RetrogeneDB ID:

retro_hsap_2396

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:2:232298636..232299140(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000172799
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:ZBTB8OS
Ensembl ID:ENSG00000176261
Aliases:None
Description:zinc finger and BTB domain containing 8 opposite strand [Source:HGNC Symbol;Acc:24094]


Retrocopy-Parental alignment summary:






>retro_hsap_2396
GTCATGGCGCAGGCAGAGGAAGATGTTAGAGATTACAATTTGACTGAGGAACAGAAGGCGATCAAGGCCAAGTATCCGCC
AGTCAATAGGAAGTACGAGTATTTGGATCATACGGCGGATGTGCAGTTACACGCATGGGGAGATACTCTGGAGGAAGCAT
TCGAGCAATGTGCAATGGCCATGTTTGGTTACATGACAGATACTGGGACAGTGGAGCCCCTCCCAACAGTAGAAGTAGAA
ACCCAAGGAAATGACTTACAGACTCTTCTGTTTCACTTTTTGGATGAATGGCTTTATAAGTTCAGTGCTGATGAATTCTT
CATACCCCGGAAAGTGAAAGTACTTAGTATTGATCAAAGAAATTTCAAATTATGATCAATTGGGTGGGGAGAAGAGTTTT
CATTGTCCAAGCATCCTCAGGGAACAGAAGTCAAGGCAATAACATATTCAGCAATGCAGGTCTATAATGAAGAGAAGCTG
GAAGTTTTTGTGATCATTGGCATT

ORF - retro_hsap_2396 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 94.64 %
Parental protein coverage: 93.85 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalVMAQEEEDVRDYNLTEEQKAIKAKYPPVNRKYEYLDHTADVQLHAWGDTLEEAFEQCAMAMFGYMTDTGT
VMAQ.EEDVRDYNLTEEQKAIKAKYPPVNRKYEYLDHTADVQLHAWGDTLEEAFEQCAMAMFGYMTDTGT
RetrocopyVMAQAEEDVRDYNLTEEQKAIKAKYPPVNRKYEYLDHTADVQLHAWGDTLEEAFEQCAMAMFGYMTDTGT
ParentalVEPLQTVEVETQGDDLQSLLFHFLDEWLYKFSADEFFIPREVKVLSIDQRNFKLRSIGWGEEFSLSKHPQ
VEPL.TVEVETQG.DLQ.LLFHFLDEWLYKFSADEFFIPR.VKVLSIDQRNFKL.SIGWGEEFSLSKHPQ
RetrocopyVEPLPTVEVETQGNDLQTLLFHFLDEWLYKFSADEFFIPRKVKVLSIDQRNFKL*SIGWGEEFSLSKHPQ
ParentalGTEVKAITYSAMQVYNEENPEVFVIIDI
GTEVKAITYSAMQVYNEE..EVFVII.I
RetrocopyGTEVKAITYSAMQVYNEEKLEVFVIIGI

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
bodymap2_adipose 0 .00 RPM 11 .15 RPM
bodymap2_adrenal 0 .16 RPM 29 .58 RPM
bodymap2_brain 0 .00 RPM 14 .44 RPM
bodymap2_breast 0 .02 RPM 16 .65 RPM
bodymap2_colon 0 .00 RPM 13 .15 RPM
bodymap2_heart 0 .02 RPM 9 .69 RPM
bodymap2_kidney 0 .14 RPM 16 .67 RPM
bodymap2_liver 0 .00 RPM 12 .72 RPM
bodymap2_lung 0 .12 RPM 9 .85 RPM
bodymap2_lymph_node 0 .00 RPM 15 .31 RPM
bodymap2_ovary 0 .10 RPM 14 .34 RPM
bodymap2_prostate 0 .26 RPM 14 .84 RPM
bodymap2_skeletal_muscle 0 .00 RPM 7 .68 RPM
bodymap2_testis 0 .08 RPM 15 .72 RPM
bodymap2_thyroid 0 .00 RPM 23 .88 RPM
bodymap2_white_blood_cells 0 .02 RPM 18 .74 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2396 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2396 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2396 retrocopy 5' end.

Lab - click to see more details

Experiment type: PCR amplification
Forward primer: GAGTATTTGGATCATACGGCGGATGTG (27 nt long)
Reverse primer: TGCCAATGATCACAAAAACTTCCAGC (26 nt long)
Anneling temperature: 62 °C
(Expected) product size: 406
Electrophoresis gel image:
Additional comment: Red arrow indicates PCR product of retrogene in pooled cDNA from 16 human tissues (Clontech). Red number of lane indicates particular retrogene; L - GeneRuler 100 bp DNA Ladder (Thermo Fisher Scientific); N - No template control (water instead of cDNA)

Retrocopy orthology:
Retrocopy retro_hsap_2396 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pongo abelii retro_pabe_13
Parental genes homology:
Parental genes homology involve 16 parental genes, and 27 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000105501 retrocopy
retro_cfam_2152,
Choloepus hoffmanni ENSCHOG000000040612 retrocopies
retro_chof_1005, retro_chof_1158,
Cavia porcellus ENSCPOG000000153492 retrocopies
retro_cpor_356, retro_cpor_903,
Dasypus novemcinctus ENSDNOG000000018612 retrocopies
retro_dnov_1056, retro_dnov_2193,
Equus caballus ENSECAG000000209821 retrocopy
retro_ecab_610,
Felis catus ENSFCAG000000007001 retrocopy
retro_fcat_703,
Homo sapiens ENSG00000176261 2 retrocopies
retro_hsap_2396 , retro_hsap_2992,
Gorilla gorilla ENSGGOG000000075192 retrocopies
retro_ggor_2072, retro_ggor_231,
Myotis lucifugus ENSMLUG000000007455 retrocopies
retro_mluc_1961, retro_mluc_2533, retro_mluc_2570, retro_mluc_2617, retro_mluc_2622,
Macaca mulatta ENSMMUG000000099391 retrocopy
retro_mmul_1915,
Monodelphis domestica ENSMODG000000174192 retrocopies
retro_mdom_400, retro_mdom_901,
Mus musculus ENSMUSG000000575721 retrocopy
retro_mmus_2631,
Oryctolagus cuniculus ENSOCUG000000009401 retrocopy
retro_ocun_492,
Otolemur garnettii ENSOGAG000000116301 retrocopy
retro_ogar_3231,
Pongo abelii ENSPPYG000000015892 retrocopies
retro_pabe_13, retro_pabe_2478,
Tursiops truncatus ENSTTRG000000149681 retrocopy
retro_ttru_1200,

Expression level across human populations :
image/svg+xml GBR_HG00142 GBR_HG00099 GBR_HG00114 GBR_HG00143 GBR_HG00131 GBR_HG00137 GBR_HG00133 GBR_HG00119 GBR_HG00111 GBR_HG00134 FIN_HG00378 FIN_HG00338 FIN_HG00349 FIN_HG00375 FIN_HG00315 FIN_HG00277 FIN_HG00328 FIN_HG00321 FIN_HG00377 FIN_HG00183 TSI_NA20756 TSI_NA20538 TSI_NA20798 TSI_NA20532 TSI_NA20765 TSI_NA20518 TSI_NA20513 TSI_NA20512 TSI_NA20771 TSI_NA20786 YRI_NA19114 YRI_NA19099 YRI_NA18870 YRI_NA18907 YRI_NA19223 YRI_NA19214 YRI_NA18916 YRI_NA19093 YRI_NA19118 YRI_NA19213 Toscaniin Italia: Finnish inFinland: British in England and Scotland: Utah Residents (CEPH) with Northernand Western European Ancestry: Yoruba in Ibadan, Nigeria: CEU_NA12760 CEU_NA12827 CEU_NA12872 CEU_NA12751 CEU_NA12873 CEU_NA12400 CEU_NA11930 CEU_NA12004 CEU_NA11831 CEU_NA11843 No expression ( = 0 RPM ) > 0 RPM = 1.51 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .02 RPM
CEU_NA11843 0 .03 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .04 RPM
CEU_NA12751 0 .02 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .03 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .02 RPM
FIN_HG00338 0 .04 RPM
FIN_HG00349 0 .03 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .02 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .02 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .04 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .03 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 1 .11 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .02 RPM
TSI_NA20771 0 .03 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .74 RPM
YRI_NA18907 0 .83 RPM
YRI_NA18916 0 .67 RPM
YRI_NA19093 0 .62 RPM
YRI_NA19099 1 .07 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .91 RPM
YRI_NA19213 0 .74 RPM
YRI_NA19214 0 .69 RPM
YRI_NA19223 1 .51 RPM

Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).





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