RetrogeneDB ID:

retro_cjac_2181

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:3:124237452..124238589(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:FAM126B
Ensembl ID:ENSCJAG00000004465
Aliases:None
Description:family with sequence similarity 126, member B [Source:HGNC Symbol;Acc:28593]


Retrocopy-Parental alignment summary:






>retro_cjac_2181
GAAGGGGCATTATGTCAGCATGATCTTGTTAGAGTTGTTTATAGTGATCTTCATCCTCAGAGGGAAAGATTCACTGCACA
GACCAGTTTGCAGTCCTGAGTTTTCTCACGCTGTGTTACAATTCTGCTATTGTATACATGCCTGCTTCATCTTACCGATC
TCTTTGTCGGATGGGTTCCAGGGTTTGTGTGACTGGGTTTCCATGGCAACATGAAACATATTGGAAAGAACTCTGTGGTT
GAATAGTATTGGATCCTGAATTTATGGTGACACTTCTCACATGGCTTTATTATGCCATGTATAATGGACAATGGGACCTT
GGCCAGGAAGTTCTTGATGGCATCATTTATAGAGCTCAGCTAGAGCTTTTTTCTCAGCCACTATTGGTTGTCAATACCAT
GAAAAACTCATCACCATTTGATGCTCCTGATTCTTCACAAGAAGGCCAGAAAGTCCTTAAAGTTGAAGTCACTCCAACAG
TGCTGAGGATTTCTTGGACTGCAATTGTAACAGCTTCAATCTCGCTGGAGGAGAGAAAATGCTGAGGGTGTAAATGGAAG
AGAGGAGTCTGTAAACCTGAATGATGCAGATGAAGGATTTTCATCAGGGGCTTCCCTCAGCAGTCAGCCATTTGGGACCA
AACCATCCTCCTCTTCTCAGAGGGGAAGCTTAAGGAAAGTAGCAACTGAGTATTCAGCCGAGGATAAAGAAACAGCCTCT
GCTATCAAATCCAGTGAGAGTCCTCAAGATTCAGTAGTTCGCAAGCAGTATGTATAGCAATGAACTGATCTTAGTGTAAA
TTCAGTTGAGCTGACACCAAAGAAGAAATGCCTGAGCCTGCCTGCTGGCCAGGTGATACCAAAAACTAGTAGTTTAAGTC
TAATCCGGACAGCCAGTGCTTCCTCAAGTAAATCATTTGACTATGTAAATAGCAGTCAAGCAAGTATCAGCCTTAGGGTT
GGCATTGAGGGAGGTACTAATTTAGCAGGTAACAATACTAATCGATACTCAAATATCAGTCTGCAGGAAGACTGGCTAGG
TCAAGATGGTGAAGGTAAAGAGCTACTCAGCCCAGGAGCCCCCTTAACCAAGCAGTCTCGATCCCCAAGTTTCAATATGC
AGCTAATATCCCAGGTA

ORF - retro_cjac_2181 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 82.55 %
Parental protein coverage: 72.08 %
Number of stop codons detected: 3
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalEGALCQHDLIRVVYSDLHPQRETFTAQ-NRFEVLSFLMLCYNSAIVYMPASSYQSLCRMGSRVCVSGFPR
EGALCQHDL.RVVYSDLHPQRE.FTAQ...F.VLSFL.LCYNSAIVYMPASSY.SLCRMGSRVCV.GFP.
RetrocopyEGALCQHDLVRVVYSDLHPQRERFTAQ<DQFAVLSFLTLCYNSAIVYMPASSYRSLCRMGSRVCVTGFPW
ParentalQHEKHWKELCGRIVLDPEFMVQLLTGVYYAMYNGQWDLGQEVLDDIIYRAQLELFSQPLLVANAMKNSLP
QHE..WKELCG.IVLDPEFMV.LLT..YYAMYNGQWDLGQEVLD.IIYRAQLELFSQPLLV.N.MKNS.P
RetrocopyQHETYWKELCG*IVLDPEFMVTLLTWLYYAMYNGQWDLGQEVLDGIIYRAQLELFSQPLLVVNTMKNSSP
ParentalFDAPDSSQEGQKVLKVEVTPTVPRISRTAITTASIR-RHRWRREGAEGVNGGEESVNLNDADEGFSSGAS
FDAPDSSQEGQ...KV......P...R...T........RWRRE.AEGVNG.EESVNLNDADEGFSSGAS
RetrocopyFDAPDSSQEGQ---KVLKVEVTPTVLRISWTAIVTA>QSRWRRENAEGVNGREESVNLNDADEGFSSGAS
ParentalLSSQPIGTKPSSSSQRGSLRKVATGRSAKDKETASAIKSSESPRDSVIRKQYVQQPTDLSVDSVELTPMK
LSSQP.GTKPSSSSQRGSLRKVAT..SA.DKETASAIKSSESP.DSV.RKQYV.Q.TDLSV.SVELTP.K
RetrocopyLSSQPFGTKPSSSSQRGSLRKVATEYSAEDKETASAIKSSESPQDSVVRKQYV*Q*TDLSVNSVELTPKK
ParentalKHLSLPAGQVVPKTNSLSLIRTASASSSKSFDYVNGSQASTSIGVGTEGGTNLAGNNANRYSTISLQEDR
K.LSLPAGQV.PKT.SLSLIRTASASSSKSFDYVN.SQAS.S..VG.EGGTNLAGNN.NRYS.ISLQED.
RetrocopyKCLSLPAGQVIPKTSSLSLIRTASASSSKSFDYVNSSQASISLRVGIEGGTNLAGNNTNRYSNISLQEDW
ParentalLGQAGEGKELLSPGAPLTKQSRSPSFNMQLISQV
LGQ.GEGKELLSPGAPLTKQSRSPSFNMQLISQV
RetrocopyLGQDGEGKELLSPGAPLTKQSRSPSFNMQLISQV

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






RNA-Seq - click to see more details

(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 29 .84 RPM
SRP051959_heart 0 .00 RPM 24 .08 RPM
SRP051959_kidney 0 .02 RPM 38 .09 RPM
SRP051959_liver 0 .02 RPM 57 .10 RPM
SRP051959_lung 0 .02 RPM 47 .11 RPM
SRP051959_lymph_node 0 .00 RPM 36 .32 RPM
SRP051959_skeletal_muscle 0 .02 RPM 15 .48 RPM
SRP051959_spleen 0 .00 RPM 38 .24 RPM

ChIP-Seq - click to see more details

Callithrix jacchus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_cjac_2181 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_2181 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_2181 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG00000004465 1 retrocopy
retro_cjac_2181 ,


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