RetrogeneDB ID:

retro_hsap_1468

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:14:106916256..106916980(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000228966
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:HOMER2
Ensembl ID:ENSG00000103942
Aliases:HOMER2, ACPD, CPD, HOMER-2, VESL-2
Description:homer homolog 2 (Drosophila) [Source:HGNC Symbol;Acc:17513]


Retrocopy-Parental alignment summary:






>retro_hsap_1468
ATGGAAGAACAGCCCATCTTCACCACCGGAGCACAGGTCTTCCAGATTGACCCCAACACCAAAAAGCACTGGATGCCTGC
GAGCAACAGGCGGCCACCGTTTCTTACTTCTATGATGTCACAAGGAACATCTATGGGATCGTCAGTGTGGACGGAGCCAA
GGTGACCATAAACAGCACAATCACACCGAATATGACCTTCACCAATGTGTCACAGACGTCTGGGCAGTGGGCCGACAGCA
GAGCCAACACGGTGTTTGGTTTGGGGTTTTCCTCTGAGCAGCAGCTGACAAAGTTTTCAGAGAAATTCCAGGAGGTGGAG
GAAGCGGCCAAGACAGCCAAAGACAAGACCCAGGAGAACATGGAGCCCTCGAGTAATAATCCCGAGAATCCGGGCATGGA
GCCCCATCTTCTACTCCGGCATCCAGTGTCAACGGGACGGACGATGAAAGGCCTCTCAGGCCGCTGCAGCTGACACGCAC
CTGCAGTCTGGGAACCACAAGCTGAAGGCGGCCTCGACGCAAAGAGCTGCCCACGGGAAGAGGTGGGAGATGGAGCTGCA
GACCCGGCGGGAGAGCGACGCCCGGCTGCCCACGGCGCTGCAGGAGTCGGTGGCCAGCGTGGAGCAGAGGAAGAGGCCGT
GAGATCCACAGAGAGGAGAAGAACACGCAGCTGAAGAGGAAGATAGAGGAGCTGGAGGCGGAGCTCCGAGAAAACGAGAA
AGAG

ORF - retro_hsap_1468 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 72.76 %
Parental protein coverage: 68.36 %
Number of stop codons detected: 1
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalMGEQPIFTTRAHVFQIDPNTKKNWMPAS-KQAVTVSYFYDVTRNSYRIISVDGAKVIINSTITPNMTFTK
M.EQPIFTT.A.VFQIDPNTKK.WMPAS..QA.TVSYFYDVTRN.Y.I.SVDGAKV.INSTITPNMTFT.
RetrocopyMEEQPIFTTGAQVFQIDPNTKKHWMPAS<QQAATVSYFYDVTRNIYGIVSVDGAKVTINSTITPNMTFTN
ParentalTSQKFGQWADSRANTVFGLGFSSEQQLTKFAEKFQEVKEAAKIAKDKTQEKIETSSNH-SQESGRETPSS
.SQ..GQWADSRANTVFGLGFSSEQQLTKF.EKFQEV.EAAK.AKDKTQE..E.SSN..S.ESG...PSS
RetrocopyVSQTSGQWADSRANTVFGLGFSSEQQLTKFSEKFQEVEEAAKTAKDKTQENMEPSSNN<SRESGHGAPSS
ParentalTQASSVNGTDDE-KASHAGPANTHLKSENDKLKIALTQSAANVKKWEIELQTLRESNARLTTALQESAAS
T.ASSVNGTDDE.KAS.A..A.THL.S.N.KLK.A.TQ.AA..K.WE.ELQT.RES.ARL.TALQES.AS
RetrocopyTPASSVNGTDDE<KASQAAAADTHLQSGNHKLKAASTQRAAHGKRWEMELQTRRESDARLPTALQESVAS
ParentalVEQWKRQFSICRDE-NDRLRNKIDELEEQCSEINRE
VEQ.KR.....R.E.N..L..KI.ELE....E...E
RetrocopyVEQRKRP*DPQRGE>NTQLKRKIEELEAELRENEKE

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 1 .29 RPM
bodymap2_adrenal 0 .00 RPM 2 .33 RPM
bodymap2_brain 0 .00 RPM 24 .26 RPM
bodymap2_breast 0 .00 RPM 18 .00 RPM
bodymap2_colon 0 .00 RPM 12 .84 RPM
bodymap2_heart 0 .00 RPM 28 .78 RPM
bodymap2_kidney 0 .00 RPM 12 .14 RPM
bodymap2_liver 0 .00 RPM 41 .68 RPM
bodymap2_lung 0 .00 RPM 7 .70 RPM
bodymap2_lymph_node 0 .02 RPM 3 .22 RPM
bodymap2_ovary 0 .00 RPM 10 .45 RPM
bodymap2_prostate 0 .00 RPM 18 .55 RPM
bodymap2_skeletal_muscle 0 .00 RPM 66 .22 RPM
bodymap2_testis 0 .47 RPM 18 .49 RPM
bodymap2_thyroid 0 .00 RPM 82 .14 RPM
bodymap2_white_blood_cells 0 .06 RPM 4 .10 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1468 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1468 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1468 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1468 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1468 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pongo abelii retro_pabe_1210
Parental genes homology:
Parental genes homology involve 7 parental genes, and 15 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000158843 retrocopies
retro_cjac_3556, retro_cjac_3614, retro_cjac_3871,
Cavia porcellus ENSCPOG000000146881 retrocopy
retro_cpor_35,
Equus caballus ENSECAG000000236193 retrocopies
retro_ecab_1046, retro_ecab_661, retro_ecab_692,
Homo sapiens ENSG00000103942 1 retrocopy
retro_hsap_1468 ,
Macaca mulatta ENSMMUG000000082971 retrocopy
retro_mmul_2278,
Nomascus leucogenys ENSNLEG000000109531 retrocopy
retro_nleu_3002,
Pongo abelii ENSPPYG000000067355 retrocopies
retro_pabe_1209, retro_pabe_1210, retro_pabe_1217, retro_pabe_3566, retro_pabe_3568,

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 = 0.05 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 .02 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 .02 RPM
FIN_HG00349 0 .03 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .02 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 .03 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 .05 RPM
TSI_NA20756 0 .03 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 .02 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .02 RPM
YRI_NA19223 0 .00 RPM

Indel association:

The presence of retro_hsap_1468 across human populations is associated with 5 indels. The percentage values indicate the frequencies of retro_hsap_1468 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. 14:106689962..107182000 98.36 98.3 99.48 100 99.09 100 93.53 100 100 100 100 98.88 98.97 100
2. 14:106800263..107276000 98.36 100 99.48 100 100 100 97.06 100 100 100 100 98.88 100 100
3. 14:106855178..106937000 95.08 98.86 98.45 98.48 100 100 95.29 100 99.44 97.85 99.49 98.31 99.48 100
4. 14:106879059..107097000 98.36 99.43 98.45 99.24 99.09 99.17 94.12 100 99.44 99.46 97.45 98.88 100 100
5. 14:106885900..106918000 87.7 84.09 81.44 92.42 92.73 89.17 77.06 85.71 82.58 75.81 88.78 96.63 97.94 100

Indel #1, located at the genomic coordinates 14:106689962..107182000.

image/svg+xml Mexican Ancestryfrom Los Angeles USA MXL 100 % Puerto Ricansfrom Puerto Rico PUR 99.09 % Colombians fromMedellin, Colombia CLM 100 % Americans of AfricanAncestry in SW USA ASW 98.36 % Yoruba in Ibadan,Nigeria YRI 98.3 % Luhya in Webuye,Kenya LWK 99.48 % Utah Residents (CEPH)with Northern andWestern European Ancestry CEU 93.53 % Iberian Populationin Spain IBS 100 % British in Englandand Scotland GBR 100 % Finnish in Finland FIN 100 % Toscani in Italia TSI 100 % Han Chinese in Bejing,China CHB 98.97 % Japanese in Tokyo,Japan 98.88 % Southern Han Chinese CHS 100 % JPT EUROPE AMERICAS AFRICA EAST ASIA


Indel #2, located at the genomic coordinates 14:106800263..107276000.

image/svg+xml Mexican Ancestryfrom Los Angeles USA MXL 100 % Puerto Ricansfrom Puerto Rico PUR 100 % Colombians fromMedellin, Colombia CLM 100 % Americans of AfricanAncestry in SW USA ASW 98.36 % Yoruba in Ibadan,Nigeria YRI 100 % Luhya in Webuye,Kenya LWK 99.48 % Utah Residents (CEPH)with Northern andWestern European Ancestry CEU 97.06 % Iberian Populationin Spain IBS 100 % British in Englandand Scotland GBR 100 % Finnish in Finland FIN 100 % Toscani in Italia TSI 100 % Han Chinese in Bejing,China CHB 100 % Japanese in Tokyo,Japan 98.88 % Southern Han Chinese CHS 100 % JPT EUROPE AMERICAS AFRICA EAST ASIA


Indel #3, located at the genomic coordinates 14:106855178..106937000.

image/svg+xml Mexican Ancestryfrom Los Angeles USA MXL 98.48 % Puerto Ricansfrom Puerto Rico PUR 100 % Colombians fromMedellin, Colombia CLM 100 % Americans of AfricanAncestry in SW USA ASW 95.08 % Yoruba in Ibadan,Nigeria YRI 98.86 % Luhya in Webuye,Kenya LWK 98.45 % Utah Residents (CEPH)with Northern andWestern European Ancestry CEU 95.29 % Iberian Populationin Spain IBS 100 % British in Englandand Scotland GBR 99.44 % Finnish in Finland FIN 97.85 % Toscani in Italia TSI 99.49 % Han Chinese in Bejing,China CHB 99.48 % Japanese in Tokyo,Japan 98.31 % Southern Han Chinese CHS 100 % JPT EUROPE AMERICAS AFRICA EAST ASIA


Indel #4, located at the genomic coordinates 14:106879059..107097000.

image/svg+xml Mexican Ancestryfrom Los Angeles USA MXL 99.24 % Puerto Ricansfrom Puerto Rico PUR 99.09 % Colombians fromMedellin, Colombia CLM 99.17 % Americans of AfricanAncestry in SW USA ASW 98.36 % Yoruba in Ibadan,Nigeria YRI 99.43 % Luhya in Webuye,Kenya LWK 98.45 % Utah Residents (CEPH)with Northern andWestern European Ancestry CEU 94.12 % Iberian Populationin Spain IBS 100 % British in Englandand Scotland GBR 99.44 % Finnish in Finland FIN 99.46 % Toscani in Italia TSI 97.45 % Han Chinese in Bejing,China CHB 100 % Japanese in Tokyo,Japan 98.88 % Southern Han Chinese CHS 100 % JPT EUROPE AMERICAS AFRICA EAST ASIA


Indel #5, located at the genomic coordinates 14:106885900..106918000.

image/svg+xml Mexican Ancestryfrom Los Angeles USA MXL 92.42 % Puerto Ricansfrom Puerto Rico PUR 92.73 % Colombians fromMedellin, Colombia CLM 89.17 % Americans of AfricanAncestry in SW USA ASW 87.7 % Yoruba in Ibadan,Nigeria YRI 84.09 % Luhya in Webuye,Kenya LWK 81.44 % Utah Residents (CEPH)with Northern andWestern European Ancestry CEU 77.06 % Iberian Populationin Spain IBS 85.71 % British in Englandand Scotland GBR 82.58 % Finnish in Finland FIN 75.81 % Toscani in Italia TSI 88.78 % Han Chinese in Bejing,China CHB 97.94 % Japanese in Tokyo,Japan 96.63 % Southern Han Chinese CHS 100 % JPT EUROPE AMERICAS AFRICA EAST ASIA




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