RetrogeneDB ID: retro_cjac_4095

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:83183453..83183780(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000008256
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FAM133B
• Ensembl ID: ENSCJAG00000013910
• Aliases: None
• Description: family with sequence similarity 133, member B [Source:HGNC Symbol;Acc:28629]

Sequence

>retro_cjac_4095
ATGGGGAAGCGGGATAATCGGGTAGCTTATATGAATCCTATAGCAATGGCCAGATGGAGAGGCCCAACTCAATCTGTGGG
CCCAACAATCCAAGATTATCTGAATCGACCAAGGCCCACCTGGGAAGAAGTAAAGAAACAATTAGAAAATAAAAAAAGAG
GCTCAAAAGCATTAGCTGAATTTGAAGAAAAAATGAATGAAAATTGGAAGAAAGAACTTGAAAAAAGCAGACAGAAATTA
TTAAGTGGAAATGAGAGCTCCTCTAAAAAAAAAGAAAGAAAGAGAAAGAGAAAGAAGAAATCTTGTCGGTCTTCATCTCC
TTCATCA

Alignment

ORF - retro_cjac_4095 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.49 %
• Parental protein coverage: 98.2 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGKRDNRVAYMNPIAMARSRGPIQSSGPTIQDYLNRPRPTWEEVKEQLEKKKKGSKALAEFEEKMNENWK
          MGKRDNRVAYMNPIAMAR.RGP.QS.GPTIQDYLNRPRPTWEEVK.QLE.KK.GSKALAEFEEKMNENWK
Retrocopy MGKRDNRVAYMNPIAMARWRGPTQSVGPTIQDYLNRPRPTWEEVKKQLENKKRGSKALAEFEEKMNENWK

Parental  KELEKHREKLLSGSESSSKKRQRKKKEKKKSGRVSKSFS
          KELEK.R.KLLSG.ESSSKK..RK.K.KKKS.R.S...S
Retrocopy KELEKSRQKLLSGNESSSKKKERKRKRKKKSCRSSSPSS

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	7.06 RPM
SRP051959_heart	0.00 RPM	7.23 RPM
SRP051959_kidney	0.00 RPM	9.54 RPM
SRP051959_liver	0.00 RPM	5.98 RPM
SRP051959_lung	0.00 RPM	9.39 RPM
SRP051959_lymph_node	0.00 RPM	12.19 RPM
SRP051959_skeletal_muscle	0.00 RPM	5.28 RPM
SRP051959_spleen	0.00 RPM	12.29 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4095 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4095 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4095 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007438	1 retrocopy	retro_amel_102,
Callithrix jacchus	ENSCJAG00000013910	3 retrocopies	retro_cjac_1084, retro_cjac_1163, retro_cjac_4095 ,
Equus caballus	ENSECAG00000026810	1 retrocopy	retro_ecab_95,
Homo sapiens	ENSG00000234545	4 retrocopies	retro_hsap_2336, retro_hsap_3179, retro_hsap_55, retro_hsap_577,
Loxodonta africana	ENSLAFG00000029755	1 retrocopy	retro_lafr_594,
Myotis lucifugus	ENSMLUG00000005933	1 retrocopy	retro_mluc_2301,
Macaca mulatta	ENSMMUG00000019802	4 retrocopies	retro_mmul_1415, retro_mmul_226, retro_mmul_420, retro_mmul_765,
Mus musculus	ENSMUSG00000058503	2 retrocopies	retro_mmus_3481, retro_mmus_3519,
Nomascus leucogenys	ENSNLEG00000015333	1 retrocopy	retro_nleu_14,
Pongo abelii	ENSPPYG00000025825	1 retrocopy	retro_pabe_225,
Rattus norvegicus	ENSRNOG00000009163	1 retrocopy	retro_rnor_2891,
Sus scrofa	ENSSSCG00000015317	1 retrocopy	retro_sscr_49,
Ictidomys tridecemlineatus	ENSSTOG00000028195	1 retrocopy	retro_itri_12,
Tupaia belangeri	ENSTBEG00000011674	1 retrocopy	retro_tbel_1,