RetrogeneDB ID:

retro_hsap_879

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:11:58563709..58564330(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000255265
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:TMA16
Ensembl ID:ENSG00000198498
Aliases:TMA16, C4orf43
Description:translation machinery associated 16 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:25638]


Retrocopy-Parental alignment summary:






>retro_hsap_879
ACCATGCCTAAAGCATCAAAGGGAAAAAGTGCAGGACCGGAAAAAAAAAAGTAACCCATCCATTTAGTAGAAAAGCAGCT
CAAATTACGAGAGAGGCCCACAAACAAGAAAAACAGAAAATTGAAGAATGAAAAAGCCTTGTGTGAGGCTTTTTTCAACC
TTATTTGTGAAAACCTGCAGTGGTTTCAAAATCATCTTGATCCCCCAAAAAAGGGATATTTAAAGAAAGATGCTTGTGAA
CTAATTGAAAGATATTAAAATCGATTCAGCAGTGAGCTGGAGCAGACTGAGTTACGTAACAGTATCAGGGACAGGCAGGG
GAGGTGGCACTGTTCCCGGGAGACTGTCAATAAGCAGACGATGGAGCGGGAGTGAGAGCAGTATGAAGGATATGGTCTTG
AGATTCCAGACATTCTAAATGCAAGTAACCTGTAAACGTTTAGGGAATGTGACTTTAATCTGAAGAAATTGCCAAACACT
AACATAAGAAAAACTTGTGCTAATGATGCAATTCCCAAGAAGTGCAAGAGGAAAACTATTATAACTGTAGACCAAGATTT
AGGGGAATTGGAACTTAACAATGAATCAAGTGACTCCGATGAGGAAATGACTGCAGTGGCA

ORF - retro_hsap_879 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78.1 %
Parental protein coverage: 84.3 %
Number of stop codons detected: 3
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalTQPKAP-KGKSAGREKK-VIHPYSRKAAQITREAHKQEKKEKLK-NEKAL---RLNLVGEKLQWFQNHLD
T.PKA..KGK........V.HP.SRKAAQITREAHKQEK..K...NEKAL.....NL..E.LQWFQNHLD
RetrocopyTMPKAS<KGKKCRTXXXXVTHPFSRKAAQITREAHKQEK-QKIE>NEKALCEAFFNLICENLQWFQNHLD
ParentalPQKKRYSKKDACELIERYLNRFSSELEQIELHNSIRDRQGRRHCSRETVIKQTMERERQQFEGYGLEIPD
P.KK.Y.KKDACELIERY.NRFSSELEQ.EL.NSIRDRQGR.HCSRETV.KQTMERE..Q.EGYGLEIPD
RetrocopyPPKKGYLKKDACELIERY*NRFSSELEQTELRNSIRDRQGRWHCSRETVNKQTMERE*EQYEGYGLEIPD
ParentalILNASNLKTFREWDFDLKKLPNIKMRKICANDAIPKTCKRKTIITVDQDLGELELNDESSDSDEEMTAVA
ILNASNL.TFRE.DF.LKKLPN...RK.CANDAIPK.CKRKTIITVDQDLGELELN.ESSDSDEEMTAVA
RetrocopyILNASNL*TFRECDFNLKKLPNTNIRKTCANDAIPKKCKRKTIITVDQDLGELELNNESSDSDEEMTAVA

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 21 .51 RPM
bodymap2_adrenal 0 .00 RPM 23 .40 RPM
bodymap2_brain 0 .05 RPM 7 .38 RPM
bodymap2_breast 0 .00 RPM 17 .92 RPM
bodymap2_colon 0 .00 RPM 19 .30 RPM
bodymap2_heart 0 .00 RPM 7 .27 RPM
bodymap2_kidney 0 .00 RPM 13 .63 RPM
bodymap2_liver 0 .00 RPM 7 .67 RPM
bodymap2_lung 0 .00 RPM 7 .65 RPM
bodymap2_lymph_node 0 .00 RPM 14 .89 RPM
bodymap2_ovary 0 .00 RPM 25 .70 RPM
bodymap2_prostate 0 .00 RPM 18 .74 RPM
bodymap2_skeletal_muscle 0 .00 RPM 5 .27 RPM
bodymap2_testis 0 .00 RPM 24 .94 RPM
bodymap2_thyroid 0 .00 RPM 17 .44 RPM
bodymap2_white_blood_cells 0 .00 RPM 18 .33 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_879 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_879 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_879 retrocopy 5' end.

Lab - click to see more details

retro_hsap_879 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_879 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_3035
Gorilla gorilla retro_ggor_713
Parental genes homology:
Parental genes homology involve 19 parental genes, and 37 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000067022 retrocopies
retro_chof_1717, retro_chof_2104,
Cavia porcellus ENSCPOG000000011191 retrocopy
retro_cpor_444,
Dasypus novemcinctus ENSDNOG000000068201 retrocopy
retro_dnov_489,
Echinops telfairi ENSETEG000000097341 retrocopy
retro_etel_1378,
Homo sapiens ENSG00000198498 2 retrocopies
retro_hsap_378, retro_hsap_879 ,
Gorilla gorilla ENSGGOG000000253241 retrocopy
retro_ggor_713,
Macropus eugenii ENSMEUG000000011343 retrocopies
retro_meug_1830, retro_meug_1895, retro_meug_396,
Macaca mulatta ENSMMUG000000044822 retrocopies
retro_mmul_184, retro_mmul_276,
Monodelphis domestica ENSMODG000000021701 retrocopy
retro_mdom_881,
Mus musculus ENSMUSG000000255912 retrocopies
retro_mmus_299, retro_mmus_329,
Nomascus leucogenys ENSNLEG000000064662 retrocopies
retro_nleu_1631, retro_nleu_2590,
Otolemur garnettii ENSOGAG000000018601 retrocopy
retro_ogar_3308,
Pongo abelii ENSPPYG000000151671 retrocopy
retro_pabe_329,
Pan troglodytes ENSPTRG000000236182 retrocopies
retro_ptro_294, retro_ptro_3035,
Rattus norvegicus ENSRNOG000000141883 retrocopies
retro_rnor_2309, retro_rnor_845, retro_rnor_846,
Sorex araneus ENSSARG000000037801 retrocopy
retro_sara_168,
Ictidomys tridecemlineatus ENSSTOG000000247633 retrocopies
retro_itri_1085, retro_itri_1372, retro_itri_715,
Tupaia belangeri ENSTBEG000000172247 retrocopies
retro_tbel_168, retro_tbel_2196, retro_tbel_2345, retro_tbel_2474, retro_tbel_3235, retro_tbel_3987, retro_tbel_4393,
Tarsius syrichta ENSTSYG000000082841 retrocopy
retro_tsyr_686,

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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