RetrogeneDB ID: retro_cjac_3566

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: ACFV01184814.1:6355..6853(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LTBP4
• Ensembl ID: ENSCJAG00000037941
• Aliases: None
• Description: None

Sequence

>retro_cjac_3566
AATCTCAGCTCACTGCAACTTCTGCTTCCCAGGTTGAAGCAGTTCCCCTGACTCAGCCTCCCAAGTAGCTGGGATTACAG
GCACGCGCCACCATGTTTGCCTAATTTTGTATTTTTAGTAGAAATAGGGTTTCTGCATGTTGGTCAGGCTGCTCTTGAAC
TCCTGACCTCAGGTGATCCATTCACCTTGGCCTCCCAAAGTGCTGAGATTACAGGCATGAGCCACCACACCGGGTTTTGT
TTTTGAGATGGAGTCTTGCTCTGTCTTCCAGGCTGAAGTGCAGTGGGATGATCTCGGAACACTACAACCTCCACCTCCTA
GGTTCAAGCAATTCTCCTGCCTCAGCTTCCTGAGTAGCTGAGATTGTAGGCACGTGCCACCACGCTGGGCTGATTTTTGT
AGTTTTAGTGGAGTCAGGGTTTCACCATGTTGGCCAGGCTGGTCTTGAACTTCTGACCTCAGGTGATTCACCCACCTCAG
CCTCCCAAAGTGCTGGGA

Alignment

ORF - retro_cjac_3566 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.8 %
• Parental protein coverage: 92.22 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DLGSLQPPPPGFKRFSCLSLPSSWDYRRTPPCPANFLVLLPTGFCHVGKAGLKFLASSDPPIFASQSAGI
          .L.SLQ...P..K.F..LSLPSSWDYR..PPC..NF..L...GF.HVG.A.L..L.S.DP...ASQSA.I
Retrocopy NLSSLQLLLPRLKQFP*LSLPSSWDYRHAPPCLPNFVFLVEIGFLHVGQAALELLTSGDPFTLASQSAEI

Parental  TGVSHSAENRLNIRVSLPLP-RLERNGAILAHCNLHLLGSGNSPASASRVAGITGTRHHAQLIF-FLVET
          TG.SH.........V.L.LP.RL...G.I..H.NLHLLGS.NSPASAS.VA.I.GT.HHA.LIF..LVE.
Retrocopy TGMSHHTGFCF*DGVLLCLP<RLKCSGMISEHYNLHLLGSSNSPASAS*VAEIVGTCHHAGLIFVVLVES

Parental  GFHHVDQDGWSST-PDLVIHPPRPPKVLG
          GFHHV.Q.G.....P.....P..PPKVLG
Retrocopy GFHHVGQAGLELL>PQVIHPP-QPPKVLG

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	13.16 RPM
SRP051959_heart	0.02 RPM	81.88 RPM
SRP051959_kidney	0.00 RPM	6.41 RPM
SRP051959_liver	0.00 RPM	1.04 RPM
SRP051959_lung	0.00 RPM	17.91 RPM
SRP051959_lymph_node	0.02 RPM	4.06 RPM
SRP051959_skeletal_muscle	0.00 RPM	8.63 RPM
SRP051959_spleen	0.00 RPM	13.36 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3566 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3566 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3566 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017963	3 retrocopies	retro_cjac_3822, retro_cjac_3823, retro_cjac_3993,
Callithrix jacchus	ENSCJAG00000037941	35 retrocopies	retro_cjac_3343, retro_cjac_3355, retro_cjac_3369, retro_cjac_3372, retro_cjac_3389, retro_cjac_3391, retro_cjac_3423, retro_cjac_3425, retro_cjac_3430, retro_cjac_3445, retro_cjac_3456, retro_cjac_3474, retro_cjac_3476, retro_cjac_3477, retro_cjac_3487, retro_cjac_3491, retro_cjac_3543, retro_cjac_3545, retro_cjac_3547, retro_cjac_3549, retro_cjac_3566 , retro_cjac_3583, retro_cjac_3598, retro_cjac_3609, retro_cjac_3616, retro_cjac_3622, retro_cjac_3633, retro_cjac_3641, retro_cjac_3656, retro_cjac_3672, retro_cjac_3674, retro_cjac_3677, retro_cjac_3682, retro_cjac_3733, retro_cjac_3736,