RetrogeneDB ID: retro_cjac_2447

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:63151378..63151816(-)
• Located in intron of: ENSCJAG00000031425

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM98
• Ensembl ID: ENSCJAG00000014550
• Aliases: None
• Description: transmembrane protein 98 [Source:HGNC Symbol;Acc:24529]

Sequence

>retro_cjac_2447
CTGCTCCAGCACTATTATTCCAAGCCCATTTTGAGTCTCTTGGGTAACATGGATACCCAATCTGAACTCACTGAGTTAGA
ATTGAATTATGTCACTACCAACTCCCGCATAGAGGTCATTCTGGAGAATGAAGACTGGATCTAGGATGCCTTGGGTCTCA
TGTCCCACTGCATTGTCATCTTGAAGATTTGTCACACTTGGAGAGAAAAACTTGTTGCCATGACAATGGGCTCAGAGGCT
GAGAAGAAGACTTCAGTCAGTGTCAGCAACATCATTGTGGCAGCCACGTGGATCATTCCCAGAGTAGATAATGTTGTGAA
ATCAATGTACCCTCTGTTGGGCACCAAACTCCTGAATTTGTGTATGACTGCTCTGCTCCTATCTGTTAGTCATCAGGTGC
TGGTGACCAGAAATGCCTGCCATCTGACCAGGGGCCTC

Alignment

ORF - retro_cjac_2447 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.79 %
• Parental protein coverage: 65.04 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LLQRYDSKPIVDLIGAMETQSEPSELELDDVVITNPHIEAILENEDWIEDASGLMSHCIAILKICHTLTE
          LLQ.Y.SKPI..L.G.M.TQSE..ELEL...V.TN..IE.ILENEDWI.DA.GLMSHCI.ILKICHT..E
Retrocopy LLQHYYSKPILSLLGNMDTQSELTELELN-YVTTNSRIEVILENEDWI*DALGLMSHCIVILKICHTWRE

Parental  KLVAMTMGSGAKMKTSASVSDIIVVAKRISPRVDDVVKSMYPPLDPKLLDARTTALLLSVSHLVLVTRNA
          KLVAMTMGS.A..KTS.SVS.IIV.A..I.PRVD.VVKSMYP.L..KLL....TALLLSVSH.VLVTRNA
Retrocopy KLVAMTMGSEAEKKTSVSVSNIIVAATWIIPRVDNVVKSMYPLLGTKLLNLCMTALLLSVSHQVLVTRNA

Parental  CHLTGGL
          CHLT.GL
Retrocopy CHLTRGL

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	9.56 RPM
SRP051959_heart	0.00 RPM	8.05 RPM
SRP051959_kidney	0.00 RPM	3.31 RPM
SRP051959_liver	0.00 RPM	0.63 RPM
SRP051959_lung	0.00 RPM	11.01 RPM
SRP051959_lymph_node	0.00 RPM	1.16 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.37 RPM
SRP051959_spleen	0.00 RPM	3.47 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2447 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2447 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2447 has 6 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3605
Pan troglodytes	retro_ptro_2436
Pan troglodytes	retro_ptro_2990
Gorilla gorilla	retro_ggor_2432
Pongo abelii	retro_pabe_2961
Macaca mulatta	retro_mmul_1835

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014550	1 retrocopy	retro_cjac_2447 ,
Homo sapiens	ENSG00000006042	2 retrocopies	retro_hsap_1421, retro_hsap_3605,
Gorilla gorilla	ENSGGOG00000013333	2 retrocopies	retro_ggor_1098, retro_ggor_2432,
Myotis lucifugus	ENSMLUG00000001191	1 retrocopy	retro_mluc_130,
Macaca mulatta	ENSMMUG00000022356	2 retrocopies	retro_mmul_1835, retro_mmul_2256,
Nomascus leucogenys	ENSNLEG00000006038	3 retrocopies	retro_nleu_1233, retro_nleu_1840, retro_nleu_2635,
Pongo abelii	ENSPPYG00000008166	2 retrocopies	retro_pabe_1175, retro_pabe_2961,
Pan troglodytes	ENSPTRG00000008993	3 retrocopies	retro_ptro_2436, retro_ptro_2990, retro_ptro_971,