RetrogeneDB ID:

retro_hsap_3364

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:5:110284188..110286477(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000248966
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:BCLAF1
Ensembl ID:ENSG00000029363
Aliases:BCLAF1, BTF, bK211L9.1
Description:BCL2-associated transcription factor 1 [Source:HGNC Symbol;Acc:16863]


Retrocopy-Parental alignment summary:






>retro_hsap_3364
GGTCGCTCCAATTCTAGATCACATTCTTCAAGGTCAAAGTCTAGATGACAGTCTAGTTCTCGATCAAGATCAAGATCTCA
TTCTAGAAAGAAGCGACACAGTTCTAGGTCTCGTTCCAGAACATATTCAAGGTCTTGGAGTAGAGATCGTATGTATTCTA
GAGATGATCGTCGTGAGTACAGAAATAATAGAGGAATGAAATGACCTTATGGGTACAGAGGAAGGGGTAGAGGGTATTAT
CAAGGAGGAGGAGGTAGATATCATCTAGGTGGTTATAGACCTGTCCGGAATAGGAGGCACTCTAGGAGTCCTAGACGAGG
TCGTTCACATTCCAGGAGTCCAAAAAGAAGATCCGTTTCTTCTCAAAGATCCAGAAGCAGATCTCACTGGTCATATAGCT
CTTCTAGGTCTCCAAGATCATTCTCTTCTCGTTCTTCATCTCCATATAGCAAATCTCCTGTTTCTAAAAGACGAGGGTCT
CAGGAAAAACAAGCCAAAAAAGCTGAAGGGGAACCCCAAGAAGAGAGTCCGTTGAAAACTAAATCACAGGAGGAACTGAA
AGATACATTTGAACATGATCCATCTGAGTCTATCGATGAATTTAGTAACTCATCAGCCACATCCGGTGATATTTGGCCTG
GCCTTACAGCTTATAATAATAGTCCCAGATCACCCCATAGTCCTTCACATATTGCTACACCACCTAGTCAGAGTTCATCT
TGCTCTGATGCTCCCATGCTCAGTACAGTTCACTCTGCAAAAAATACTCCTTCTCAGCATTCAAAATCCATTCAGCATAG
TCCTGAAAGGTCTGGGTCTGGTTCTGTTGGAAATGGATCTAGTCCATACAGTCCTTCTCAGAATAGTCCAGTTCATCACA
TCCCTTCACGAAGAAGTCCTGCAAAGACAATCGCACCACAGAATGCTCCAAGAGATGAGTCTAGGGGCCGTTCCTCATTT
TATCCTGATAATGGAGATCAGGAAACTGCAAAGACTGGGAAGTTCTAAAAAGGTTCACAGATGAAGAGTCTAGAGTATTC
CTGCTTGATAGGGGTAATGCCAGGGATAAAGAGGCTTCAAAAGAGAAAGGATCAGAGAAAGGGAGGGCAGAGGGAGAATG
GGAAGATCAGGAAGCTCTAGATTACTTCAGTGATAAAGAGTCTGGAAAACAAAGTTTAATGATTCAGAAGGGGATGGCAC
AGAGGAGACAGAGGATTATAGACAGTTCAGGAAGTCAGTCCTCACAGATCAAGGTAAAAGTTTTGCTGCTGCATCTCACC
GGAATACTGAGGAGGAAGGACTCAAGTACAAGTCCAAAGTTTCACTGAAAGGCAATAGAGAAAGTGGTGGATTTAGAGAA
GAAAAAAATTATGAACTTAAAGAAGCTGGATATGTAGTGGAAAGGCCTAGCACTACAAAAGATAAGCACAAAGAAGAAGA
CAAAAATTCTGAAAGAATAATAGTAAAGAAAGAAACTCAGTCACCTGAGCAGGTAAAGTCTGAAAAGCTCAAAGACCTCT
TTGATTACAATCCCCCTCTACACAAGAATCTGGATGCATGAGAAAGTCTACCTTCAGAGAGGAAAGCCCACTTAGGATCA
AAATGATAGCAAGTGATTCTCATCATCCTGAAGTCAAACTCAAAATGGCACCTGTTCCTCTTGATGATTCTAACAGACCT
GCTTCCTTGACTAAAGACAGGCGGCTTGCTAGTACACTTGTCCATTCTGTCAAGAAGGAGCAAGAATTCTGATCCATCTT
TGACCACATTAAGTTGCCACAGGCCAGCAAAAGCACTTCAGAGTCATTTATTTAACACATTGTGTTCTTGGTTCATCATG
TTAAAGAGCAATACTTCAGGTCAGCTGCAATGACCCTAAACAAGCGGTTTACTTCCCATCAGAAAGCCACTGAAGAACAT
AGTACTCGGCAAAAGAGCCCTGAAATACACAGGAGAATTGACATCTCACCAAGTACCCTGAGGAAGCATACCCATTTAGC
AGGGGACGAGAGAGTTTTTAAAGAAGAAAATCAAAAGGGAGATAAAAAAAAATTAAGGTGTGACTCTGCTGACCTTCAGC
ATGACATTGATCACCGTAGAAAAGAAATAAGTAAAGAACGGGGAAATTCCAAGGGCCCCAGGGAATCCAGTGGATCAAGA
AAGCAGGAAAAAACTCCAAAAGATTACAAGGAATACAAATCTTACAAAGATGACAGTAAACATAAAAATAGAGAGCAAGA
TCATTCTCGATCTTCATCCTCTTCACCATCACCTTCTTCTCCCAGTTCT

ORF - retro_hsap_3364 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.31 %
Parental protein coverage: 87.49 %
Number of stop codons detected: 5
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalGRSNSRSHSSRSKSRSQSSSRSRSRSHSRKKRYSSRSRSRTYSRSRSRDRMYSRDYRRDYRNNRGMRRPY
GRSNSRSHSSRSKSR.QSSSRSRSRSHSRKKR.SSRSRSRTYSRS.SRDRMYSRD.RR.YRNNRGM..PY
RetrocopyGRSNSRSHSSRSKSR*QSSSRSRSRSHSRKKRHSSRSRSRTYSRSWSRDRMYSRDDRREYRNNRGMK*PY
ParentalGYRGRGRGYYQGGGGRYHRGGYRPVWNRRHSRSPRRGRSRSRSPKRRSVSSQRSRSRSRRSYRSSRSPRS
GYRGRGRGYYQGGGGRYH.GGYRPV.NRRHSRSPRRGRS.SRSPKRRSVSSQRSRSRS..SY.SSRSPRS
RetrocopyGYRGRGRGYYQGGGGRYHLGGYRPVRNRRHSRSPRRGRSHSRSPKRRSVSSQRSRSRSHWSYSSSRSPRS
ParentalSSSRSSSPYSKSPVSKRRGSQEKQTKKAEGEPQEESPLKSKSQEEPKDTFEHDPSESIDEFNKSSATSGD
.SSRSSSPYSKSPVSKRRGSQEKQ.KKAEGEPQEESPLK.KSQEE.KDTFEHDPSESIDEF..SSATSGD
RetrocopyFSSRSSSPYSKSPVSKRRGSQEKQAKKAEGEPQEESPLKTKSQEELKDTFEHDPSESIDEFSNSSATSGD
ParentalIWPGLSAYDNSPRSPHSPSPIATPPSQSSSCSDAPMLSTVHSAKNTPSQHSHSIQHSPERSGSGSVGNGS
IWPGL.AY.NSPRSPHSPS.IATPPSQSSSCSDAPMLSTVHSAKNTPSQHS.SIQHSPERSGSGSVGNGS
RetrocopyIWPGLTAYNNSPRSPHSPSHIATPPSQSSSCSDAPMLSTVHSAKNTPSQHSKSIQHSPERSGSGSVGNGS
ParentalSRYSPSQNSPIHHIPSRRSPAKTIAPQNAPRDESRGRSSFYPDGGDQETAKTGKF-LKRFTDEESRVFLL
S.YSPSQNSP.HHIPSRRSPAKTIAPQNAPRDESRGRSSFYPD.GDQETAKTGKF.LKRFTDEESRVFLL
RetrocopySPYSPSQNSPVHHIPSRRSPAKTIAPQNAPRDESRGRSSFYPDNGDQETAKTGKF<LKRFTDEESRVFLL
ParentalDRGNTRDKEASKEKGSEKGRAEGEWEDQEALDYFSDKESGKQ-KFNDSEGDDTEETEDYRQFRKSVLADQ
DRGN.RDKEASKEKGSEKGRAEGEWEDQEALDYFSDKESGKQ.KFNDSEGD.TEETEDYRQFRKSVL.DQ
RetrocopyDRGNARDKEASKEKGSEKGRAEGEWEDQEALDYFSDKESGKQ<KFNDSEGDGTEETEDYRQFRKSVLTDQ
ParentalGKSFATASHRNTEEEGLKYKSKVSLKGNRESDGFREEKNYKLKETGYVVERPSTTKDKHKEEDKNSERIT
GKSFA.ASHRNTEEEGLKYKSKVSLKGNRES.GFREEKNY.LKE.GYVVERPSTTKDKHKEEDKNSERI.
RetrocopyGKSFAAASHRNTEEEGLKYKSKVSLKGNRESGGFREEKNYELKEAGYVVERPSTTKDKHKEEDKNSERII
ParentalVKKETQSPEQVKSEKLKDLFDYSPPLHKNLDARE-KSTFREESPLRIKMIASDSHRPEVKLKMAPVPLDD
VKKETQSPEQVKSEKLKDLFDY.PPLHKNLDA.E.KSTFREESPLRIKMIASDSH.PEVKLKMAPVPLDD
RetrocopyVKKETQSPEQVKSEKLKDLFDYNPPLHKNLDA*E<KSTFREESPLRIKMIASDSHHPEVKLKMAPVPLDD
ParentalSNRPASLTKDRLLASTLVHSVKKEQEFRSIFDHIKLPQASKSTSESFIQHIVSLVHHVKEQYFKSAAMTL
SNRPASLTKDR.LASTLVHSVKKEQEF.SIFDHIKLPQASKSTSESFI.HIV.LVHHVKEQYF.SAAMTL
RetrocopySNRPASLTKDRRLASTLVHSVKKEQEF*SIFDHIKLPQASKSTSESFI*HIVFLVHHVKEQYFRSAAMTL
ParentalNERFTSYQKATEEHSTRQKSPEIHRRIDISPSTLRKHTRLAGEERVFKEENQKGD-KKLRCDSADLRHDI
N.RFTS.QKATEEHSTRQKSPEIHRRIDISPSTLRKHT.LAG.ERVFKEENQKGD...LRCDSADL.HDI
RetrocopyNKRFTSHQKATEEHSTRQKSPEIHRRIDISPSTLRKHTHLAGDERVFKEENQKGDXXXLRCDSADLQHDI
ParentalDRRRKERSKERGDSKGSRESSGSRKQEKTPKDYKEYKSYKDDSKHK-REQDHSRSSSSSASPSSPSS
D.RRKE.SKERG.SKG.RESSGSRKQEKTPKDYKEYKSYKDDSKHK.REQDHSRSSSSS.SPSSPSS
RetrocopyDHRRKEISKERGNSKGPRESSGSRKQEKTPKDYKEYKSYKDDSKHKNREQDHSRSSSSSPSPSSPSS

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 124 .91 RPM
bodymap2_adrenal 0 .02 RPM 198 .55 RPM
bodymap2_brain 0 .02 RPM 247 .27 RPM
bodymap2_breast 0 .02 RPM 128 .46 RPM
bodymap2_colon 0 .00 RPM 124 .21 RPM
bodymap2_heart 0 .02 RPM 104 .29 RPM
bodymap2_kidney 0 .00 RPM 164 .64 RPM
bodymap2_liver 0 .04 RPM 51 .90 RPM
bodymap2_lung 0 .00 RPM 112 .15 RPM
bodymap2_lymph_node 0 .00 RPM 187 .41 RPM
bodymap2_ovary 0 .02 RPM 288 .11 RPM
bodymap2_prostate 0 .00 RPM 208 .05 RPM
bodymap2_skeletal_muscle 0 .05 RPM 76 .86 RPM
bodymap2_testis 0 .08 RPM 227 .05 RPM
bodymap2_thyroid 0 .00 RPM 303 .26 RPM
bodymap2_white_blood_cells 0 .00 RPM 217 .18 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3364 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3364 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3364 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3364 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3364 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2287
Pongo abelii retro_pabe_2767
Macaca mulatta retro_mmul_2102
Parental genes homology:
Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species Parental gene accession Retrocopies number
Felis catus ENSFCAG000000276141 retrocopy
retro_fcat_978,
Homo sapiens ENSG00000029363 1 retrocopy
retro_hsap_3364 ,
Gorilla gorilla ENSGGOG000000018241 retrocopy
retro_ggor_2279,
Macaca mulatta ENSMMUG000000037101 retrocopy
retro_mmul_2102,
Pongo abelii ENSPPYG000000170321 retrocopy
retro_pabe_2767,
Pan troglodytes ENSPTRG000000186351 retrocopy
retro_ptro_2287,
Tupaia belangeri ENSTBEG000000148861 retrocopy
retro_tbel_628,

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 .04 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .02 RPM
CEU_NA12760 0 .09 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .08 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .04 RPM
FIN_HG00315 0 .03 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .07 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .06 RPM
FIN_HG00375 0 .05 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .02 RPM
GBR_HG00099 0 .06 RPM
GBR_HG00111 0 .02 RPM
GBR_HG00114 0 .05 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .09 RPM
GBR_HG00133 0 .02 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .05 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .06 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .08 RPM
TSI_NA20532 0 .03 RPM
TSI_NA20538 0 .09 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .06 RPM
TSI_NA20771 0 .03 RPM
TSI_NA20786 0 .03 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .03 RPM
YRI_NA18916 0 .06 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .03 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .05 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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