RetrogeneDB ID:

retro_cjac_2201

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:3:166361559..166362413(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCJAG00000013118
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCJAG00000015267
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_2201
GGGATGGGCGGAGGCCCCGGGGGCCCCGGGATGGGGAACCGCGGTGGCTTCCGCAGAGGTTTCGGCAGTGGCATCCGGGG
CCGGGGTCGCGGCCATGGACGGGGCCAGGCGAGGCCGCGGAGCTCGCGGAGGCAAAGCCGAGGATAAGGAATGGATGCCT
GTCACCAAGTTGGGCCGCCTGGTCAAAGACATGAAGATTAAATCTCTGGAGGAGACCTATCTCTTCTCTCTGCCCATCAA
GGAATCTGAGATCATTGACTTTTTCCTGGGAGCCTCTCTCAAGGATGAGGTTTTGAAGATTATGCTGGTGCAGAAGCAGA
CCCGTGCTGGCCAGCGCACCAGGTTCAAGGCGTTTGTTGCTATTGGGGACTACAATGGTCACGTTGGTCTGGGTGTTAAG
TGTTCCAAGGAGATGGCCACTGCCATTCGTGGGGCCATCATCCTGGCCAAGCTCTCCATTGTCCCCGTGCCTAGAGGCTA
CTGGGGGAACAAGATTGATTGGCAAGCCCCACACCGTCCCCTGCAAGGTGACAGGCCGCTGTGGTTCTGTGCTGGTGTGC
CTCATCCCTGTGCCGAGGGGCACTGGGATAGTCTCAGCACCTGTGCCCAAGAAGTTGCTTATGATGGCTGGTATCGATGA
CTGCTACACCTCAGCTAGAGGCACTGCCACCTTGGGCAACTTTGCCAAGGCCACCTTTGATGCCATTTCTAAGACTTACA
GCTACCTGACCCCTGATCTCTGGAAGGAGACTGTGTTCACCAAGCCTCCCTATCAGGAATTCACTGACCACCTTGTCAAG
ACCCACACCAGAGTCTCCGTGCAGAGGACCCAAGCTCCAGCTGTGGCTACAACA

ORF - retro_cjac_2201 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 93.43 %
Parental protein coverage: 97.27 %
Number of stop codons detected: 0
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalGAPGGPGGPGMGNRGGFRGGFGSGIRGRGRGRGR-GRG-RGRGARGGKAEDKEWMPVTKLGRLVKDMKIK
G..GGPGGPGMGNRGGFR.GFGSGIRGRGRG.GR.G.G.RGRGARGGKAEDKEWMPVTKLGRLVKDMKIK
RetrocopyGMGGGPGGPGMGNRGGFRRGFGSGIRGRGRGHGR<GPG<RGRGARGGKAEDKEWMPVTKLGRLVKDMKIK
ParentalSLEEIYLFSLPIKESEIIDFFLGASLKDEVLKIMPVQKQTRAGQRTRFKAFVAIGDYNGHVGLGVKCSKE
SLEE.YLFSLPIKESEIIDFFLGASLKDEVLKIM.VQKQTRAGQRTRFKAFVAIGDYNGHVGLGVKCSKE
RetrocopySLEETYLFSLPIKESEIIDFFLGASLKDEVLKIMLVQKQTRAGQRTRFKAFVAIGDYNGHVGLGVKCSKE
ParentalVATAIRGAIILAKLSIVPVRRGYW-GNK-IGKPHTVPCKVTGRCGSVLVRLIPAPRGTGIVSAPVPKKLL
.ATAIRGAIILAKLSIVPV.RGYW.G...IGKPHTVPCKVTGRCGSVLV.LIP.PRGTGIVSAPVPKKLL
RetrocopyMATAIRGAIILAKLSIVPVPRGYW>GTRLIGKPHTVPCKVTGRCGSVLVCLIPVPRGTGIVSAPVPKKLL
ParentalMMAGIDDCYTSARGCTATLGNFAKATFDAISKTYSYLTPDLWKETVFTKSPYQEFTDHLVKTHTRVSVQR
MMAGIDDCYTSARG.TATLGNFAKATFDAISKTYSYLTPDLWKETVFTK.PYQEFTDHLVKTHTRVSVQR
RetrocopyMMAGIDDCYTSARG-TATLGNFAKATFDAISKTYSYLTPDLWKETVFTKPPYQEFTDHLVKTHTRVSVQR
ParentalTQAPAVATT
TQAPAVATT
RetrocopyTQAPAVATT

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 .02 RPM 103 .33 RPM
SRP051959_heart 0 .00 RPM 66 .13 RPM
SRP051959_kidney 0 .00 RPM 86 .90 RPM
SRP051959_liver 0 .02 RPM 169 .21 RPM
SRP051959_lung 0 .02 RPM 76 .34 RPM
SRP051959_lymph_node 0 .02 RPM 130 .47 RPM
SRP051959_skeletal_muscle 0 .04 RPM 155 .73 RPM
SRP051959_spleen 0 .00 RPM 120 .76 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2201 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2201 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_2201 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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