RetrogeneDB ID:

retro_hsap_3307

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:5:39719085..39720797(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000250492
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:INTS6
Ensembl ID:ENSG00000102786
Aliases:INTS6, DBI-1, DDX26, DDX26A, DICE1, HDB, INT6, Notchl2
Description:integrator complex subunit 6 [Source:HGNC Symbol;Acc:14879]


Retrocopy-Parental alignment summary:






>retro_hsap_3307
GAACCAATGGTTATTGATAAACTTCCTTTTGACAAATACGAGTTGGAACCTTCATCACTGACTCAATTTATCCTGGAAAG
GAAATCTCCTCAAACATGTTGGCAGGTGTACGTCAGCAATAGTGCAAAATACAGTGAACTTGGTCATCCTTTTGGTTACT
TGAAAGCCAGTATGGCACTGAACTGTGTCAATGTATTTGTGATGCCTTACAATTACCCAGTCCTTCCCCTCTTAGATGAC
TTGCTTAAAGTGCATAAAGCAAAACCAACACTGAAGTGGAGACAGTCATTTGAAAGTTATTTGAAGACCGTGCCTCCCTA
CTATCTCGGGCCCTTCAAGAAAGCTGTTAGTATGATGGGAGCACCTAACCTAATAGCAGACAGTATGGAATATGGACTTA
GTTACAGTGTCATTTCATACCTCAAAAAACTGAGTCAACAGGCCAAAATAGAATCTGATCGAGTCATTGGATCTGTAGGC
AAAAAAGGAGTACAGGAAACTGAAATAAAAGTCTGGAGCCAATCACATGGTTTATCAAGGGCATATAGGAAAGATTTTCA
ACAGCTCCTCCAGGGAATTTCAGATGTCCCTCACAGACTGCTAGACCTTAATATGAAGGAATACGCTGGGTTCCACGTTG
CTTTGCTGAATAAGGATTTGAAGCCACAGACATTTAGAAATGCTTATGACATTCCAAGACGAAATCTTTTGGATCACTTA
ACAAGAATGAGATCTAATCTTTTGAAGCACACTCGCAGATTTCTTAAAGGACAGGACGAAGATCAAGTGCAGTGTTCCTA
TAGCACAAATGGGGAACTACCAGGAATACCTCAAGCAAGTTACCTTCTCCACTAAGAGAACTTGATCCTGATCAGCCGCA
AAGGTTACATACATTTGGCAATTCCTTTAAGCTGGATAAAAAGGGTATGATGACAGATGAAGCAGATGAATTTGTGGCTG
GACCTCAAAATAAACATAAATGACCTGGAGAATCAAATATGCAAGGGATCCCTAAAAGACGTCAGTGTATGTCTCCACTA
CTAAGAGGCAGACAGCAGAATCCTGTTGTAAACAATCATATCGGGGGAAAAGGACCACCTGCACCTACAACTCAAGCACA
GCCAGATCTTATTAAGCTTCTTCCTCTTCATAAAATTTCAGAAACCACTAATGATTCGATAATACATGATGTGGTTGAAA
ATCATGTTGCAGACCAACTTTCGTCAGACATTACACCAAATGCTATGGATACTGAATTTTCAACATCTTCTCCAGCCAGT
TTACTGGAAGGGCCAACCAATCATATGGAGGCTCCTGGTCATGACAATTTAGGAACGAATGACCTCACTGTTGGTGGATT
TTTAGAAAATCATGAGGAGCCAAGAGATAAAGAACAATGTGCTGAAGAGAACATACCAGCATCTTCACTCAACAAAGGAA
AGAAATTGATCCATTGCAGAAGCCATGAAGAGGTCAATATCGAACTAAAACCACAAATAATGAAAGAGATCTGAAAGCCA
GGGAGAAAATATGAAAGAATCTTCACTTTACTGAAGCATGTGCAAGGCAGTTTACAAACAAGACTAATATTTTTACAAAA
TGTTATTAAAGAAGCATCAAGGTTTTAAAAACGAATGCTAATAGAACAACTGGAGAACTTCTTGGATGAAATTCATCGAA
GAGCCAATCAGATCAACCATATTAATAGCAAT

ORF - retro_hsap_3307 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.52 %
Parental protein coverage: 64.6 %
Number of stop codons detected: 3
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalEPMVIDKLPFDKYELEPSPLTQFILERKSPQTCWQVYVSNSAKYSELGHPFGYLKASTALNCVNLFVMPY
EPMVIDKLPFDKYELEPS.LTQFILERKSPQTCWQVYVSNSAKYSELGHPFGYLKAS.ALNCVN.FVMPY
RetrocopyEPMVIDKLPFDKYELEPSSLTQFILERKSPQTCWQVYVSNSAKYSELGHPFGYLKASMALNCVNVFVMPY
ParentalNYPVLLPLLDDLFKVHKAKPTLKWRQSFESYLKTMPPYYLGPLKKAVRMMGAPNLIADSMEYGLSYSVIS
NYPVL.PLLDDL.KVHKAKPTLKWRQSFESYLKT.PPYYLGP.KKAV.MMGAPNLIADSMEYGLSYSVIS
RetrocopyNYPVL-PLLDDLLKVHKAKPTLKWRQSFESYLKTVPPYYLGPFKKAVSMMGAPNLIADSMEYGLSYSVIS
ParentalYLKKLSQQAKIESDRVIGSVGKKVVQETGIKVRSRSHGLSMAYRKDFQQLLQGISEDVPHRLLDLNMKEY
YLKKLSQQAKIESDRVIGSVGKK.VQET.IKV.S.SHGLS.AYRKDFQQLLQGIS.DVPHRLLDLNMKEY
RetrocopyYLKKLSQQAKIESDRVIGSVGKKGVQETEIKVWSQSHGLSRAYRKDFQQLLQGIS-DVPHRLLDLNMKEY
ParentalTGFQVALLNKDLKPQTFRNAYDIPRRNLLDHLTRMRSNLLKSTRR-FLKGQDEDQVHSVPIAQMGNYQEY
.GF.VALLNKDLKPQTFRNAYDIPRRNLLDHLTRMRSNLLK.TRR.FLK........SVPIAQMGNYQEY
RetrocopyAGFHVALLNKDLKPQTFRNAYDIPRRNLLDHLTRMRSNLLKHTRR>FLKDRTKIKC-SVPIAQMGNYQEY
ParentalLKQV-PSPLRELDPDQPRRLHTFGNPFKLDKKGMMIDEADEFVAGPQNKHKRPGEPNMQGIPKRRRCMSP
LKQV.PSPLRELDPDQP.RLHTFGN.FKLDKKGMM.DEADEFVAGPQNKHK.PGE.NMQGIPKRR.CMSP
RetrocopyLKQV>PSPLRELDPDQPQRLHTFGNSFKLDKKGMMTDEADEFVAGPQNKHK*PGESNMQGIPKRRQCMSP
ParentalLLRGRQQNPVVNNHIGGKGPPAPTTQAQPDLIKPLPLHKISETTNDSIIHDVVENHVADQLSSDITPNAM
LLRGRQQNPVVNNHIGGKGPPAPTTQAQPDLIK.LPLHKISETTNDSIIHDVVENHVADQLSSDITPNAM
RetrocopyLLRGRQQNPVVNNHIGGKGPPAPTTQAQPDLIKLLPLHKISETTNDSIIHDVVENHVADQLSSDITPNAM
ParentalDTEFSASSPASLLERPTNHMEALGHDHLGTNDLTVGGFLENHEEPRDKEQCAEENIPASSLNKGKKLMHC
DTEFS.SSPASLLE.PTNHMEA.GHD.LGTNDLTVGGFLENHEEPRDKEQCAEENIPASSLNKGKKL.HC
RetrocopyDTEFSTSSPASLLEGPTNHMEAPGHDNLGTNDLTVGGFLENHEEPRDKEQCAEENIPASSLNKGKKLIHC
ParentalRSHEEVNTELKAQIMKEIRKPGRKYERIFTLLKHVQGSLQTRLIFLQNVIKEASRFKKRMLIEQLENFLD
RSHEEVN.ELK.QIMKEI.KPGRKYERIFTLLKHVQGSLQTRLIFLQNVIKEASRF.KRMLIEQLENFLD
RetrocopyRSHEEVNIELKPQIMKEI*KPGRKYERIFTLLKHVQGSLQTRLIFLQNVIKEASRF*KRMLIEQLENFLD
ParentalEIHRRANQINHINSN
EIHRRANQINHINSN
RetrocopyEIHRRANQINHINSN

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 19 .42 RPM
bodymap2_adrenal 0 .00 RPM 17 .26 RPM
bodymap2_brain 0 .00 RPM 14 .65 RPM
bodymap2_breast 0 .00 RPM 22 .78 RPM
bodymap2_colon 0 .00 RPM 26 .26 RPM
bodymap2_heart 0 .00 RPM 24 .22 RPM
bodymap2_kidney 0 .00 RPM 31 .52 RPM
bodymap2_liver 0 .08 RPM 20 .60 RPM
bodymap2_lung 0 .00 RPM 24 .75 RPM
bodymap2_lymph_node 0 .00 RPM 35 .85 RPM
bodymap2_ovary 0 .02 RPM 31 .67 RPM
bodymap2_prostate 0 .00 RPM 41 .71 RPM
bodymap2_skeletal_muscle 0 .00 RPM 17 .97 RPM
bodymap2_testis 0 .04 RPM 128 .28 RPM
bodymap2_thyroid 0 .00 RPM 28 .59 RPM
bodymap2_white_blood_cells 0 .00 RPM 46 .52 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3307 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3307 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3307 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3307 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3307 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2164
Gorilla gorilla retro_ggor_1307
Pongo abelii retro_pabe_2727
Parental genes homology:
Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000102786 1 retrocopy
retro_hsap_3307 ,
Homo sapiens ENSG000002422841 retrocopy
retro_hsap_3362,
Gorilla gorilla ENSGGOG000000011761 retrocopy
retro_ggor_1307,
Pongo abelii ENSPPYG000000053811 retrocopy
retro_pabe_2727,
Pan troglodytes ENSPTRG000000058901 retrocopy
retro_ptro_2164,

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 = 0.09 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .06 RPM
CEU_NA11930 0 .03 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .04 RPM
CEU_NA12751 0 .00 RPM
CEU_NA12760 0 .04 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .03 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .03 RPM
FIN_HG00328 0 .05 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .09 RPM
FIN_HG00375 0 .05 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 .02 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .07 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 .06 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .09 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 .03 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .03 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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