RetrogeneDB ID:

retro_hsap_2814

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:3:93795158..93795809(-)
Located in intron of:ENSG00000178694
Retrocopy
information
Ensembl ID:ENSG00000242457
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RBBP4
Ensembl ID:ENSG00000162521
Aliases:RBBP4, NURF55, RBAP48
Description:retinoblastoma binding protein 4 [Source:HGNC Symbol;Acc:9887]


Retrocopy-Parental alignment summary:






>retro_hsap_2814
ACACACACATTGGATGAACAAAAACATCTTGTTATAGCCAGTGTGCAACTCCCTAATGATGATGCTCATTTTGATGCATC
ACACTACGACAGTGAGAAAGGAGAATTTGGAGGTTTTGGTTCAGTTAGTGGAAAAATTGAAATAGAAATCAAGATCAACC
ATGAAGGAGAAGTAAACAGGGCCCGTTATATGCCCCAGAATCCTTGTATTATCACAACAAAGACTCCTTCCAGTGATGTT
CTTATCTTGGACTATACAAAACATCCTAAACCAGATCTTTCTGGAGACTGCAACTCAGACTTGCGTCTCCATGGACATCA
GAAAAAAGGCTATGGGCTTTCTTGGCCAAATCTCAGTGGGCACTTACTTAGTGCTTCAGATGATCACACCATCTACCCGT
GGGACATCAGTGCTGTTCCAAAGGAGGGAAATGTGGTGGATGCAAAGACCATCTTTACAGGGCATACAGTAGTAGTAGAA
GATGTTTCCTGGCATCTGTTCCATAAGTCTCTGTTTGGGTCAGTTGCTGATCATCAGAAACTTATGATTTGGGATACTTG
TTCAAACAATACTTCCAAACCAAGCCACTCAGTTGACGCTCACACTGCTGAAGTGAACTGCCTTTCAATCCTTATAGTGA
GTTCATTCTTG

ORF - retro_hsap_2814 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.67 %
Parental protein coverage: 51.65 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalTHTSDEQNHLVIASVQLPNDDAQFDASHYDSEKGEFGGFGSVSGKIEIEIKINHEGEVNRARYMPQNPCI
THT.DEQ.HLVIASVQLPNDDA.FDASHYDSEKGEFGGFGSVSGKIEIEIKINHEGEVNRARYMPQNPCI
RetrocopyTHTLDEQKHLVIASVQLPNDDAHFDASHYDSEKGEFGGFGSVSGKIEIEIKINHEGEVNRARYMPQNPCI
ParentalIATKTPSSDVLVFDYTKHPSKPDPSGECNPDLRLRGHQKEGYGLSWNPNLSGHLLSASDDHTICLWDISA
I.TKTPSSDVL..DYTKHP.KPD.SG.CN.DLRL.GHQK.GYGLSW.PNLSGHLLSASDDHTI..WDISA
RetrocopyITTKTPSSDVLILDYTKHP-KPDLSGDCNSDLRLHGHQKKGYGLSW-PNLSGHLLSASDDHTIYPWDISA
ParentalVPKEGKVVDAKTIFTGHTAVVEDVSWHLLHESLFGSVADDQKLMIWDTRSNNTSKPSHSVDAHTAEVNCL
VPKEG.VVDAKTIFTGHT.VVEDVSWHL.H.SLFGSVAD.QKLMIWDT.SNNTSKPSHSVDAHTAEVNCL
RetrocopyVPKEGNVVDAKTIFTGHTVVVEDVSWHLFHKSLFGSVADHQKLMIWDTCSNNTSKPSHSVDAHTAEVNCL
ParentalSFNPYSEFI
S....S.F.
RetrocopySILIVSSFL

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 .02 RPM 91 .76 RPM
bodymap2_adrenal 0 .08 RPM 97 .54 RPM
bodymap2_brain 0 .07 RPM 113 .83 RPM
bodymap2_breast 0 .02 RPM 83 .95 RPM
bodymap2_colon 0 .04 RPM 80 .13 RPM
bodymap2_heart 0 .00 RPM 55 .03 RPM
bodymap2_kidney 0 .08 RPM 90 .89 RPM
bodymap2_liver 0 .04 RPM 36 .06 RPM
bodymap2_lung 0 .00 RPM 84 .88 RPM
bodymap2_lymph_node 0 .00 RPM 106 .13 RPM
bodymap2_ovary 0 .06 RPM 190 .32 RPM
bodymap2_prostate 0 .00 RPM 102 .43 RPM
bodymap2_skeletal_muscle 0 .00 RPM 66 .29 RPM
bodymap2_testis 0 .06 RPM 173 .60 RPM
bodymap2_thyroid 0 .04 RPM 114 .14 RPM
bodymap2_white_blood_cells 0 .00 RPM 150 .67 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2814 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2814 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2814 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2814 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2814 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1909
Parental genes homology:
Parental genes homology involve 21 parental genes, and 55 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000059042 retrocopies
retro_btau_1610, retro_btau_630,
Canis familiaris ENSCAFG000000105271 retrocopy
retro_cfam_1550,
Choloepus hoffmanni ENSCHOG000000040666 retrocopies
retro_chof_1382, retro_chof_1649, retro_chof_1867, retro_chof_2116, retro_chof_2327, retro_chof_908,
Callithrix jacchus ENSCJAG000000010217 retrocopies
retro_cjac_1157, retro_cjac_1787, retro_cjac_1873, retro_cjac_244, retro_cjac_2557, retro_cjac_2719, retro_cjac_2939,
Cavia porcellus ENSCPOG000000153523 retrocopies
retro_cpor_154, retro_cpor_27, retro_cpor_899,
Equus caballus ENSECAG000000227841 retrocopy
retro_ecab_767,
Echinops telfairi ENSETEG000000200084 retrocopies
retro_etel_1088, retro_etel_1462, retro_etel_1877, retro_etel_676,
Felis catus ENSFCAG000000270171 retrocopy
retro_fcat_1507,
Homo sapiens ENSG00000162521 6 retrocopies
retro_hsap_1305, retro_hsap_2675, retro_hsap_2814 , retro_hsap_3292, retro_hsap_3600, retro_hsap_3601,
Macropus eugenii ENSMEUG000000143791 retrocopy
retro_meug_1032,
Myotis lucifugus ENSMLUG000000007492 retrocopies
retro_mluc_2275, retro_mluc_892,
Macaca mulatta ENSMMUG000000099401 retrocopy
retro_mmul_75,
Mustela putorius furoENSMPUG000000152141 retrocopy
retro_mputfur_104,
Mus musculus ENSMUSG000000572361 retrocopy
retro_mmus_356,
Nomascus leucogenys ENSNLEG000000028056 retrocopies
retro_nleu_1061, retro_nleu_1179, retro_nleu_1194, retro_nleu_1356, retro_nleu_1379, retro_nleu_2982,
Petromyzon marinus ENSPMAG000000071891 retrocopy
retro_pmar_26,
Pongo abelii ENSPPYG000000015886 retrocopies
retro_pabe_1093, retro_pabe_2210, retro_pabe_2720, retro_pabe_2958, retro_pabe_3529, retro_pabe_3611,
Pteropus vampyrus ENSPVAG000000109812 retrocopies
retro_pvam_1094, retro_pvam_902,
Rattus norvegicus ENSRNOG000000214921 retrocopy
retro_rnor_1270,
Sarcophilus harrisii ENSSHAG000000109231 retrocopy
retro_shar_399,
Ictidomys tridecemlineatus ENSSTOG000000120111 retrocopy
retro_itri_1168,

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 = 0.29 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .09 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .16 RPM
CEU_NA12004 0 .08 RPM
CEU_NA12400 0 .04 RPM
CEU_NA12751 0 .15 RPM
CEU_NA12760 0 .04 RPM
CEU_NA12827 0 .24 RPM
CEU_NA12872 0 .19 RPM
CEU_NA12873 0 .06 RPM
FIN_HG00183 0 .11 RPM
FIN_HG00277 0 .15 RPM
FIN_HG00315 0 .14 RPM
FIN_HG00321 0 .09 RPM
FIN_HG00328 0 .07 RPM
FIN_HG00338 0 .09 RPM
FIN_HG00349 0 .03 RPM
FIN_HG00375 0 .10 RPM
FIN_HG00377 0 .08 RPM
FIN_HG00378 0 .13 RPM
GBR_HG00099 0 .12 RPM
GBR_HG00111 0 .19 RPM
GBR_HG00114 0 .11 RPM
GBR_HG00119 0 .26 RPM
GBR_HG00131 0 .29 RPM
GBR_HG00133 0 .07 RPM
GBR_HG00134 0 .15 RPM
GBR_HG00137 0 .14 RPM
GBR_HG00142 0 .14 RPM
GBR_HG00143 0 .03 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .15 RPM
TSI_NA20518 0 .06 RPM
TSI_NA20532 0 .17 RPM
TSI_NA20538 0 .09 RPM
TSI_NA20756 0 .12 RPM
TSI_NA20765 0 .17 RPM
TSI_NA20771 0 .11 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .22 RPM
YRI_NA18870 0 .17 RPM
YRI_NA18907 0 .17 RPM
YRI_NA18916 0 .08 RPM
YRI_NA19093 0 .05 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .21 RPM
YRI_NA19118 0 .08 RPM
YRI_NA19213 0 .22 RPM
YRI_NA19214 0 .10 RPM
YRI_NA19223 0 .10 RPM

Indel association:

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



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