RetrogeneDB ID:

retro_hsap_4076

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:8:74189596..74190281(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000254213
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:FAM213A
Ensembl ID:ENSG00000122378
Aliases:FAM213A, C10orf58, PAMM
Description:family with sequence similarity 213, member A [Source:HGNC Symbol;Acc:28651]


Retrocopy-Parental alignment summary:






>retro_hsap_4076
ATGTCTTTCTTCCAGAACCCAAGTTTCCTCACCATGGGCATGTGGTCCCTCGGTGCAAGAGCCCTGGGGGCTGCTGCCTT
GGCATTGTTGCTGGCCAACACAGACATGTTTCTCTCTAAGCCCCAGAAAGCGGCACTGGAGTACCTGGAGGATATAGACC
TGAAAATGCTGGAGAAGGAACCAAGGACTTTGAAAGCAAAGCAGCTATGGGAAAAGAAAATGGACCTGTGATTATGGCTG
TGCGGAGGCCAGGCTGTTTCCTCTGTTGAGGGGAAGCTGCGGATCTGTCCTCCCTAAAACCCATGTGGACGAGCTGGGTG
TCCCCCTCTATGCAGTGGTAAAGGAGCACATCAGGAATGAAGTGAAGGATTTCCAGCCTTATTTTAAAAGAGAAACCTTC
CTGGATGAAAAGAAAAAGTTCTATGGTCCACAAAGGCAGAAGATGATGTTTATGGGATTTATCTGTCTGGGAGTGTGGTA
CTTCTGAGCCTGGAATGGAGGCTTCTCTGGAAACCTGGAAGGAGAAGGCTTCATCCTCAGGGAAGTTTTCGTGGTGGCAT
CAGGAAACCAGGGGATTCTTCTCGAGCACCGAGAAAAAGAATTTGGAGACAAAGTAAACCTACTTTGTCTGGTTCTGGAG
GCTGCTAAGATGATCAAACCACAGACTTTGGCCTCAGAGAAAAAA

ORF - retro_hsap_4076 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.12 %
Parental protein coverage: 100. %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMSFLQDPSFFTMGMWSIGAGALGAAALALLLANTDVFLSKPQKAALEYLEDIDLKTLEKEPRT-FKAKE-
MSF.Q.PSF.TMGMWS.GA.ALGAAALALLLANTD.FLSKPQKAALEYLEDIDLK.LEKEPRT.F..K..
RetrocopyMSFFQNPSFLTMGMWSLGARALGAAALALLLANTDMFLSKPQKAALEYLEDIDLKMLEKEPRT<FESKAA
ParentalLWEKNGAVIMAVRRPGCFLCREEAADLSSLKSM-LDQLGVPLYAVVKEHIRTEVKDFQPYFKGEIFLDEK
....NG.VIMAVRRPGCFLC..EAADLSSLK.M..D.LGVPLYAVVKEHIR.EVKDFQPYFK.E.FLDEK
RetrocopyMGKENGPVIMAVRRPGCFLC*GEAADLSSLKPM<VDELGVPLYAVVKEHIRNEVKDFQPYFKRETFLDEK
ParentalKKFYGPQRRKMMFMGFIRLGVWYNFFRAWNGGFSGNLEGEGFILGGVFVVGSGKQGILLEHREKEFGDKV
KKFYGPQR.KMMFMGFI.LGVWY..F.AWNGGFSGNLEGEGFIL..VFVV.SG.QGILLEHREKEFGDKV
RetrocopyKKFYGPQRQKMMFMGFICLGVWY--F*AWNGGFSGNLEGEGFILREVFVVASGNQGILLEHREKEFGDKV
ParentalNLLS-VLEAAKMIKPQTLASEKK
NLL..VLEAAKMIKPQTLASEKK
RetrocopyNLLCLVLEAAKMIKPQTLASEKK

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 .12 RPM 336 .69 RPM
bodymap2_adrenal 0 .00 RPM 48 .21 RPM
bodymap2_brain 0 .12 RPM 130 .16 RPM
bodymap2_breast 0 .04 RPM 334 .83 RPM
bodymap2_colon 0 .00 RPM 102 .09 RPM
bodymap2_heart 0 .00 RPM 58 .26 RPM
bodymap2_kidney 0 .00 RPM 85 .37 RPM
bodymap2_liver 0 .00 RPM 38 .38 RPM
bodymap2_lung 0 .02 RPM 21 .66 RPM
bodymap2_lymph_node 0 .00 RPM 56 .85 RPM
bodymap2_ovary 0 .02 RPM 35 .18 RPM
bodymap2_prostate 0 .07 RPM 82 .39 RPM
bodymap2_skeletal_muscle 0 .00 RPM 17 .55 RPM
bodymap2_testis 0 .15 RPM 80 .45 RPM
bodymap2_thyroid 0 .00 RPM 85 .66 RPM
bodymap2_white_blood_cells 0 .00 RPM 4 .31 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4076 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4076 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4076 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4076 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4076 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2763
Gorilla gorilla retro_ggor_2733
Pongo abelii retro_pabe_3345
Macaca mulatta retro_mmul_2351
Parental genes homology:
Parental genes homology involve 13 parental genes, and 30 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000008131 retrocopy
retro_chof_878,
Callithrix jacchus ENSCJAG000000036571 retrocopy
retro_cjac_3312,
Dasypus novemcinctus ENSDNOG000000019813 retrocopies
retro_dnov_1843, retro_dnov_1901, retro_dnov_868,
Homo sapiens ENSG00000122378 2 retrocopies
retro_hsap_1135, retro_hsap_4076 ,
Gorilla gorilla ENSGGOG000000132462 retrocopies
retro_ggor_2733, retro_ggor_886,
Microcebus murinus ENSMICG000000074852 retrocopies
retro_mmur_1346, retro_mmur_1481,
Macaca mulatta ENSMMUG000000217733 retrocopies
retro_mmul_2351, retro_mmul_2409, retro_mmul_881,
Mus musculus ENSMUSG000000217921 retrocopy
retro_mmus_2227,
Otolemur garnettii ENSOGAG000000136387 retrocopies
retro_ogar_2126, retro_ogar_2435, retro_ogar_2562, retro_ogar_3327, retro_ogar_420, retro_ogar_580, retro_ogar_784,
Procavia capensis ENSPCAG000000096961 retrocopy
retro_pcap_281,
Pongo abelii ENSPPYG000000258624 retrocopies
retro_pabe_3345, retro_pabe_643, retro_pabe_738, retro_pabe_944,
Pan troglodytes ENSPTRG000000026852 retrocopies
retro_ptro_2763, retro_ptro_774,
Rattus norvegicus ENSRNOG000000111401 retrocopy
retro_rnor_1517,

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 = 0.27 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .04 RPM
CEU_NA11843 0 .03 RPM
CEU_NA11930 0 .03 RPM
CEU_NA12004 0 .11 RPM
CEU_NA12400 0 .11 RPM
CEU_NA12751 0 .02 RPM
CEU_NA12760 0 .04 RPM
CEU_NA12827 0 .14 RPM
CEU_NA12872 0 .05 RPM
CEU_NA12873 0 .06 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .07 RPM
FIN_HG00315 0 .17 RPM
FIN_HG00321 0 .09 RPM
FIN_HG00328 0 .21 RPM
FIN_HG00338 0 .04 RPM
FIN_HG00349 0 .14 RPM
FIN_HG00375 0 .07 RPM
FIN_HG00377 0 .05 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .12 RPM
GBR_HG00111 0 .13 RPM
GBR_HG00114 0 .05 RPM
GBR_HG00119 0 .12 RPM
GBR_HG00131 0 .06 RPM
GBR_HG00133 0 .12 RPM
GBR_HG00134 0 .17 RPM
GBR_HG00137 0 .08 RPM
GBR_HG00142 0 .03 RPM
GBR_HG00143 0 .06 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .12 RPM
TSI_NA20518 0 .08 RPM
TSI_NA20532 0 .07 RPM
TSI_NA20538 0 .05 RPM
TSI_NA20756 0 .06 RPM
TSI_NA20765 0 .27 RPM
TSI_NA20771 0 .03 RPM
TSI_NA20786 0 .03 RPM
TSI_NA20798 0 .12 RPM
YRI_NA18870 0 .07 RPM
YRI_NA18907 0 .10 RPM
YRI_NA18916 0 .08 RPM
YRI_NA19093 0 .05 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .05 RPM
YRI_NA19118 0 .19 RPM
YRI_NA19213 0 .02 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .14 RPM

Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).





Copyright © RetrogeneDB 2014-2017