RetrogeneDB ID:

retro_cjac_2464

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:4:110855728..110856517(-)
Located in intron of:ENSCJAG00000005204
Retrocopy
information
Ensembl ID:ENSCJAG00000005207
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:APOOL
Ensembl ID:ENSCJAG00000008249
Aliases:None
Description:apolipoprotein O-like [Source:HGNC Symbol;Acc:24009]


Retrocopy-Parental alignment summary:






>retro_cjac_2464
ATGGGAAAACTGACAACCATGCTGGCAGGTCTGATTTATGCATCTGTAAGTGTACATGCAACCAAAGAAGAGGAATCCAA
AAAGCAGCTAGTGAAACCAGAGCAGCTCCCCATGTATACTGCACCACCGCTCCAGTCTAAACATGTTGAAGAGCAGCCTG
GTCATTTACAAATGAGCTTTGCTTCCATCCACACTGCAACTGGTCGTTATATTGGCTGGTGCAAGGGTGTTTATGTCTTT
GCAAAAAATGGGATAATGGATACAGTACAATTTGGAAAAGATGACTATGTCTATCTGAAGAATCCTCCTCAAGATATTCT
TCTGAAAATGGGAGTTATTATAGTTTCAGGATTGGTGGGCTTGGTTTCAGAGAGAAAAGGTTCTAAGTTTAAGAAAATTA
CTTATCCTCTGGGACTGGCCACTTTAGGAGCAACTGTTTGCTACCCAATTCAGTCAGTAATAATTGCTAAGGTAACAGGG
AAAAAGATATATGCTACAAGCCAGCAAATTTTTGAAACAATTAAATCGCTGTGGACAAAAAGCAACAAAAAAGAGTCACT
TCGTCAACCTAAGGAAAAAACTAAGCTAGGATCCTCTGCCGAAACAGAAGTATCTGCAAAAACAACTCACGTCTTGAAAC
ACTCAGTGCCTTTGCCAACAGAACTCAGCTCTGAAGCAAAGACCAAATCAGTATCCACCTCAGGTGCTACACCGTTTATG
CCTGACCCCAACCTCATGGATCACAGGCAGTCCCATCCAGAAGATACAGATATGTACAGCACTAGAAGC

ORF - retro_cjac_2464 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 89.35 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMGKLTTMPAGLIYASVSVHSTKEEESKKQLVKPEQLPIYTAPPLQSKYVEEQPGHLQMGFASIRTATGRY
MGKLTTM.AGLIYASVSVH.TKEEESKKQLVKPEQLP.YTAPPLQSK.VEEQPGHLQM.FASI.TATGRY
RetrocopyMGKLTTMLAGLIYASVSVHATKEEESKKQLVKPEQLPMYTAPPLQSKHVEEQPGHLQMSFASIHTATGRY
ParentalIGWCKGVYVFVKNGITNTVQFGKDAYVYLKSPPQDFLPKMGVITVSGLVGLVSARKGSKFKKITYPLGLA
IGWCKGVYVF.KNGI..TVQFGKD.YVYLK.PPQD.L.KMGVI.VSGLVGLVS.RKGSKFKKITYPLGLA
RetrocopyIGWCKGVYVFAKNGIMDTVQFGKDDYVYLKNPPQDILLKMGVIIVSGLVGLVSERKGSKFKKITYPLGLA
ParentalTLGATVCYPVQSVIITKVTGKKIYATSQQTFETVKSLWTKSNKKESLPQPKEKTKLGSSAEIEAFAKTTH
TLGATVCYP.QSVII.KVTGKKIYATSQQ.FET.KSLWTKSNKKESL.QPKEKTKLGSSAE.E..AKTTH
RetrocopyTLGATVCYPIQSVIIAKVTGKKIYATSQQIFETIKSLWTKSNKKESLRQPKEKTKLGSSAETEVSAKTTH
ParentalVLKHSVPLPAELSSEAKTKSVSTSGATQFMPDPKLMDHGQSHPEDIDMYSTRS
VLKHSVPLP.ELSSEAKTKSVSTSGAT.FMPDP.LMDH.QSHPED.DMYSTRS
RetrocopyVLKHSVPLPTELSSEAKTKSVSTSGATPFMPDPNLMDHRQSHPEDTDMYSTRS

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 .24 RPM 7 .01 RPM
SRP051959_heart 0 .47 RPM 9 .70 RPM
SRP051959_kidney 2 .13 RPM 9 .21 RPM
SRP051959_liver 0 .11 RPM 12 .13 RPM
SRP051959_lung 0 .07 RPM 5 .50 RPM
SRP051959_lymph_node 0 .14 RPM 3 .65 RPM
SRP051959_skeletal_muscle 2 .88 RPM 9 .22 RPM
SRP051959_spleen 0 .57 RPM 5 .40 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_2464 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_2464 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_2464 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 19 parental genes, and 33 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000008291 retrocopy
retro_amel_1035,
Canis familiaris ENSCAFG000000173831 retrocopy
retro_cfam_1490,
Callithrix jacchus ENSCJAG000000049098 retrocopies
retro_cjac_1360, retro_cjac_1417, retro_cjac_1448, retro_cjac_1767, retro_cjac_1792, retro_cjac_1896, retro_cjac_2038, retro_cjac_2063,
Callithrix jacchus ENSCJAG00000008249 2 retrocopies
retro_cjac_1783, retro_cjac_2464 ,
Dipodomys ordii ENSDORG000000110451 retrocopy
retro_dord_373,
Equus caballus ENSECAG000000092291 retrocopy
retro_ecab_577,
Homo sapiens ENSG000001550081 retrocopy
retro_hsap_3253,
Gorilla gorilla ENSGGOG000000163291 retrocopy
retro_ggor_2213,
Loxodonta africana ENSLAFG000000088441 retrocopy
retro_lafr_1035,
Microcebus murinus ENSMICG000000158441 retrocopy
retro_mmur_1511,
Myotis lucifugus ENSMLUG000000113841 retrocopy
retro_mluc_1364,
Macaca mulatta ENSMMUG000000043351 retrocopy
retro_mmul_2045,
Mustela putorius furoENSMPUG000000018993 retrocopies
retro_mputfur_606, retro_mputfur_734, retro_mputfur_874,
Nomascus leucogenys ENSNLEG000000026341 retrocopy
retro_nleu_1702,
Pongo abelii ENSPPYG000000205161 retrocopy
retro_pabe_2697,
Pan troglodytes ENSPTRG000000220671 retrocopy
retro_ptro_2200,
Sus scrofa ENSSSCG000000124591 retrocopy
retro_sscr_610,
Tupaia belangeri ENSTBEG000000101475 retrocopies
retro_tbel_2037, retro_tbel_2609, retro_tbel_2840, retro_tbel_3361, retro_tbel_3737,
Tursiops truncatus ENSTTRG000000004291 retrocopy
retro_ttru_1337,


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