RetrogeneDB ID:

retro_cjac_1840

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:2:127553116..127553560(+)
Located in intron of:ENSCJAG00000019548
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:MAGOHB
Ensembl ID:ENSCJAG00000021662
Aliases:None
Description:mago-nashi homolog B (Drosophila) [Source:HGNC Symbol;Acc:25504]


Retrocopy-Parental alignment summary:






>retro_cjac_1840
ATGTCTATGGCTAGCGATTTCTACCTGCGCTACTACGTAGGGCACAAGGGCAAGTTTGGGCACAAGTTTCTGGAGTTCGA
ATTTCGGCCGGATGGAAAGCTTAGATATGCCAACAACAGCAATTACAAAAATGACGTAATGATCAGAAAAGAGGCTTATG
TACACAAGAGTGTAATGGAAGAACTGAAGAGAATTATTGATGTCAGTGAAATTACAAAAGAAGATGATGCTTTGTGGCCT
CCCCCTGACAGGGTTGGCCGTCAGGAGCTTGAAATTGTCATTGGAGATAAGCACATATCTTTTACCACATGAAAAATAGG
TTCTCTTATTGATGTGAACCAGTCGAAGGATCCTGAAGGCCTTCGAGTATTTTACTATTTGGTACAAGACTTGAAATGTT
TAGTTTTCAGTCTCATTGGATTACACTTCAAGATTAAACCAATT

ORF - retro_cjac_1840 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 97.3 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMSMASDFYLRYYVGHKGKFGHEFLEFEFRPDGKLRYANNSNYKNDVMIRKEAYVHKSVMEELKRIIDDSE
MSMASDFYLRYYVGHKGKFGH.FLEFEFRPDGKLRYANNSNYKNDVMIRKEAYVHKSVMEELKRIID.SE
RetrocopyMSMASDFYLRYYVGHKGKFGHKFLEFEFRPDGKLRYANNSNYKNDVMIRKEAYVHKSVMEELKRIIDVSE
ParentalITKEDDALWPPPDRVGRQELEIVIGDEHISFTTSKIGSLIDVNQSKDPEGLRVFYYLVQDLKCLVFSLIG
ITKEDDALWPPPDRVGRQELEIVIGD.HISFTT.KIGSLIDVNQSKDPEGLRVFYYLVQDLKCLVFSLIG
RetrocopyITKEDDALWPPPDRVGRQELEIVIGDKHISFTT*KIGSLIDVNQSKDPEGLRVFYYLVQDLKCLVFSLIG
ParentalLHFKIKPI
LHFKIKPI
RetrocopyLHFKIKPI

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 .07 RPM 2 .84 RPM
SRP051959_heart 0 .05 RPM 2 .35 RPM
SRP051959_kidney 0 .24 RPM 3 .82 RPM
SRP051959_liver 0 .17 RPM 3 .81 RPM
SRP051959_lung 0 .08 RPM 3 .20 RPM
SRP051959_lymph_node 0 .18 RPM 2 .85 RPM
SRP051959_skeletal_muscle 0 .13 RPM 2 .23 RPM
SRP051959_spleen 0 .02 RPM 3 .07 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1840 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1840 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_1840 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 15 parental genes, and 40 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000043821 retrocopy
Callithrix jacchus ENSCJAG000000045381 retrocopy
Callithrix jacchus ENSCJAG00000021662 7 retrocopies
Dasypus novemcinctus ENSDNOG000000059974 retrocopies
Echinops telfairi ENSETEG000000165913 retrocopies
Homo sapiens ENSG000001111961 retrocopy
Macropus eugenii ENSMEUG000000017821 retrocopy
Macaca mulatta ENSMMUG000000050821 retrocopy
Monodelphis domestica ENSMODG000000004621 retrocopy
Nomascus leucogenys ENSNLEG000000033551 retrocopy
Ochotona princeps ENSOPRG000000005482 retrocopies
Pan troglodytes ENSPTRG000000046792 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000008351 retrocopy
Tupaia belangeri ENSTBEG000000148207 retrocopies
Tarsius syrichta ENSTSYG000000104527 retrocopies



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