RetrogeneDB ID:

retro_cjac_3456

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:ACFV01180525.1:2601..3099(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:LTBP4
Ensembl ID:ENSCJAG00000037941
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_3456
AATCTCAGCTCACTGCAACTTCTGCTTCCCAGGTTGAAGCAGTTCCCCTGACTCAGCCTCCCAAGTAGCTGGGATTACAG
GCACGCACCACCATGTTTGCCTAATTTTGTATTTTTAGTAGAGATAGGGTTTCTGCATGTTGGTCAGGCTGCTCTTGAAC
TCCTGACCTCAGGTGATCCATTCACCTTGGCCTCCCAAAGTGCTGAGATTACAGGCATGAGACACCACACCGGGTTTTGT
TTTTGAGATGGAGTCTTGCTCTGTCTTCCAGGCTGGAGTGCAGTGGGATGATCTCGGCACACTACAACCTCCACCTCCTG
GGCTCAAGCAATTCTCCTGCCTCAGCTTCCTGAGTAGCTGAGATTGTAGGCACGTGCCACCACGCTGGGCTGATTTTTGT
AGTTTTAGTGGAGTCAGGGTTTCACCATGTTGGCCAGGCTGGTCTTGAACTTCTGACCTCAGGTGATTCACCCACCTCGG
CCTCCCAAAGTGCTGGGA

ORF - retro_cjac_3456 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 57.99 %
Parental protein coverage: 92.22 %
Number of stop codons detected: 3
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalDLGSLQPPPPGFKRFSCLSLPSSWDYRRTPPCPANFLVLLPTGFCHVGKAGLKFLASSDPPIFASQSAGI
.L.SLQ...P..K.F..LSLPSSWDYR..PPC..NF..L...GF.HVG.A.L..L.S.DP...ASQSA.I
RetrocopyNLSSLQLLLPRLKQFP*LSLPSSWDYRHAPPCLPNFVFLVEIGFLHVGQAALELLTSGDPFTLASQSAEI
ParentalTGVSHSAENRLNIRVSLPLP-RLERNGAILAHCNLHLLGSGNSPASASRVAGITGTRHHAQLIF-FLVET
TG..H.........V.L.LP.RLE..G.I.AH.NLHLLGS.NSPASAS.VA.I.GT.HHA.LIF..LVE.
RetrocopyTGMRHHTGFCF*DGVLLCLP<RLECSGMISAHYNLHLLGSSNSPASAS*VAEIVGTCHHAGLIFVVLVES
ParentalGFHHVDQDGWSST-PDLVIHPPRPPKVLG
GFHHV.Q.G.....P.....P.RPPKVLG
RetrocopyGFHHVGQAGLELL>PQVIHPP-RPPKVLG

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP051959_colon 0 .00 RPM 13 .16 RPM
SRP051959_heart 0 .04 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 .00 RPM 4 .06 RPM
SRP051959_skeletal_muscle 0 .00 RPM 8 .63 RPM
SRP051959_spleen 0 .00 RPM 13 .36 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3456 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3456 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_3456 has 0 orthologous retrocopies within eutheria group .


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

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000179633 retrocopies
Callithrix jacchus ENSCJAG00000037941 35 retrocopies



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