RetrogeneDB ID:

retro_hsap_37

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:12907260..12908142(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000179172
Aliases:HNRNPCL1, HNRPCL1
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:RALY
Ensembl ID:ENSG00000125970
Aliases:RALY, HNRPCL2, P542
Description:RNA binding protein, autoantigenic (hnRNP-associated with lethal yellow homolog (mouse)) [Source:HGNC Symbol;Acc:15921]


Retrocopy-Parental alignment summary:






>retro_hsap_37
ATGGCCAGCAACGTTACCAACAAGATGGATCCTCACTCCATGAACTCCCGTGTGTTCATTGGGAATCTCAACACTCTTGT
TGTCAAGAAATCGGATGTGGAGGCGATCTTTTCCAAGTATGGCAAAATTGCGGGCTGCTCTGTTCATAAGGGCTTTGCCT
TCGTTCAATATGATAAGGAGAAAAATGCCCGGGCTGCTGTAGCAGGAGAGGATGGCAGAATGATTGCTAGCCAGGTTGTA
GATATTAACCTGGCTGCAGAGCCAAAAGTGAACCGAGGAAACGCAGGTGTGAAACGATCAGCAGCGGAGATGTACGGCTC
CTCTTTTGACTTGGACTATGGCTTTCAACGGGATTATTATGATGGAATGTACAGTTTCCCAGCACGTGTACCTCCTCCTC
CTCCCATTGCTCTGGCTGTAGTGCCCTCGAAACGTCAACGTCTATCAGGAAACACCTCACGAAGGGGCAAAAGTGGCTTC
AATTCTAAGAGTGGAAAGCGGGGATCTTCCAAGTCTGGAAAGTTGAAAGGTGATGACCTTCAGGCCATTAAGCAGGAGTT
GACCCAGATAAAACAGAAAGTGGATTCTCTCCTGGAAAACCTGGAAAAAATTGAAAAGGAACAGAGCAAACAAGAGGTAG
AGGTGAAAAATGCTAAGTCAGAAGAGGAGCAGAGCAGTAGCTCCATGAAGAAAGATGAGACTCATGTGAAGATGGAGTCT
GAGGGGGGTGCAGAAGACTCTGCTGAGGAGGGGGACCCACTGGATGATGATGTTAATGAAGATCAGGGGGATGACCAGCT
GGAGTTGATCAAGGATGATGAAAAAGAGGCTGAGGAAGGAGAGGATGACAGAGACAGCACCAATGGCCAGGATGACTCTT
AA

ORF - retro_hsap_37 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 53.99 %
Parental protein coverage: 68.3 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHKGYAFVQYSNERHARAAVLGEN
ASNVTNK.DP.S.NSRVFIGNLNT..VKKSDVE.IFSKYG..AGCSVHKG.AFVQY..E..ARAAV.GE.
RetrocopyASNVTNKMDPHSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIAGCSVHKGFAFVQYDKEKNARAAVAGED
ParentalGRVLAGQTLDINMAGEPKPDRPK-GLKRAASAIYSGYIFDYDY-YRDDFYDRLFDYRGRLSPVP--VPRA
GR..A.Q..DIN.A.EPK..R...G.KR.A...Y.G..FD.DY....D.YD.......R..P.P......
RetrocopyGRMIASQVVDINLAAEPKVNRGNAGVKRSAAEMY-GSSFDLDYGFQRDYYDGMYSFPARVPPPPPIALAV
ParentalVPVKRPRVTVPLVRRVKTNVPVKLFARSTAVTTSSAKIKLKSSELQAIKTELTQIKSNIDALLSRLEQIA
VP.KR.R......RR.K.....K...R.......S.K.K.....LQAIK.ELTQIK...D.LL..LE.I.
RetrocopyVPSKRQRLSGNTSRRGKSGFNSKSGKRG---SSKSGKLK--GDDLQAIKQELTQIKQKVDSLLENLEKIE
ParentalAEQ
.EQ
RetrocopyKEQ

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 .02 RPM 59 .93 RPM
bodymap2_adrenal 0 .04 RPM 66 .77 RPM
bodymap2_brain 0 .00 RPM 24 .19 RPM
bodymap2_breast 0 .00 RPM 40 .10 RPM
bodymap2_colon 0 .00 RPM 51 .28 RPM
bodymap2_heart 0 .00 RPM 29 .39 RPM
bodymap2_kidney 0 .00 RPM 47 .09 RPM
bodymap2_liver 0 .00 RPM 19 .56 RPM
bodymap2_lung 0 .00 RPM 82 .95 RPM
bodymap2_lymph_node 0 .00 RPM 66 .97 RPM
bodymap2_ovary 0 .08 RPM 49 .29 RPM
bodymap2_prostate 0 .00 RPM 65 .78 RPM
bodymap2_skeletal_muscle 0 .00 RPM 51 .33 RPM
bodymap2_testis 0 .06 RPM 76 .83 RPM
bodymap2_thyroid 0 .04 RPM 66 .42 RPM
bodymap2_white_blood_cells 0 .00 RPM 91 .51 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_37 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_37 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_37 retrocopy 5' end.

Lab - click to see more details

retro_hsap_37 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_37 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG000000921992 retrocopies
retro_hsap_1624, retro_hsap_3740,
Homo sapiens ENSG00000125970 1 retrocopy
retro_hsap_37 ,

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 = 0.28 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .13 RPM
CEU_NA11843 0 .06 RPM
CEU_NA11930 0 .10 RPM
CEU_NA12004 0 .08 RPM
CEU_NA12400 0 .11 RPM
CEU_NA12751 0 .07 RPM
CEU_NA12760 0 .04 RPM
CEU_NA12827 0 .19 RPM
CEU_NA12872 0 .03 RPM
CEU_NA12873 0 .03 RPM
FIN_HG00183 0 .14 RPM
FIN_HG00277 0 .07 RPM
FIN_HG00315 0 .14 RPM
FIN_HG00321 0 .03 RPM
FIN_HG00328 0 .17 RPM
FIN_HG00338 0 .15 RPM
FIN_HG00349 0 .03 RPM
FIN_HG00375 0 .17 RPM
FIN_HG00377 0 .13 RPM
FIN_HG00378 0 .17 RPM
GBR_HG00099 0 .12 RPM
GBR_HG00111 0 .24 RPM
GBR_HG00114 0 .16 RPM
GBR_HG00119 0 .07 RPM
GBR_HG00131 0 .06 RPM
GBR_HG00133 0 .24 RPM
GBR_HG00134 0 .09 RPM
GBR_HG00137 0 .03 RPM
GBR_HG00142 0 .08 RPM
GBR_HG00143 0 .13 RPM
TSI_NA20512 0 .28 RPM
TSI_NA20513 0 .05 RPM
TSI_NA20518 0 .17 RPM
TSI_NA20532 0 .03 RPM
TSI_NA20538 0 .09 RPM
TSI_NA20756 0 .09 RPM
TSI_NA20765 0 .10 RPM
TSI_NA20771 0 .06 RPM
TSI_NA20786 0 .24 RPM
TSI_NA20798 0 .19 RPM
YRI_NA18870 0 .03 RPM
YRI_NA18907 0 .17 RPM
YRI_NA18916 0 .11 RPM
YRI_NA19093 0 .05 RPM
YRI_NA19099 0 .13 RPM
YRI_NA19114 0 .10 RPM
YRI_NA19118 0 .17 RPM
YRI_NA19213 0 .10 RPM
YRI_NA19214 0 .17 RPM
YRI_NA19223 0 .18 RPM

Indel association:

The presence of retro_hsap_37 across human populations is associated with 3 indels. The percentage values indicate the frequencies of retro_hsap_37 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. 1:12853864..12919400 100 100 98.45 98.48 98.18 95.83 97.06 96.43 97.75 98.92 97.96 93.82 97.42 96.5
2. 1:12898652..13013300 100 98.86 99.48 97.73 99.09 95.83 98.82 100 98.88 100 99.49 97.75 99.48 98.5
3. 1:12907341..13183100 100 99.43 98.97 100 100 100 100 100 100 100 100 98.88 98.45 99.5

Indel #1, located at the genomic coordinates 1:12853864..12919400.

image/svg+xml Mexican Ancestryfrom Los Angeles USA MXL 98.48 % Puerto Ricansfrom Puerto Rico PUR 98.18 % Colombians fromMedellin, Colombia CLM 95.83 % Americans of AfricanAncestry in SW USA ASW 100 % Yoruba in Ibadan,Nigeria YRI 100 % Luhya in Webuye,Kenya LWK 98.45 % Utah Residents (CEPH)with Northern andWestern European Ancestry CEU 97.06 % Iberian Populationin Spain IBS 96.43 % British in Englandand Scotland GBR 97.75 % Finnish in Finland FIN 98.92 % Toscani in Italia TSI 97.96 % Han Chinese in Bejing,China CHB 97.42 % Japanese in Tokyo,Japan 93.82 % Southern Han Chinese CHS 96.5 % JPT EUROPE AMERICAS AFRICA EAST ASIA


Indel #2, located at the genomic coordinates 1:12898652..13013300.

image/svg+xml Mexican Ancestryfrom Los Angeles USA MXL 97.73 % Puerto Ricansfrom Puerto Rico PUR 99.09 % Colombians fromMedellin, Colombia CLM 95.83 % Americans of AfricanAncestry in SW USA ASW 100 % Yoruba in Ibadan,Nigeria YRI 98.86 % Luhya in Webuye,Kenya LWK 99.48 % Utah Residents (CEPH)with Northern andWestern European Ancestry CEU 98.82 % Iberian Populationin Spain IBS 100 % British in Englandand Scotland GBR 98.88 % Finnish in Finland FIN 100 % Toscani in Italia TSI 99.49 % Han Chinese in Bejing,China CHB 99.48 % Japanese in Tokyo,Japan 97.75 % Southern Han Chinese CHS 98.5 % JPT EUROPE AMERICAS AFRICA EAST ASIA


Indel #3, located at the genomic coordinates 1:12907341..13183100.

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 100 % Yoruba in Ibadan,Nigeria YRI 99.43 % Luhya in Webuye,Kenya LWK 98.97 % Utah Residents (CEPH)with Northern andWestern European Ancestry CEU 100 % 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 98.45 % Japanese in Tokyo,Japan 98.88 % Southern Han Chinese CHS 99.5 % JPT EUROPE AMERICAS AFRICA EAST ASIA




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