RetrogeneDB ID: retro_cjac_2744

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:95780366..95780815(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000031153
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ARPC5L
• Ensembl ID: ENSCJAG00000006730
• Aliases: None
• Description: actin related protein 2/3 complex, subunit 5-like [Source:HGNC Symbol;Acc:23366]

Sequence

>retro_cjac_2744
GTGGCCCGGAACACGCTGTCCTCGCGTTTCTGCCGGGTGGGCATAGACGAATTTGACGAGAACAAATTTGCGGACGAGTA
GGAGGAGGCGGCGGCGGCGGAGCCAGGCCCGGACCCGAGCGAGGTGGAAGGGCTTCTGCGGCAAGGGACATACTTCAGGC
ATTCCAGGCAGGCTTGCGGAACTCTCCCGTCAACACCAAGAATCAAGCCGTGAAGGAAAGAGCCCAGGGTGTGGTGCTGA
AAGTGCTCACAAACTTCAAGAGCAGCGAGATTGAGCAGGCTGTGCAGTCACTGGACAGAAACGGCGTTGACTTGTTAATG
AAGTACATTTATAAAGGCTTTGAGACGCTCACAGAAAATAGCGCAGTGCTGCTCCAGTGGCATGAAAAGGCCTTAGCAGT
AGGAAGACTAGGCTCCATTATAAGAGTTCTTACAGCAAGAAAGACTGTT

Alignment

ORF - retro_cjac_2744 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.96 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MARNTLSSRFRRVDIDEFDENKFVDEQEEAAAAAAEPGPDPSEVDGLLRQG-DMLRAFHAALRNSPVNTK
          .ARNTLSSRF.RV.IDEFDENKF.DE.EEAAAA..EPGPDPSEV.GLLRQG.D.L.AF.A.LRNSPVNTK
Retrocopy VARNTLSSRFCRVGIDEFDENKFADE*EEAAAA--EPGPDPSEVEGLLRQG<DILQAFQAGLRNSPVNTK

Parental  NQAVKERAQGVVLKVLTNFKSSEIEQAVQSLDRNGVDLLMKYIYKGFEKPTENSSAVLLQWHEKALAVGG
          NQAVKERAQGVVLKVLTNFKSSEIEQAVQSLDRNGVDLLMKYIYKGFE..TEN.SAVLLQWHEKALAVG.
Retrocopy NQAVKERAQGVVLKVLTNFKSSEIEQAVQSLDRNGVDLLMKYIYKGFETLTEN-SAVLLQWHEKALAVGR

Parental  LGSIIRVLTARKTV
          LGSIIRVLTARKTV
Retrocopy LGSIIRVLTARKTV

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	0.02 RPM	10.32 RPM
SRP051959_heart	0.02 RPM	9.73 RPM
SRP051959_kidney	0.02 RPM	6.52 RPM
SRP051959_liver	0.00 RPM	6.76 RPM
SRP051959_lung	0.05 RPM	8.62 RPM
SRP051959_lymph_node	0.02 RPM	13.58 RPM
SRP051959_skeletal_muscle	0.02 RPM	9.65 RPM
SRP051959_spleen	0.02 RPM	8.68 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2744 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2744 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2744 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016540	1 retrocopy	retro_amel_1798,
Callithrix jacchus	ENSCJAG00000006730	4 retrocopies	retro_cjac_1282, retro_cjac_1725, retro_cjac_2744 , retro_cjac_3941,
Felis catus	ENSFCAG00000028753	1 retrocopy	retro_fcat_1316,
Macaca mulatta	ENSMMUG00000020628	2 retrocopies	retro_mmul_1650, retro_mmul_623,
Mustela putorius furo	ENSMPUG00000013924	1 retrocopy	retro_mputfur_1532,
Oryctolagus cuniculus	ENSOCUG00000002997	1 retrocopy	retro_ocun_518,
Procavia capensis	ENSPCAG00000013936	1 retrocopy	retro_pcap_274,
Pan troglodytes	ENSPTRG00000021362	1 retrocopy	retro_ptro_2185,
Rattus norvegicus	ENSRNOG00000014317	1 retrocopy	retro_rnor_2730,
Ictidomys tridecemlineatus	ENSSTOG00000007907	2 retrocopies	retro_itri_275, retro_itri_767,
Tupaia belangeri	ENSTBEG00000008398	1 retrocopy	retro_tbel_442,