RetrogeneDB ID: retro_cjac_2486

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:150066869..150067168(-)
• Located in intron of: ENSCJAG00000019580

Retrocopy information

• Ensembl ID: ENSCJAG00000032986
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FABP12
• Ensembl ID: ENSCJAG00000000433
• Aliases: None
• Description: fatty acid binding protein 12 [Source:HGNC Symbol;Acc:34524]

Sequence

>retro_cjac_2486
CTGTCGATCAGCAGAAATGGAGATGTGATCTCTACAAAAATGAAAAGCATCTTTAAAAATAACGAAATTGCTTTTAAACC
TAGAAAAGAATTTGAGGAAACCACACCAGGTGGCCATAAAATCAAGAGTATCCCACCCTTAGATAATGACTCCTTGATTC
AGGTTCGGGACTGGGATCACAAGGATACCCCAATGGGAGAAAGTTGGTGGTTGAGAAAGTGGGGGTAGCAAATGCCGTGA
ACAATATTACCTATGCTCAGATATAGGAGAGAGAATGAACAAATTCAGCCTCAATCTCT

Alignment

ORF - retro_cjac_2486 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.46 %
• Parental protein coverage: 71.43 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VTISTDGDVITIKTKSIFKNNEISFKLGEEFEEVTPAGHKTKNKVTLDNESLIQVQDWDGKETTI-TRKL
          ..IS..GDVI..K.KSIFKNNEI.FK...EFEE.TP.GHK.K....LDN.SLIQV.DWD.K.T....RKL
Retrocopy LSISRNGDVISTKMKSIFKNNEIAFKPRKEFEETTPGGHKIKSIPPLDNDSLIQVRDWDHKDTPM<GRKL

Parental  VDGKMVVESTVNNVICTRTYEKVSSNSVSNS
          V..K..V...VNN.......E....NS.S.S
Retrocopy VVEKVGVANAVNNITYAQI*ERE*TNSASIS

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	0.00 RPM
SRP051959_heart	0.00 RPM	0.00 RPM
SRP051959_kidney	0.00 RPM	0.00 RPM
SRP051959_liver	0.00 RPM	0.00 RPM
SRP051959_lung	0.00 RPM	0.07 RPM
SRP051959_lymph_node	0.00 RPM	0.00 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.00 RPM
SRP051959_spleen	0.00 RPM	0.00 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2486 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2486 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2486 has 6 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3679
Pan troglodytes	retro_ptro_2493
Gorilla gorilla	retro_ggor_2488
Pongo abelii	retro_pabe_3016
Macaca mulatta	retro_mmul_1787
Equus caballus	retro_ecab_761

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014554	1 retrocopy	retro_amel_945,
Callithrix jacchus	ENSCJAG00000000433	1 retrocopy	retro_cjac_2486 ,
Callithrix jacchus	ENSCJAG00000000444	4 retrocopies	retro_cjac_1832, retro_cjac_2227, retro_cjac_2816, retro_cjac_4084,
Equus caballus	ENSECAG00000023552	1 retrocopy	retro_ecab_761,
Homo sapiens	ENSG00000197416	1 retrocopy	retro_hsap_3679,
Gorilla gorilla	ENSGGOG00000016835	1 retrocopy	retro_ggor_2488,
Latimeria chalumnae	ENSLACG00000008511	3 retrocopies	retro_lcha_37, retro_lcha_45, retro_lcha_57,
Microcebus murinus	ENSMICG00000005319	1 retrocopy	retro_mmur_1131,
Macaca mulatta	ENSMMUG00000019337	1 retrocopy	retro_mmul_1787,
Nomascus leucogenys	ENSNLEG00000002515	1 retrocopy	retro_nleu_528,
Oryzias latipes	ENSORLG00000008282	1 retrocopy	retro_olat_7,
Pongo abelii	ENSPPYG00000018703	1 retrocopy	retro_pabe_3016,
Pan troglodytes	ENSPTRG00000022654	1 retrocopy	retro_ptro_2493,