RetrogeneDB ID:

retro_hsap_1434

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:14:68119148..68119372(-)
Located in intron of:ENSG00000100568
Retrocopy
information
Ensembl ID:ENSG00000258626
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:COX7A2
Ensembl ID:ENSG00000112695
Aliases:COX7A2, COX7AL, COX7AL1, COXVIIAL, COXVIIa-L, VIIAL
Description:cytochrome c oxidase subunit VIIa polypeptide 2 (liver) [Source:HGNC Symbol;Acc:2288]


Retrocopy-Parental alignment summary:






>retro_hsap_1434
TTGTGGAGTTGTCAGGGTTCTTGGGCAGTAACTGAGTCAAGATGCTGCAGAATCTGCTGGCACTGTCAGGTTGCCCAGAG
GACCATGAGCATTGCTTCATGCAGGCATTTTGAAAATAAAGGTCCAGAAAACACAAGCTGTTTCAGGAGAAGAATGGAAT
TCCAGTGCATCTAAAGGGTGGTAGAGCTGATGACCTCCTGTATAGAGCCACCATGGTTCTCAGT

ORF - retro_hsap_1434 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 55.26 %
Parental protein coverage: 65.22 %
Number of stop codons detected: 0
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalVFSCGGCWSVTAKMLRNLLALRQIGQRTISTASRRHFKNKVPE-KQKLFQEDDEIPLYLKGGVADALLYR
..SC.G.W.VT...........Q..QRT.S.AS.RHF.NK.PE.K.KLFQE...IP..LKGG.AD.LLYR
RetrocopyLWSCQGSWAVTESRCCRICWHCQVAQRTMSIASCRHFENKGPE<KHKLFQEKNGIPVHLKGGRADDLLYR
ParentalATMILT
ATM.L.
RetrocopyATMVLS

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 45 .58 RPM
bodymap2_adrenal 0 .10 RPM 60 .63 RPM
bodymap2_brain 0 .12 RPM 94 .28 RPM
bodymap2_breast 0 .00 RPM 70 .80 RPM
bodymap2_colon 0 .02 RPM 85 .93 RPM
bodymap2_heart 0 .00 RPM 107 .17 RPM
bodymap2_kidney 0 .45 RPM 124 .17 RPM
bodymap2_liver 0 .00 RPM 86 .94 RPM
bodymap2_lung 0 .00 RPM 73 .40 RPM
bodymap2_lymph_node 0 .05 RPM 63 .28 RPM
bodymap2_ovary 0 .10 RPM 44 .18 RPM
bodymap2_prostate 0 .31 RPM 66 .32 RPM
bodymap2_skeletal_muscle 0 .11 RPM 25 .79 RPM
bodymap2_testis 0 .02 RPM 218 .79 RPM
bodymap2_thyroid 0 .40 RPM 61 .47 RPM
bodymap2_white_blood_cells 0 .00 RPM 51 .68 RPM

ChIP-Seq - click to see more details

RNA Polymerase II activity near the 5' end of retro_hsap_1434 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1434 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1434 retrocopy 5' end.

Lab - click to see more details

Experiment type: PCR amplification
Forward primer: TGCCCTTCATGGGAGTCAG (19 nt long)
Reverse primer: CTGTGCCCAAGGTCACGTA (19 nt long)
Annealing temperature: 58 °C
(Expected) product size: 616
Electrophoresis gel image:
Additional comment: Red arrow indicates PCR product of retrogene in pooled cDNA from 16 human tissues (Clontech). Red number of lane indicates particular retrogene; L - GeneRuler 100 bp DNA Ladder (Thermo Fisher Scientific); N - No template control (water instead of cDNA)

Retrocopy orthology:
Retrocopy retro_hsap_1434 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_1104
Pongo abelii retro_pabe_1187
Parental genes homology:
Parental genes homology involve 18 parental genes, and 47 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000144531 retrocopy
retro_amel_723,
Bos taurus ENSBTAG000000050966 retrocopies
retro_btau_1071, retro_btau_1230, retro_btau_1436, retro_btau_1469, retro_btau_1703, retro_btau_507,
Callithrix jacchus ENSCJAG000000103052 retrocopies
retro_cjac_1523, retro_cjac_4129,
Cavia porcellus ENSCPOG000000074042 retrocopies
retro_cpor_1300, retro_cpor_527,
Dipodomys ordii ENSDORG000000154252 retrocopies
retro_dord_701, retro_dord_790,
Homo sapiens ENSG00000112695 2 retrocopies
retro_hsap_1434 , retro_hsap_2961,
Homo sapiens ENSG000001159441 retrocopy
retro_hsap_825,
Gorilla gorilla ENSGGOG000000058652 retrocopies
retro_ggor_1104, retro_ggor_2051,
Loxodonta africana ENSLAFG000000023131 retrocopy
retro_lafr_811,
Microcebus murinus ENSMICG000000157473 retrocopies
retro_mmur_381, retro_mmur_548, retro_mmur_799,
Nomascus leucogenys ENSNLEG000000049492 retrocopies
retro_nleu_1412, retro_nleu_735,
Pongo abelii ENSPPYG000000167812 retrocopies
retro_pabe_1187, retro_pabe_2456,
Pteropus vampyrus ENSPVAG000000104016 retrocopies
retro_pvam_1144, retro_pvam_1408, retro_pvam_443, retro_pvam_57, retro_pvam_656, retro_pvam_741,
Rattus norvegicus ENSRNOG000000429031 retrocopy
retro_rnor_52,
Sus scrofa ENSSSCG000000044801 retrocopy
retro_sscr_296,
Ictidomys tridecemlineatus ENSSTOG000000025365 retrocopies
retro_itri_435, retro_itri_464, retro_itri_608, retro_itri_890, retro_itri_892,
Tupaia belangeri ENSTBEG000000072947 retrocopies
retro_tbel_1177, retro_tbel_178, retro_tbel_3617, retro_tbel_4102, retro_tbel_4330, retro_tbel_738, retro_tbel_781,
Tursiops truncatus ENSTTRG000000078741 retrocopy
retro_ttru_669,

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 .04 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 .03 RPM
FIN_HG00183 0 .03 RPM
FIN_HG00277 0 .04 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .02 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 .03 RPM
GBR_HG00111 0 .06 RPM
GBR_HG00114 0 .05 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .02 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .03 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .02 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .02 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .03 RPM
TSI_NA20798 0 .03 RPM
YRI_NA18870 0 .03 RPM
YRI_NA18907 0 .03 RPM
YRI_NA18916 0 .02 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .03 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .04 RPM

Indel association:

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



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