RetrogeneDB ID:

retro_hsap_1529

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:15:97300218..97301823(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000214424
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:FAM149B1
Ensembl ID:ENSG00000138286
Aliases:None
Description:family with sequence similarity 149, member B1 [Source:HGNC Symbol;Acc:29162]


Retrocopy-Parental alignment summary:






>retro_hsap_1529
TCCAGATACACTCGGGAAGGCGATGCCACAGAGCTTGGAGCTGAAAGGAATAACAAAACATGCTCTTAACCATCATCTCC
CTCCCGAGAAGCTGGAGGAAATTTCCCCCACCAGTGACAGTCATGAGAAAGACATAAGTTCCCAAAGCGAGTCTGACATC
ACAAGAGAATCACCTTTTACATCAGCCGATGCTGGGAATTCACTGTCTGCTTTTCCAAGTTATACAGGCGCAGGGATATC
TACTGAAGGCAACTCAGACTTCTCCTGGGAATATGGTGAACTCGATCAAAATGCCACTGAAAAAGCCTAGGCAATGTTCA
CAGCCATTGATGAACCCTTGTATGAGCAGAAGTTGAGTGTGCATACCAAGAGTCTACAAGAAGAGCGCCAACAGTGGACA
GCTAGCTTTCCTCACCTCAGGATTCTAGGTAGGCAGATAATCATTCCAAGTGAAGGTTATAGATTGTATCCTAGATCCCC
TTCTGCTGTTTCAGCTTCATATGAAACAACCTTGTCTCAAGAAAGAGATTCTACTATATTTGGTATAAGGGGAAAGAAGT
TACATTTTTCATCTTCGTATGCTCATAAAGCATCTTCTATTGCCAAATCCTCCAGCTTTTCTTTTATGGAAAGAGACGAG
GAAGACTCTATAATCATCTCCGAAGGAATAATTGAGGAATACCTAGCATTCGATTGCACAGATATGGAAGAGGGATTTCA
TGGGAAGAAATCAGAAGCAGCTACAGAGAAACAGAAATTAGGGTATCCTCCCATTGCTCCATTTTACTGCATGAAAGAAG
ATGTCCTTGTTTATGTGTTTGACAATGTATGGAGCAAGGTTGTGAGCTGTATGGAGCAGTTGACACGTAGTCACTGGGAA
GGATTTGCCCACCATGATGAGAGTAATGTTGCAGTTACCAGACCCGTTTCAGAAAGTTTCTGTGTGCTGAGTGAGCCACA
TCCTTTGGTGTTACCACGAGTGCCACAGTCTAAGGTGCTGTCCGTTACCTCAAATCCAATGAGTCTCTGTCAAGCAAGTA
GTCATCAGCCAAATGTTAATGGTCTCTTGGTTTATGGGATGCCTCTACAGCCAAGAAATCTCTCCCTAATGGACAAGCTC
CTAGATCTTGATGACAAGCTACTTATGAGGCCTGGGTCCAGTACCATCCTTTCAACTCGAAATTGGCCAAATCGAGCTGT
GGAGTTTTTAGTACATCATCTCTGTCATACACAGTGCAGTCCACCAAGAGACGCAATCCATCGCCACGAACCCTTCATCC
GATCAGCACAAGCCATTCACGTGCTGGAATACCAAGACTTGTGGAAGAAATCCTCAGAGGAGCCCGAGTCCCAGCGGCAG
CCAACTGGCTCTCCTCTCCCTCACCAATGTCCCTGAGTCGAAATAATCTGCTACCACCTACTAGCACAGCTGAAGTGGAA
CTTGTGAGCACTGTGGGGCCACAAAGACAGACGGAGCCCCGTGGCGACTCCAGTCGAGCTCCAAGTGTGGTGGTGGATGA
ACTTAACTATCAGCAGCCACAAGAAAGGCTCCTTTTGCCCAACTTTTTCTCCAGGCCCAACACAACTCAATCATTTTTGG
TAGAG

ORF - retro_hsap_1529 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.59 %
Parental protein coverage: 91.75 %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalSRYTR-KAVPQSLELKGITKHALNHHPPPEKLEEISPTSDSHEKDTSSQSKSDITRESSFTSADTGNSLS
SRYTR.KA.PQSLELKGITKHALNHH.PPEKLEEISPTSDSHEKD.SSQS.SDITRES.FTSAD.GNSLS
RetrocopySRYTR>KAMPQSLELKGITKHALNHHLPPEKLEEISPTSDSHEKDISSQSESDITRESPFTSADAGNSLS
ParentalAFPSYTGAGISTEGSSDFSWGYGELDQNATEKVQTMFTAIDELLYEQKLSVHTKSLQEECQQWTASFPHL
AFPSYTGAGISTEG.SDFSW.YGELDQNATEK...MFTAIDE.LYEQKLSVHTKSLQEE.QQWTASFPHL
RetrocopyAFPSYTGAGISTEGNSDFSWEYGELDQNATEKA*AMFTAIDEPLYEQKLSVHTKSLQEERQQWTASFPHL
ParentalRILGRQIITPSEGYRLYPRSPSAVSASYETTLSQERDSTIFGIRGKKLHFSSSYAHKASSIAKSSSFCSM
RILGRQII.PSEGYRLYPRSPSAVSASYETTLSQERDSTIFGIRGKKLHFSSSYAHKASSIAKSSSF..M
RetrocopyRILGRQIIIPSEGYRLYPRSPSAVSASYETTLSQERDSTIFGIRGKKLHFSSSYAHKASSIAKSSSFSFM
ParentalERDEEDSIIVSEGIIEEYLAFDHIDIEEGFHGKKSEAATEKQKLGYPPIAPFYCMKEDVLAYVFDSVWCK
ERDEEDSII.SEGIIEEYLAFD..D.EEGFHGKKSEAATEKQKLGYPPIAPFYCMKEDVL.YVFD.VW.K
RetrocopyERDEEDSIIISEGIIEEYLAFDCTDMEEGFHGKKSEAATEKQKLGYPPIAPFYCMKEDVLVYVFDNVWSK
ParentalVVSCMEQLTRSHWEGFASDDESNVAVTRPDSESSCVLSELHPLVLPRVPQSKVLYITSNPMSLCQASRHQ
VVSCMEQLTRSHWEGFA..DESNVAVTRP.SES.CVLSE.HPLVLPRVPQSKVL..TSNPMSLCQAS.HQ
RetrocopyVVSCMEQLTRSHWEGFAHHDESNVAVTRPVSESFCVLSEPHPLVLPRVPQSKVLSVTSNPMSLCQASSHQ
ParentalPNVNDLLVHGMPLQPRNLSLMDKLLDLDDKLLMRPGSSTILSTRNWPNRAVEFSTSSLSYTVQS-TRRRN
PNVN.LLV.GMPLQPRNLSLMDKLLDLDDKLLMRPGSSTILSTRNWPNRAVEF....L..T..S....R.
RetrocopyPNVNGLLVYGMPLQPRNLSLMDKLLDLDDKLLMRPGSSTILSTRNWPNRAVEFLVHHLCHTQCS<STKRR
ParentalPP-PRTLHPISTSHSCAETPRSVEEILRGARVPVAPDSLSSPSPTPLSRNNLLPPIGTAEVEHVSTVGPQ
.P.PRTLHPISTSHS.A..PR.VEEILRGARVP.A...LSSPSP..LSRNNLLPP..TAEVE.VSTVGPQ
RetrocopyNPSPRTLHPISTSHSRAGIPRLVEEILRGARVPAAANWLSSPSPMSLSRNNLLPPTSTAEVELVSTVGPQ
ParentalRQMKPHGDSSRAQSAVVDEPNYQQPQERLLLPDFFPRPNTTQSFLLD
RQ..P.GDSSRA.S.VVDE.NYQQPQERLLLP.FF.RPNTTQSFL..
RetrocopyRQTEPRGDSSRAPSVVVDELNYQQPQERLLLPNFFSRPNTTQSFLVE

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 17 .83 RPM
bodymap2_adrenal 0 .00 RPM 18 .61 RPM
bodymap2_brain 0 .02 RPM 26 .96 RPM
bodymap2_breast 0 .02 RPM 22 .32 RPM
bodymap2_colon 0 .14 RPM 26 .08 RPM
bodymap2_heart 0 .00 RPM 14 .92 RPM
bodymap2_kidney 0 .00 RPM 32 .99 RPM
bodymap2_liver 0 .00 RPM 15 .06 RPM
bodymap2_lung 0 .00 RPM 25 .12 RPM
bodymap2_lymph_node 0 .00 RPM 23 .83 RPM
bodymap2_ovary 0 .00 RPM 30 .84 RPM
bodymap2_prostate 0 .00 RPM 41 .10 RPM
bodymap2_skeletal_muscle 0 .00 RPM 9 .28 RPM
bodymap2_testis 0 .25 RPM 47 .92 RPM
bodymap2_thyroid 0 .00 RPM 21 .98 RPM
bodymap2_white_blood_cells 0 .14 RPM 19 .83 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1529 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1529 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1529 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1529 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1529 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1036
Parental genes homology:
Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000138286 1 retrocopy
retro_hsap_1529 ,
Macaca mulatta ENSMMUG000000112811 retrocopy
retro_mmul_2158,
Nomascus leucogenys ENSNLEG000000165751 retrocopy
retro_nleu_1938,
Pan troglodytes ENSPTRG000000026232 retrocopies
retro_ptro_1036, retro_ptro_2950,
Rattus norvegicus ENSRNOG000000065541 retrocopy
retro_rnor_2124,
Ictidomys tridecemlineatus ENSSTOG000000021421 retrocopy
retro_itri_429,

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 = 0.02 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 .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 .00 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .02 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .02 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 .00 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 .02 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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