RetrogeneDB ID:

retro_cjac_274

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:ACFV01175094.1:656..1400(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCJAG00000035066
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCJAG00000015267
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_274
GGCCGCGGAGCTCGCAGAGGCAAAGCCAAGGATAAGGAATGGATGCCTGTCACTAAGTTGGGCCGCCTGGTCAAAGACAT
GAAGATTAAATCTCTGGAGGAGATCTATCTCTTCTCTCTGCCCATCAAGGAATCTGAGATCATTGACTTTTTCCTGGGGG
CCTCTCTCAAGGATGAGGTTTTGAAGATTATGCCGGTGCAGAAGCAGACCCGTGCTGGCCAGCACACCAGGTTCAAGGCA
TTTGTTGCTATTGGGGACCACAATGGTCACGTCGGTCTGGGTGTTAAGTGTTCCAAGGAGGTGGCCACCGCTATCCATGG
GGCCATGATCCTGGCCAAGCTCTCCATTGTCCCCATGCGCAGAGGCTACTGGGGGAACAAGATTGGCAAGCCCCACACTG
TCCCTTGCAAGGTGAAAGGCCGCTGTGGTTCTGTGCTGGTGTATCTCATCCCCGTGCCCAGGGGTACTGGCATCGTCTCA
GCACCTGTGCCCAAGAAGCTGCTTATGATGGTTGGTGTTGATGACTGCTACACCTCAGCTAGGGGCTGCACTGCCACCTT
GGGCAACTTTGCCAAGGCCACCTTTGATGCCATCTCTAAGACTTACAGCTACCTGACCCCTGATCTCTGGAAGGAGACTG
TGTTCACCAAGTCTCCCTATCAGGAATTCACTGACCACCTTGTAAAGACCCACACCAGAGTCTCCGTGCAGAGGACCCAA
GCTCCAGCTGTGGCTACAACATAG

ORF - retro_cjac_274 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 95.14 %
Parental protein coverage: 84.3 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalGRGARGGKAEDKEWMPVTKLGRLVKDMKIKSLEEIYLFSLPIKESEIIDFFLGASLKDEVLKIMPVQKQT
GRGAR.GKA.DKEWMPVTKLGRLVKDMKIKSLEEIYLFSLPIKESEIIDFFLGASLKDEVLKIMPVQKQT
RetrocopyGRGARRGKAKDKEWMPVTKLGRLVKDMKIKSLEEIYLFSLPIKESEIIDFFLGASLKDEVLKIMPVQKQT
ParentalRAGQRTRFKAFVAIGDYNGHVGLGVKCSKEVATAIRGAIILAKLSIVPVRRGYWGNKIGKPHTVPCKVTG
RAGQ.TRFKAFVAIGD.NGHVGLGVKCSKEVATAI.GA.ILAKLSIVP.RRGYWGNKIGKPHTVPCKV.G
RetrocopyRAGQHTRFKAFVAIGDHNGHVGLGVKCSKEVATAIHGAMILAKLSIVPMRRGYWGNKIGKPHTVPCKVKG
ParentalRCGSVLVRLIPAPRGTGIVSAPVPKKLLMMAGIDDCYTSARGCTATLGNFAKATFDAISKTYSYLTPDLW
RCGSVLV.LIP.PRGTGIVSAPVPKKLLMM.G.DDCYTSARGCTATLGNFAKATFDAISKTYSYLTPDLW
RetrocopyRCGSVLVYLIPVPRGTGIVSAPVPKKLLMMVGVDDCYTSARGCTATLGNFAKATFDAISKTYSYLTPDLW
ParentalKETVFTKSPYQEFTDHLVKTHTRVSVQRTQAPAVATT
KETVFTKSPYQEFTDHLVKTHTRVSVQRTQAPAVATT
RetrocopyKETVFTKSPYQEFTDHLVKTHTRVSVQRTQAPAVATT

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 .16 RPM 103 .33 RPM
SRP051959_heart 0 .54 RPM 66 .13 RPM
SRP051959_kidney 0 .13 RPM 86 .90 RPM
SRP051959_liver 0 .04 RPM 169 .21 RPM
SRP051959_lung 0 .41 RPM 76 .34 RPM
SRP051959_lymph_node 0 .14 RPM 130 .47 RPM
SRP051959_skeletal_muscle 0 .24 RPM 155 .73 RPM
SRP051959_spleen 0 .19 RPM 120 .76 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_274 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_274 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_274 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 8 parental genes, and 88 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000025491 retrocopy
Callithrix jacchus ENSCJAG00000015267 15 retrocopies
Felis catus ENSFCAG000000291916 retrocopies
Macropus eugenii ENSMEUG000000045082 retrocopies
Microcebus murinus ENSMICG0000001276528 retrocopies
Monodelphis domestica ENSMODG000000160771 retrocopy
Sarcophilus harrisii ENSSHAG000000152135 retrocopies
Tupaia belangeri ENSTBEG0000000672630 retrocopies



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