACAGATGCTGATCCTAATTCCCGACGTGGCTTTTTCTTCTCTCACGTGGGCTGGCTGCTTGTGC
GCAAACACCCAGCTGTCAAAGAGAAGGGCCTTATGCTGGACTTGTCTGACCTAAAAGCTGAGAAACTGGTGATGTTCCAG
AGGAGGTTCTACAAACCCGGCGTGGTGCTGATGTGCTTCATCCTGCCCACACTTGTGCCCTTTTATTTCTGGGGTGAAAC
TTTTCAACACAGCTTGTATGTTGCCACTTTCTTGCTATATGCTGTAGTGCTTAATGCCACCTGGCTAGTGAACAGTGCTG
CCTACCTCTACAGATATCGTCCTTATGACAAGAACATTAGCCCCTGGGAGAATGTCCTGGTTTCGCTTGGAGCTGTGGGT
GAGGGCTTCCACAACTACCACCACTCCTTTCCCTATGACTACTCTGCCAGTGAGTACCGCTGGCACATCAACTTAACCAC
ATTCTTCATTGATTGCGTGGCTGCCCTCAGTCTGGCCTATGACCGGAAGAAAGTCTCCAAGGCCACCATCTTGGCCAGGA
TTAAAAGAACTGGAGATGGAAGCTACAAGAGTGGC

Alignment

ORF - retro_cjac_2348 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.11 %
• Parental protein coverage: 99.72 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PGPAPQVQISSSYTTTTT-ITAPPSRVPQNGGDKLEKTPLYLEEDIRPDMKDDIYDPTYKDKEGPRPKVE
          P....Q..ISSSYTTTTT.ITAPPSRVPQNGG.KLEKTPLYLEEDIRPD.KDDIYDPTYKDKEGPRPKVE
Retrocopy PAHLLQEEISSSYTTTTTTITAPPSRVPQNGGYKLEKTPLYLEEDIRPDIKDDIYDPTYKDKEGPRPKVE

Parental  YVWRNIILMSLLHLGALYGIILIPTCKFYTWLWGLFYYFVSALGITAGVHRLWSHRTYKARLPLRVFLII
          YVWRNIILMSL.HLGALYGIILIP.CKFYTWLWGLFYYFVSALGITAGVHRLWSHRT.KAR.PLRVFLI.
Retrocopy YVWRNIILMSLQHLGALYGIILIPICKFYTWLWGLFYYFVSALGITAGVHRLWSHRT*KARPPLRVFLIV

Parental  ANTMAFQNDVF-EWARDHRAHHKFSETDADPHNSRRGFFFSHVGWLLVRKHPAVKEKGGTLDLSDLKAEK
          ANTMAFQNDVF.EWA.DH.AHHKFSETDADP.NSRRGFFFSHVGWLLVRKHPAVKEKG..LDLSDLKAEK
Retrocopy ANTMAFQNDVF>EWACDHHAHHKFSETDADP-NSRRGFFFSHVGWLLVRKHPAVKEKGLMLDLSDLKAEK

Parental  LVMFQRRYYKPGVLLMCFILPTLVPFYFWGETFQHSLYVATFLRYAVVLNATWLVNSAAHLYGYRPYDKN
          LVMFQRR.YKPGV.LMCFILPTLVPFYFWGETFQHSLYVATFL.YAVVLNATWLVNSAA.LY.YRPYDKN
Retrocopy LVMFQRRFYKPGVVLMCFILPTLVPFYFWGETFQHSLYVATFLLYAVVLNATWLVNSAAYLYRYRPYDKN

Parental  ISPRENILVSFGAVGEGFHNYHHSFPYDYSASEYRWHINLTTFFIDCMALLGLAYDRKKVSKAAILARIK
          ISP.EN.LVS.GAVGEGFHNYHHSFPYDYSASEYRWHINLTTFFIDC.A.L.LAYDRKKVSKA.ILARIK
Retrocopy ISPWENVLVSLGAVGEGFHNYHHSFPYDYSASEYRWHINLTTFFIDCVAALSLAYDRKKVSKATILARIK

Parental  RTGDGSYKSG
          RTGDGSYKSG
Retrocopy RTGDGSYKSG

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	29.60 RPM
SRP051959_heart	0.00 RPM	126.52 RPM
SRP051959_kidney	0.00 RPM	22.14 RPM
SRP051959_liver	0.50 RPM	2504.81 RPM
SRP051959_lung	0.00 RPM	49.47 RPM
SRP051959_lymph_node	0.02 RPM	4.09 RPM
SRP051959_skeletal_muscle	0.07 RPM	41.34 RPM
SRP051959_spleen	0.00 RPM	12.27 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2348 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2348 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2348 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017338	2 retrocopies	retro_cjac_1077, retro_cjac_2348 ,
Homo sapiens	ENSG00000099194	1 retrocopy	retro_hsap_1733,
Macaca mulatta	ENSMMUG00000010817	1 retrocopy	retro_mmul_1636,
Pongo abelii	ENSPPYG00000002566	1 retrocopy	retro_pabe_1545,
Pan troglodytes	ENSPTRG00000002847	1 retrocopy	retro_ptro_3058,
Drosophila melanogaster	FBgn0086687	1 retrocopy	retro_dmel_78,