RetrogeneDB ID:

retro_cjac_311

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:13:35597886..35598555(-)
Located in intron of:ENSCJAG00000002768
Retrocopy
information
Ensembl ID:ENSCJAG00000002782
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCJAG00000005111
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_311
ATGCCGAAAGTAGTGTCTCGGTCAGTAGTCTGCTCTGACACTCGGAACCGGGAGGAATATGATGATGGCGAGAAGCCCCT
CCATGTGTACTATTGTTTGTGCGGCCAGATGGTCCTACTGCTGGACTGTCAGTTAGAGAAACTGCCCATGAGGCCCCGGG
ACCGGTCCCGTGTGATTGATGCTGCCAAACATGCCCGTAAGTTTTGTAACACAGAAGACCAGGAGACTGTGTATCTGCGG
AGACCTGAAGGCACTGAACGACAGCACAGAAAGAAATGTGCAAAGTGTGGACTGCTGCTCTTCTACCAATCCCAGCCGAA
TAACGCTCCTGTTACCTTCATTGTGGATGGAGCAGTAGTCAAGTTTGGCCAGGCCTTTGGGAAAACGAACATATATACTC
AGAAACAAGAGCCTCCTAAGAAGGTGATGATGACCAAATGGACCAAAGACATGGGCAAGTTCACTTCTGTCACTGTGTCT
ACCATTGATGAAGAGGAAGAGGAGATTGAGGCTAGGGAAGTTGCTGACTCCTATGCGCAGAATGCCAAAGTGATTGAAAA
ACAGCTGGAGCGCAAAGGCATGAGCAAGATGCGACTGCAAGAGCTGGCTGGACTGGAAGCCAAGAAAGCGAAAATGAAGG
GGACCTTGATTGACAACCAGTTCAAATAA

ORF - retro_cjac_311 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.56 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMPKVVSRSVVCSDTRDREEYDDGEKPLHVYYCLCGQMVLVLVSLLELIQLPMNKRDGSRYILPASWHMXL
MPKVVSRSVVCSDTR.REEYDDGEKPLHVYYCLCGQMVL.L...LE...LPM..RD.SR....A..H...
RetrocopyMPKVVSRSVVCSDTRNREEYDDGEKPLHVYYCLCGQMVLLLDCQLE--KLPMRPRDRSR-VIDAAKHARK
ParentalFQNKEKDIFHFLCRPEGIERQYRKKCAKCGLLLFYQSQPKNAPVTFIVDGAVVKFGQGFGKTNIYTQKQE
F.N.E......L.RPEG.ERQ.RKKCAKCGLLLFYQSQP.NAPVTFIVDGAVVKFGQ.FGKTNIYTQKQE
RetrocopyFCNTEDQETVYLRRPEGTERQHRKKCAKCGLLLFYQSQPNNAPVTFIVDGAVVKFGQAFGKTNIYTQKQE
ParentalPPKKVMMTKRTKDMGKFSSVTVSTIDEEEEEIEAREVADSYAQNAKVIEKQLERKGMSKRRLQELAELEA
PPKKVMMTK.TKDMGKF.SVTVSTIDEEEEEIEAREVADSYAQNAKVIEKQLERKGMSK.RLQELA.LEA
RetrocopyPPKKVMMTKWTKDMGKFTSVTVSTIDEEEEEIEAREVADSYAQNAKVIEKQLERKGMSKMRLQELAGLEA
ParentalKKAKMKGTLIDNQFK
KKAKMKGTLIDNQFK
RetrocopyKKAKMKGTLIDNQFK

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 .29 RPM 6 .17 RPM
SRP051959_heart 0 .68 RPM 5 .37 RPM
SRP051959_kidney 1 .11 RPM 5 .01 RPM
SRP051959_liver 0 .80 RPM 4 .48 RPM
SRP051959_lung 1 .17 RPM 7 .43 RPM
SRP051959_lymph_node 0 .89 RPM 6 .96 RPM
SRP051959_skeletal_muscle 1 .53 RPM 5 .28 RPM
SRP051959_spleen 0 .95 RPM 7 .31 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_311 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_311 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_311 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Macaca mulatta retro_mmul_2333
Parental genes homology:
Parental genes homology involve 15 parental genes, and 16 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG00000005111 1 retrocopy
retro_cjac_311 ,
Homo sapiens ENSG000000186101 retrocopy
retro_hsap_4044,
Gorilla gorilla ENSGGOG000000133241 retrocopy
retro_ggor_2711,
Latimeria chalumnae ENSLACG000000124681 retrocopy
retro_lcha_59,
Myotis lucifugus ENSMLUG000000157511 retrocopy
retro_mluc_72,
Macaca mulatta ENSMMUG000000226651 retrocopy
retro_mmul_2333,
Mus musculus ENSMUSG000000064231 retrocopy
retro_mmus_1715,
Nomascus leucogenys ENSNLEG000000148621 retrocopy
retro_nleu_2057,
Otolemur garnettii ENSOGAG000000124741 retrocopy
retro_ogar_145,
Pongo abelii ENSPPYG000000206701 retrocopy
retro_pabe_177,
Sorex araneus ENSSARG000000031631 retrocopy
retro_sara_5,
Sarcophilus harrisii ENSSHAG000000063191 retrocopy
retro_shar_16,
Ictidomys tridecemlineatus ENSSTOG000000115791 retrocopy
retro_itri_103,
Tarsius syrichta ENSTSYG000000080431 retrocopy
retro_tsyr_634,
Tursiops truncatus ENSTTRG000000131012 retrocopies
retro_ttru_231, retro_ttru_77,


Copyright © RetrogeneDB 2014-2017