RetrogeneDB ID: retro_cjac_2994

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:78919062..78919598(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTX3
• Ensembl ID: ENSCJAG00000019700
• Aliases: None
• Description: metaxin 3 [Source:HGNC Symbol;Acc:24812]

Sequence

>retro_cjac_2994
AATAACATTGTTTCTTAGCTGGTAAAAGTGTTAAACTTTTAAAGAAAACAGAAATATAATGCTGATTATGAACCTCCAGC
AAAAGGAAGGACAGATAGATACACTGGCTTTCACTGCTCTCCTCAAACAGAAGCTGTCTCCTTCTAGTGCTTCGCACACA
ATCAGTTGAAAGCAACAATCAGTTTACTGTGACTAAGCTGTGGTGTTGGTTTGCTTCATAGATTCCTTTTCCCTTGGGTT
TGATCCTGCCTGGAAAAATACCTGAAAGAGCACTATTAGAATTCTCCTGACCAGAAGAGAGCCTCTCCGCCTGTGCGAAG
CAGAATCACGGATCTGCAGAGACACTAAGAAGTGCCTAAATCTTCTGTCAGATAAATTGTGACCATCTCAGTTTCTCCTT
GGGGATACCCATTCTACTTTGGTTACCCACATTTGGTTTCCTTGCACCTCTGCATACGGCGCCCTCTCCTAAAGTTCAGT
TACAGGAACATTTGAAACATGTCTCCAACCTGCGATCCTTTTGCAATGCTATCCTA

Alignment

ORF - retro_cjac_2994 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.92 %
• Parental protein coverage: 57.05 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  DNIVSQPAKILNFLRKQKYNADYE-LSAKQGA-DTLAYIALLEEKLLPA-VLHTFWVESDNYFTVTKPW-
          .NIVS...K.LNF.RKQKYNADYE.L..K.G..DTLA..ALL..KL.P..VL.T..VES.N.FTVTK.W.
Retrocopy NNIVS*LVKVLNF*RKQKYNADYE>LQQKEGQIDTLAFTALLKQKLSPS>VLRTQSVESNNQFTVTKLWC

Parental  -FASQIPFPLSLILPGRMSRGALN-RILLTRGQPPLYHLREVEAQIYRDAKECLNLLSNRLGTSQ-FFFG
          .FAS.IPFPL.LILPG.....AL..RILLTR..P....L.E.E..I.RD.K.CLNLLS..L..SQ.F..G
Retrocopy WFAS*IPFPLGLILPGKIPERALL<RILLTRREP--LRLCEAESRICRDTKKCLNLLSDKL*PSQ>FSLG

Parental  NTPSTLDAYVFGFLAPLYKVRFPKIQLQEHLKQLSNLCRFCDDIL
          ..P..L....FGFLAPL.....PK.QLQEHLK..SNL..FC..IL
Retrocopy -IPILLWLPTFGFLAPLHTAPSPKVQLQEHLKHVSNLRSFCNAIL

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	2.55 RPM
SRP051959_heart	0.00 RPM	3.75 RPM
SRP051959_kidney	0.00 RPM	2.73 RPM
SRP051959_liver	0.00 RPM	2.06 RPM
SRP051959_lung	0.00 RPM	4.20 RPM
SRP051959_lymph_node	0.00 RPM	4.36 RPM
SRP051959_skeletal_muscle	0.00 RPM	1.70 RPM
SRP051959_spleen	0.00 RPM	3.97 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2994 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2994 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2994 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010893	1 retrocopy	retro_chof_1828,
Callithrix jacchus	ENSCJAG00000019700	1 retrocopy	retro_cjac_2994 ,
Macaca mulatta	ENSMMUG00000021104	1 retrocopy	retro_mmul_489,
Vicugna pacos	ENSVPAG00000009404	1 retrocopy	retro_vpac_626,