RetrogeneDB ID:

retro_cjac_2244

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:3:77935437..77935992(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPF2
Ensembl ID:ENSCJAG00000005212
Aliases:None
Description:ribosome production factor 2 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:20870]


Retrocopy-Parental alignment summary:






>retro_cjac_2244
AATGAACAAATAATAGGTCACATGTATGACTATCTTTTGCTAAATATGATAAAATTAGTCACTGAGAAATTTGTCTCATT
AAAAGACATTAAGAACAGTAAATACTCTGAGAAAATAAAACCTACGATTATATTTGCTGGTGAGGATTTTGATGTACAAG
ATGACTCTATTCGGCTAAAGAGTCTTGTTATTGCTTTCTTCAGCGGCTCAGGAGTATCAAATATCCTCCTAGCTGGATTA
GAGTATGTTTTACACTTTACCATACAGAAAGGGAAGATTTATTTTTGAAGCTATAAGTTGCTTGATGAATAAATCTTTTG
CAGAATATTACAGACTGAATTGGAGACACAGAAACCTCATTGAATTGGGTTTTGAGAAGGACATATCTGGCATCAGATGA
ACTTTATAAATTATCTATGCAAATGTCAAAAACCTTCAAGTCAAAGAAGAAGAAAATTATCTCCCATAATACTTTTGGCA
TTATTTGTGGAAGGATTCACATGTAGAATTAAGGCCTTAAGCAAACTACAAAGAGGGAAAATGAGGGGGTTGAAG

ORF - retro_cjac_2244 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 64.17 %
Parental protein coverage: 60.46 %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalNNLVIGRMYDYHVLDMIELGIENFVSLKDIKNSKCPEGTKPMLIFAGDDFDVTEDYRRLKSLLIDFFRGP
N...IG.MYDY..L.MI.L..E.FVSLKDIKNSK..E..KP..IFAG.DFDV..D..RLKSL.I.FF.G.
RetrocopyNEQIIGHMYDYLLLNMIKLVTEKFVSLKDIKNSKYSEKIKPTIIFAGEDFDVQDDSIRLKSLVIAFFSGS
ParentalAVSNIRLAGLEYVLHFTALNGKIYFRSYKLLLKKSGCRTPRIELEEMGP-SLDLVLRRTHLASDDLYKLS
.VSNI.LAGLEYVLHFT...GKIYF.SYKLL.....CR....ELE...P.SL..VLRRT.LASD.LYKLS
RetrocopyGVSNILLAGLEYVLHFTIQKGKIYF*SYKLLDE*IFCRILQTELETQKP<SLNWVLRRTYLASDELYKLS
ParentalMKMPKALKPKKKKNISHDTFGTTYGRIHM-QKQDLSKLQTRKMKGLK
M.M.K..K.KKKK.ISH.TFG...GRIHM.....LSKLQ..KM.GLK
RetrocopyMQMSKTFKSKKKKIISHNTFGIICGRIHM>RIKALSKLQRGKMRGLK

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 3 .53 RPM
SRP051959_heart 0 .00 RPM 5 .49 RPM
SRP051959_kidney 0 .00 RPM 6 .90 RPM
SRP051959_liver 0 .00 RPM 4 .96 RPM
SRP051959_lung 0 .00 RPM 4 .38 RPM
SRP051959_lymph_node 0 .00 RPM 5 .37 RPM
SRP051959_skeletal_muscle 0 .00 RPM 7 .34 RPM
SRP051959_spleen 0 .00 RPM 5 .92 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_2244 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_2244 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_2244 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pongo abelii retro_pabe_2464
Macaca mulatta retro_mmul_1903
Parental genes homology:
Parental genes homology involve 17 parental genes, and 37 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000039182 retrocopies
retro_cfam_1611, retro_cfam_903,
Callithrix jacchus ENSCJAG00000005212 6 retrocopies
retro_cjac_1675, retro_cjac_1768, retro_cjac_2244 , retro_cjac_2473, retro_cjac_606, retro_cjac_933,
Cavia porcellus ENSCPOG000000067972 retrocopies
retro_cpor_332, retro_cpor_582,
Equus caballus ENSECAG000000171211 retrocopy
retro_ecab_782,
Erinaceus europaeus ENSEEUG000000061692 retrocopies
retro_eeur_454, retro_eeur_584,
Felis catus ENSFCAG000000015271 retrocopy
retro_fcat_1584,
Homo sapiens ENSG000001974981 retrocopy
retro_hsap_2425,
Gorilla gorilla ENSGGOG000000014691 retrocopy
retro_ggor_83,
Myotis lucifugus ENSMLUG000000056762 retrocopies
retro_mluc_485, retro_mluc_921,
Macaca mulatta ENSMMUG000000215321 retrocopy
retro_mmul_1903,
Mus musculus ENSMUSG000000385101 retrocopy
retro_mmus_2234,
Nomascus leucogenys ENSNLEG000000128543 retrocopies
retro_nleu_2024, retro_nleu_2434, retro_nleu_2445,
Oryctolagus cuniculus ENSOCUG000000160281 retrocopy
retro_ocun_831,
Pongo abelii ENSPPYG000000169252 retrocopies
retro_pabe_1788, retro_pabe_2464,
Pan troglodytes ENSPTRG000000185031 retrocopy
retro_ptro_1398,
Rattus norvegicus ENSRNOG000000005871 retrocopy
retro_rnor_2336,
Tupaia belangeri ENSTBEG000000171519 retrocopies
retro_tbel_1824, retro_tbel_2243, retro_tbel_2376, retro_tbel_2576, retro_tbel_3547, retro_tbel_3635, retro_tbel_3803, retro_tbel_3876, retro_tbel_4509,




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