RetrogeneDB ID:

retro_hsap_3391

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:5:149311574..149312230(-)
Located in intron of:ENSG00000132915
Retrocopy
information
Ensembl ID:ENSG00000251583
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:MFF
Ensembl ID:ENSG00000168958
Aliases:MFF, C2orf33, GL004
Description:mitochondrial fission factor [Source:HGNC Symbol;Acc:24858]


Retrocopy-Parental alignment summary:






>retro_hsap_3391
ATGGCAGAAATTAGTCGAATTCGTACGAAATGGAATATACTGAAGGCATTAGTCAGCGAATGAGGGTCCCAGAAAAGTTA
AAAGTAGCACCGCCAAACGCCAACCTGGAACAGGGATTCCAAAAAGGAGTTCCAAATGCTAGCGTGATAATAATGCAAGT
TCCAGAGAGGATTGTTGTAGCAGGAAATAATGAGGATGTTTCATTTTCAAGACCAGCAGATCTTGACCTTATTCAGTCAA
CTCCCTTTAAACTCCTCGCACTAAAAACAGCACCTCGTGTACTTAGGCTAAGTGAAAGACCACTAGATTTTCTGGATTTA
GAAAGACCTCCTACAACCCCTCAAAATGAAGAAATCCGTGCAGTTGGCCGACTAAAAAGAGAGCGGTCTACGAGTGAAAC
TGCTGTTCGCCAAAATGGACAGCTGGTCAGAAATGATTCTCTTTATGGCATTTCAAATACAGATACAACAATTGAAGGAA
CATCAGATGACCTGACTGTTGTAGATGCAGCTTCACTAAGACGACAGATAATCAAACTAAATAGACGTCTACAACTTCCG
GACGAGGAGAACAAAGAACGTGCTAAAAGAGAAATGGTCGTGTATTCAATTACTGTAGCTTTCTGGCTGCTTAATAGCTG
GCTCTGGTTTTGCCGC

ORF - retro_hsap_3391 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 93.18 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMAEISRIQ-YEMEYTEGISQRMRVPEKLKVAPPNADLEQGFQEGVPNASV-IMQVPERIVVAGNNEDVSF
MAEISRI..YEMEYTEGISQRMRVPEKLKVAPPNA.LEQGFQ.GVPNASV.IMQVPERIVVAGNNEDVSF
RetrocopyMAEISRIR<YEMEYTEGISQRMRVPEKLKVAPPNANLEQGFQKGVPNASVIIMQVPERIVVAGNNEDVSF
ParentalSRPADLDLIQSTPFKPLALKTPPRVLTLSERPLDFLDLERPPTTPQNEEIRAVGRLKRERSMSENAVRQN
SRPADLDLIQSTPFK.LALKT.PRVL.LSERPLDFLDLERPPTTPQNEEIRAVGRLKRERS.SE.AVRQN
RetrocopySRPADLDLIQSTPFKLLALKTAPRVLRLSERPLDFLDLERPPTTPQNEEIRAVGRLKRERSTSETAVRQN
ParentalGQLVRNDSLYGISNIDTTIEGTSDDLTVVDAASLRRQIIKLNRRLQLLEEENKERAKREMVMYSITVAFW
GQLVRNDSLYGISN.DTTIEGTSDDLTVVDAASLRRQIIKLNRRLQL..EENKERAKREMV.YSITVAFW
RetrocopyGQLVRNDSLYGISNTDTTIEGTSDDLTVVDAASLRRQIIKLNRRLQLPDEENKERAKREMVVYSITVAFW
ParentalLLNSWLWFRR
LLNSWLWF.R
RetrocopyLLNSWLWFCR

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 39 .56 RPM
bodymap2_adrenal 0 .02 RPM 62 .53 RPM
bodymap2_brain 0 .00 RPM 83 .73 RPM
bodymap2_breast 0 .00 RPM 42 .94 RPM
bodymap2_colon 0 .00 RPM 60 .60 RPM
bodymap2_heart 0 .02 RPM 59 .06 RPM
bodymap2_kidney 0 .00 RPM 85 .06 RPM
bodymap2_liver 0 .00 RPM 29 .00 RPM
bodymap2_lung 0 .00 RPM 39 .52 RPM
bodymap2_lymph_node 0 .00 RPM 62 .75 RPM
bodymap2_ovary 0 .08 RPM 72 .87 RPM
bodymap2_prostate 0 .00 RPM 76 .07 RPM
bodymap2_skeletal_muscle 0 .00 RPM 64 .93 RPM
bodymap2_testis 2 .39 RPM 168 .96 RPM
bodymap2_thyroid 0 .15 RPM 53 .52 RPM
bodymap2_white_blood_cells 0 .00 RPM 50 .85 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_hsap_3391 in 2 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF002CFW POLR2A 5:149312326..149312565
ENCFF002CFX POLR2A 5:149312343..149312565

EST - click to see more details

No EST(s) were mapped for retro_hsap_3391 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3391 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3391 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3391 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000213192 retrocopies
retro_btau_1233, retro_btau_826,
Callithrix jacchus ENSCJAG000000129731 retrocopy
retro_cjac_4058,
Cavia porcellus ENSCPOG000000118811 retrocopy
retro_cpor_803,
Homo sapiens ENSG00000168958 2 retrocopies
retro_hsap_3391 , retro_hsap_347,
Microcebus murinus ENSMICG000000132001 retrocopy
retro_mmur_1002,
Nomascus leucogenys ENSNLEG000000134201 retrocopy
retro_nleu_1706,

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 = 0.06 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .03 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 .03 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .04 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .03 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 .02 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 .02 RPM
GBR_HG00134 0 .02 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .02 RPM
TSI_NA20518 0 .03 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .06 RPM
TSI_NA20765 0 .00 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .03 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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