RetrogeneDB ID:

retro_hsap_3926

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:8:1678371..1679027(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000254265
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:DFFA
Ensembl ID:ENSG00000160049
Aliases:None
Description:DNA fragmentation factor, 45kDa, alpha polypeptide [Source:HGNC Symbol;Acc:2772]


Retrocopy-Parental alignment summary:






>retro_hsap_3926
ATGGATGTGACTGGGGACACCAGGGCATGAGAACCCGGCGAGATTCAGACTCTAAAGCTGGGCCGGCTGCACCGCAACTG
CAGCCGTGAGCAGCACAGGTGGTCACCTCCCGCCTCGAGGACCTGAGCAGCAAGGCCTGTGACAGCCTGGCCATTGACAA
GTCCCTGCCACTGATCACCCTGGTCCTGCAGAGGCTGGCACCACGGTGATGAGGATTACTTCCTGTGTCTGCCTTCCAAT
ACTAAGAGTATGGCATTGACCAATAACGAGACGAGGGCATAGGACAATTCTGATGGAGATATGGCTTGGGTTTCCAGGCA
TCCTTTGATGTGGATGAACTATAGCGGGGCATGGTTGAAGCAGAAGAATGTGGCCAGGCAGCTGAACAAGGCTCCATCCA
GTGCCATCCTCCTATCAGAGGAAGACTGTCCCGTGCTCATTCATATTCTGTGTTCAGATCTGGCTCAGGAACTAAGCCAA
GGCTGTGCCACCATCCAGGTTCGCAGGACGCGCTCCAGCAGGTGCTTCACAGAGGAAGTGGTCTGTCCGGGCAGCTCCTG
GAGCTGTACCTCCTGGTTTTGGAGAAAGAGGGCAGCCTCTTGTCAAGGCAAGAGGAGTCCAAAGCAGCCTTTGGTGATGA
GGCAGAGGCAGTAGAC

ORF - retro_hsap_3926 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 64.07 %
Parental protein coverage: 67.67 %
Number of stop codons detected: 2
Number of frameshifts detected 7


Retrocopy - Parental Gene Alignment:

ParentalMEVTGDAGVPESGEIRTLKPCLLRRNYSREQHG-VAASCLEDLRSKACDILAIDKSLTPVTLVL-AEDGT
M.VTGD....E.GEI.TLK...L.RN.SREQH..V..S.LEDL.SKACD.LAIDKSL...TLVL.AE.GT
RetrocopyMDVTGDTRA*EPGEIQTLKLGRLHRNCSREQHR<VVTSRLEDLSSKACDSLAIDKSLPLITLVL<AEAGT
ParentalIV-DDDDYFLCLPSNTKFVALASNEKWAYNNSDGGTAWIS-QESFDVDE-TDSGAG-LKWKNVARQLKED
.V.D..DYFLCLPSNTK..AL..NE..A..NSDG..AW.S.Q.SFDVDE.T..G.G.LK.KNVARQL...
RetrocopyTV<DE-DYFLCLPSNTKSMALTNNETRA*DNSDGDMAWVS<QASFDVDE<TIAGHG<LKQKNVARQLNKA
ParentalLSSIILLSEEDLQMLVDAPCSDLAQELRQSCATVQ-RLQHTLQQVLDQREEVRQSKQLLQLYLQALEKEG
.SS.ILLSEED...L....CSDLAQEL.Q.CAT.Q...Q..LQQVL........S.QLL.LYL..LEKEG
RetrocopyPSSAILLSEEDCPVLIHILCSDLAQELSQGCATIQ<GSQDALQQVLHRGSGL--SGQLLELYLLVLEKEG
ParentalSLLSKQEESKAAFGEEVDAVD
SLLS.QEESKAAFG.E..AVD
RetrocopySLLSRQEESKAAFGDEAEAVD

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 50 .77 RPM
bodymap2_adrenal 0 .00 RPM 40 .26 RPM
bodymap2_brain 0 .12 RPM 36 .36 RPM
bodymap2_breast 0 .00 RPM 46 .11 RPM
bodymap2_colon 0 .00 RPM 63 .07 RPM
bodymap2_heart 0 .00 RPM 25 .88 RPM
bodymap2_kidney 0 .00 RPM 51 .45 RPM
bodymap2_liver 0 .00 RPM 22 .39 RPM
bodymap2_lung 0 .00 RPM 26 .14 RPM
bodymap2_lymph_node 0 .00 RPM 42 .72 RPM
bodymap2_ovary 0 .00 RPM 76 .72 RPM
bodymap2_prostate 0 .00 RPM 52 .71 RPM
bodymap2_skeletal_muscle 0 .00 RPM 32 .25 RPM
bodymap2_testis 0 .00 RPM 55 .50 RPM
bodymap2_thyroid 0 .00 RPM 33 .14 RPM
bodymap2_white_blood_cells 0 .00 RPM 29 .91 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3926 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3926 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3926 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3926 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3926 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_2642
Pongo abelii retro_pabe_3242
Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000135351 retrocopy
retro_btau_211,
Homo sapiens ENSG00000160049 1 retrocopy
retro_hsap_3926 ,
Gorilla gorilla ENSGGOG000000127211 retrocopy
retro_ggor_2642,
Pongo abelii ENSPPYG000000018991 retrocopy
retro_pabe_3242,

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 ) 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 .00 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 .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 .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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