RetrogeneDB ID:

retro_hsap_55

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:X:92964418..92965165(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000179083
Aliases:FAM133A, CT115
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:FAM133B
Ensembl ID:ENSG00000234545
Aliases:None
Description:family with sequence similarity 133, member B [Source:HGNC Symbol;Acc:28629]


Retrocopy-Parental alignment summary:






>retro_hsap_55
ATGGGGAAGCGGGATAATCGGGTAGCCTATATGAATCCTATAGCAATGGCCAGATGGAGAGGCCCAACTCAATCTGTGGG
CCCAACAATCCAAGATTATCTAAATCGACCAAGACCCACCTGGGAAGAAGTAAAGAAACAATTAGAAAATAAAAAAACAG
GTTCAAAAGCATTAGCTGAATTTGAAGAAAAAATGAATGAAAATTGGAAGAAAGAACTTGAAAAAAGCAGAGAGAAATTA
TTAAGTGGAAATGAGAGCTCATCTAAAAAAAGAGAAAGAAAGAAAAAGAGAAAGAAGAAATCTTGTCGGTCTTCATCTTC
TTCATCAAGCTCTGATTCTTCAAGCAGTTCTTCAGATTCTGAGGATGAGGAAAAGAAACAAGGAAAAAGGAGAAAGAAAA
AGAAGAACCGTTCATACAAATCATCCCAAAGCTCTACGCATGAATCAGAATCAGAGAGCAAGGAGTCTGTAAAAAAGAAA
AAGAAGTCAAAGGATGAAACAGAGAAAGAAAAGGATGTAAGAAGCCTCAGCAAAAAAAGAAAGAAAAGTTACCCTGATGA
TAAACCTTTATCATCTGAGTCCTCATCTGAATCAGATTATGAAGAGGATGTGCAAGCAAAAAAGAAGAGAAGGTGTGAAG
AGCGAGAACAAGCAAAGGAAAAAGTAAAGAAGAAGAAGAAGAAACAGCACAAGAAACATAGTAAGAAGAAGAAAAAGAAG
TCTGGATCAAGTCACAAGTCAAGGTAA

ORF - retro_hsap_55 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 82.04 %
Parental protein coverage: 97.98 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMGKRDNRVAYMNPIAMARSRGPIQSSGPTIQDYLNRPRPTWEEVKEQLEKKKKGSKALAEFEEKMNENWK
MGKRDNRVAYMNPIAMAR.RGP.QS.GPTIQDYLNRPRPTWEEVK.QLE.KK.GSKALAEFEEKMNENWK
RetrocopyMGKRDNRVAYMNPIAMARWRGPTQSVGPTIQDYLNRPRPTWEEVKKQLENKKTGSKALAEFEEKMNENWK
ParentalKELEKHREKLLSGSESSSKKRQRKKKEKKKSGRYSSSSSSSSDSSSSSSDSEDEDKKQGKRRKKKKNRSH
KELEK.REKLLSG.ESSSKKR.RKKK.KKKS.R.SSSSSSSSDSSSSSSDSEDE.KKQGKRRKKKKNRS.
RetrocopyKELEKSREKLLSGNESSSKKRERKKKRKKKSCR-SSSSSSSSDSSSSSSDSEDEEKKQGKRRKKKKNRSY
ParentalKSSESSMSETESDSKDSLKKKKKSKDGTEKEKDIKGLSKKR-KMYSEDKPLSSESLSESEYIEEVRAKKK
KSS.SS..E.ES.SK.S.KKKKKSKD.TEKEKD...LSKKR.K.Y..DKPLSSES.SES.Y.E.V.AKKK
RetrocopyKSSQSSTHESESESKESVKKKKKSKDETEKEKDVRSLSKKRKKSYPDDKPLSSESSSESDYEEDVQAKKK
ParentalKSSEEREKATEKTKKKKK--HKKHSKKKKKKAASS
...EERE.A.EK.KKKKK..HKKHSKKKKKK..SS
RetrocopyRRCEEREQAKEKVKKKKKKQHKKHSKKKKKKSGSS

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 4 .81 RPM
bodymap2_adrenal 0 .00 RPM 10 .52 RPM
bodymap2_brain 4 .08 RPM 13 .83 RPM
bodymap2_breast 0 .19 RPM 7 .84 RPM
bodymap2_colon 0 .15 RPM 7 .13 RPM
bodymap2_heart 0 .09 RPM 6 .18 RPM
bodymap2_kidney 0 .04 RPM 9 .18 RPM
bodymap2_liver 0 .00 RPM 3 .91 RPM
bodymap2_lung 0 .00 RPM 6 .93 RPM
bodymap2_lymph_node 0 .00 RPM 10 .12 RPM
bodymap2_ovary 0 .29 RPM 12 .43 RPM
bodymap2_prostate 0 .33 RPM 12 .47 RPM
bodymap2_skeletal_muscle 0 .00 RPM 4 .02 RPM
bodymap2_testis 17 .01 RPM 11 .46 RPM
bodymap2_thyroid 0 .06 RPM 11 .73 RPM
bodymap2_white_blood_cells 0 .00 RPM 10 .41 RPM

ChIP-Seq - click to see more details

RNA Polymerase II activity near the 5' end of retro_hsap_55 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_55 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_55 retrocopy 5' end.

Lab - click to see more details

retro_hsap_55 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_55 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 14 parental genes, and 23 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000074381 retrocopy
retro_amel_102,
Callithrix jacchus ENSCJAG000000139103 retrocopies
retro_cjac_1084, retro_cjac_1163, retro_cjac_4095,
Equus caballus ENSECAG000000268101 retrocopy
retro_ecab_95,
Homo sapiens ENSG00000234545 4 retrocopies
retro_hsap_2336, retro_hsap_3179, retro_hsap_55 , retro_hsap_577,
Loxodonta africana ENSLAFG000000297551 retrocopy
retro_lafr_594,
Myotis lucifugus ENSMLUG000000059331 retrocopy
retro_mluc_2301,
Macaca mulatta ENSMMUG000000198024 retrocopies
retro_mmul_1415, retro_mmul_226, retro_mmul_420, retro_mmul_765,
Mus musculus ENSMUSG000000585032 retrocopies
retro_mmus_3481, retro_mmus_3519,
Nomascus leucogenys ENSNLEG000000153331 retrocopy
retro_nleu_14,
Pongo abelii ENSPPYG000000258251 retrocopy
retro_pabe_225,
Rattus norvegicus ENSRNOG000000091631 retrocopy
retro_rnor_2891,
Sus scrofa ENSSSCG000000153171 retrocopy
retro_sscr_49,
Ictidomys tridecemlineatus ENSSTOG000000281951 retrocopy
retro_itri_12,
Tupaia belangeri ENSTBEG000000116741 retrocopy
retro_tbel_1,

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 = 0.03 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .00 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 .00 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .03 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .03 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .00 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .00 RPM

Indel association:

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



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