RetrogeneDB ID:

retro_hsap_3027

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:4:17553739..17554374(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000249488
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:NACA
Ensembl ID:ENSG00000196531
Aliases:NACA, NACA1, skNAC
Description:nascent polypeptide-associated complex alpha subunit [Source:HGNC Symbol;Acc:7629]


Retrocopy-Parental alignment summary:






>retro_hsap_3027
ATGCCTGGTGAAGCCACAGAAACCATTCTTGCTACAGAGCAGGAGTTGCCACAGCCCCAGGTGGAGACCGGGTCTGGAAC
AGAAGCTGACAGTGATAAATCAGTACCAGAGCTCGAGGAACAGGATTCCACAGAGATACCACACAAGCAGCCCAGCTGGC
AGCAGCAGCTGAAATCAATGAGTGTCAATCAGTAAAGCAAAACAGAGTTAGAGTGAAAAGAAGGCACGTAAGGCTATGTC
CAAACTCGGTCTTCCGTAGATAACAGGGGTTACTACAGTCACTACTGGAAATCTAAGAATATCTTCTTTGTCATCACAAA
ACCAGATGTCTACAAGAATCCTGCTTCGGATACCTATGTGTGTGTTTTTGGGGAAGCCAAGATCAAGGATTTATCTTAAC
AAGCATGGGTAGCACCTGCTAAGACACAGAGTGAGCTGTCTCAAACATTCAAGAAAACACACAGACTCCAACTATACAAG
ACGAGACTGGAGAGGAAAAGGTTGATGATACAGGTGTGGAAGTTAAGGACGTAGAATTGGTCATGTCACAAGCAAATGTA
TTGAGAGCAAAGGAAGTCCGAGCCTTGAAGAACAAGAGTAATCATATTGTAACTGCTATTACAGAATTAACAATG

ORF - retro_hsap_3027 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.27 %
Parental protein coverage: 100. %
Number of stop codons detected: 3
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalMPGEATETVPATEQELPQPQAETGSGTESDSDESVPELEEQDSTQA-TTQQAQLAAAAEIDE-EPVSKAK
MPGEATET..ATEQELPQPQ.ETGSGTE.DSD.SVPELEEQDST...TTQ.AQLAAAAEI.E....SKAK
RetrocopyMPGEATETILATEQELPQPQVETGSGTEADSDKSVPELEEQDSTEI<TTQAAQLAAAAEINE<VSISKAK
ParentalQSRSEKKARKAMSKLGLRQVTGVTRVTIR-KSKNILFVITKPDVYKSPASDTYI-VFGEAKIEDLSQQAQ
QS.SEKKARKAMSKLGL...TGVT.VT...KSKNI.FVITKPDVYK.PASDTY..VFGEAKI.DLS.QA.
RetrocopyQS*SEKKARKAMSKLGLP*ITGVTTVTTG<KSKNIFFVITKPDVYKNPASDTYVCVFGEAKIKDLS*QAW
ParentalLAAAEKFKVQGE-AVSNIQENTQTPTVQEESEEEEVDETGVEVKDIELVMSQANVSRAKAVRALKNNSND
.A.A...K.Q.E.AVSNIQENTQTPT.Q.E..EE.VD.TGVEVKD.ELVMSQANV.RAK.VRALKN.SN.
RetrocopyVAPA---KTQSE<AVSNIQENTQTPTIQDETGEEKVDDTGVEVKDVELVMSQANVLRAKEVRALKNKSNH
ParentalIVNAIMELTM
IV.AI.ELTM
RetrocopyIVTAITELTM

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 638 .30 RPM
bodymap2_adrenal 0 .00 RPM 666 .69 RPM
bodymap2_brain 0 .00 RPM 300 .74 RPM
bodymap2_breast 0 .00 RPM 528 .53 RPM
bodymap2_colon 0 .00 RPM 793 .43 RPM
bodymap2_heart 0 .00 RPM 584 .27 RPM
bodymap2_kidney 0 .00 RPM 312 .09 RPM
bodymap2_liver 0 .00 RPM 215 .55 RPM
bodymap2_lung 0 .00 RPM 519 .39 RPM
bodymap2_lymph_node 0 .00 RPM 580 .94 RPM
bodymap2_ovary 0 .00 RPM 1123 .78 RPM
bodymap2_prostate 0 .00 RPM 761 .06 RPM
bodymap2_skeletal_muscle 0 .00 RPM 2154 .57 RPM
bodymap2_testis 0 .00 RPM 575 .23 RPM
bodymap2_thyroid 0 .00 RPM 445 .42 RPM
bodymap2_white_blood_cells 0 .00 RPM 713 .96 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3027 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3027 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3027 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3027 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3027 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pongo abelii retro_pabe_2507
Parental genes homology:
Parental genes homology involve 16 parental genes, and 73 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000041753 retrocopies
retro_amel_1725, retro_amel_1821, retro_amel_643,
Canis familiaris ENSCAFG000000001418 retrocopies
retro_cfam_1502, retro_cfam_1561, retro_cfam_1884, retro_cfam_1913, retro_cfam_2096, retro_cfam_2169, retro_cfam_710, retro_cfam_974,
Callithrix jacchus ENSCJAG000000107018 retrocopies
retro_cjac_1063, retro_cjac_1452, retro_cjac_1875, retro_cjac_2202, retro_cjac_2453, retro_cjac_2696, retro_cjac_2975, retro_cjac_3232,
Dipodomys ordii ENSDORG000000145222 retrocopies
retro_dord_228, retro_dord_699,
Equus caballus ENSECAG000000152421 retrocopy
retro_ecab_785,
Homo sapiens ENSG00000196531 6 retrocopies
retro_hsap_3006, retro_hsap_3027 , retro_hsap_3968, retro_hsap_3992, retro_hsap_737, retro_hsap_77,
Loxodonta africana ENSLAFG000000045986 retrocopies
retro_lafr_1107, retro_lafr_113, retro_lafr_1251, retro_lafr_166, retro_lafr_491, retro_lafr_958,
Microcebus murinus ENSMICG000000164655 retrocopies
retro_mmur_1122, retro_mmur_450, retro_mmur_585, retro_mmur_684, retro_mmur_807,
Myotis lucifugus ENSMLUG0000000116916 retrocopies
retro_mluc_1147, retro_mluc_1653, retro_mluc_1668, retro_mluc_1756, retro_mluc_1767, retro_mluc_1851, retro_mluc_1881, retro_mluc_1941, retro_mluc_2587, retro_mluc_2600, retro_mluc_414, retro_mluc_492, retro_mluc_526, retro_mluc_641, retro_mluc_725, retro_mluc_861,
Macaca mulatta ENSMMUG000000030734 retrocopies
retro_mmul_1233, retro_mmul_1933, retro_mmul_2066, retro_mmul_889,
Mus musculus ENSMUSG000000613151 retrocopy
retro_mmus_968,
Ochotona princeps ENSOPRG000000017813 retrocopies
retro_opri_264, retro_opri_758, retro_opri_961,
Procavia capensis ENSPCAG000000070675 retrocopies
retro_pcap_150, retro_pcap_224, retro_pcap_282, retro_pcap_305, retro_pcap_324,
Sarcophilus harrisii ENSSHAG000000021751 retrocopy
retro_shar_213,
Tursiops truncatus ENSTTRG000000021502 retrocopies
retro_ttru_1157, retro_ttru_760,
Vicugna pacos ENSVPAG000000040282 retrocopies
retro_vpac_485, retro_vpac_611,

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 = 0.03 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 .02 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .03 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 .02 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:

The presence of retro_hsap_3027 across human populations is associated with 1 indel. The percentage values indicate the frequencies of retro_hsap_3027 presence in various populations. Based on Kabza et al. 2015 (PubMed).


# Indel coordinates AFR, African AMR, Ad Mixed American EUR, European EAS, East Asian
ASW YRI LWK MXL PUR CLM CEU IBS GBR FIN TSI JPT CHB CHS
1. 4:17543641..17569600 100 100 100 99.24 100 100 100 100 99.44 100 100 98.31 97.94 99

Indel #1, located at the genomic coordinates 4:17543641..17569600.

image/svg+xml Mexican Ancestryfrom Los Angeles USA MXL 99.24 % Puerto Ricansfrom Puerto Rico PUR 100 % Colombians fromMedellin, Colombia CLM 100 % Americans of AfricanAncestry in SW USA ASW 100 % Yoruba in Ibadan,Nigeria YRI 100 % Luhya in Webuye,Kenya LWK 100 % Utah Residents (CEPH)with Northern andWestern European Ancestry CEU 100 % Iberian Populationin Spain IBS 100 % British in Englandand Scotland GBR 99.44 % Finnish in Finland FIN 100 % Toscani in Italia TSI 100 % Han Chinese in Bejing,China CHB 97.94 % Japanese in Tokyo,Japan 98.31 % Southern Han Chinese CHS 99 % JPT EUROPE AMERICAS AFRICA EAST ASIA




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