RetrogeneDB ID: retro_cjac_2525

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:63577512..63578053(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RQCD1
• Ensembl ID: ENSCJAG00000011079
• Aliases: None
• Description: RCD1 required for cell differentiation1 homolog (S. pombe) [Source:HGNC Symbol;Acc:10445]

Sequence

>retro_cjac_2525
CCCACATTGACAGCACACCAAATTAACAGAGTTTGCAATGCTCTGGCATTACTGCAATGTGTAGCATCACATCCAGAAGC
CAGGTCAGCGTTTCTTGCAGCACACATCCACTTTTTTGTACCCCTTTTTTGCACACACGTCCCTTTGAGTATCTTTGACT
CACCAGCCTTGGAGTTATTGGGACCCTGGTGAAAACAGATGAACAAGGAGTAATCAACTTTTTACTGACAACAGAAATTA
TCCCTTTATGTTTGCGAATTATGGAATCTGGAAGTGAACTTTCTAAAACAGTTGCCACATTCATCCTCCAGAAGATCTTC
TTAGATGACACTGGTTTGGCTTATATATGTCAGACGTATGAGCGTTTCTCCCTTGTTGCCATGATCTTGGGTAAGATGGT
CCTGCAGTTATCCAAAGAGCCTTCTGCCCATCTGCTGAAGCATGTAGTGAGATGTTACATTCAACTCTCAGATAACCCAG
GGCACCTGAAGCACTCAGGCAGTGCCTCTCTGACCAGCTGAAGGACACAACCTTTGCTAAA

Alignment

ORF - retro_cjac_2525 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.77 %
• Parental protein coverage: 61.87 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PTLTAHQSNRVCNALALLQCVASHPETRSAFLAAHI-PLFLYPFLHTVSKTRPFEYLRLTSLGVIGALVK
          PTLTAHQ.NRVCNALALLQCVASHPE.RSAFLAAHI.PLF..PFLH....TRPFEYL.LTSLGVIG.LVK
Retrocopy PTLTAHQINRVCNALALLQCVASHPEARSAFLAAHI<PLFCTPFLH----TRPFEYL*LTSLGVIGTLVK

Parental  TDEQEVINFLLTTEIIPLCLRIMESGSELSKTVATFILQKILLDDTGLAYICQTYERFSHVAMILGKMVL
          TDEQ.VINFLLTTEIIPLCLRIMESGSELSKTVATFILQKI.LDDTGLAYICQTYERFS.VAMILGKMVL
Retrocopy TDEQGVINFLLTTEIIPLCLRIMESGSELSKTVATFILQKIFLDDTGLAYICQTYERFSLVAMILGKMVL

Parental  QLSKEPSARLLKHVVRCYLRLSDN-PRAREALRQCLPDQLKDTTFAQ
          QLSKEPSA.LLKHVVRCY..LSDN.PRA.EALRQCL.DQLKDTTFA.
Retrocopy QLSKEPSAHLLKHVVRCYIQLSDN<PRAPEALRQCLSDQLKDTTFAK

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	5.86 RPM
SRP051959_heart	0.00 RPM	4.35 RPM
SRP051959_kidney	0.00 RPM	5.79 RPM
SRP051959_liver	0.00 RPM	3.77 RPM
SRP051959_lung	0.00 RPM	6.98 RPM
SRP051959_lymph_node	0.00 RPM	7.44 RPM
SRP051959_skeletal_muscle	0.00 RPM	5.28 RPM
SRP051959_spleen	0.00 RPM	6.68 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2525 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2525 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2525 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000011079	1 retrocopy	retro_cjac_2525 ,
Drosophila melanogaster	FBgn0031047	1 retrocopy	retro_dmel_75,