RetrogeneDB ID:

retro_hsap_88

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:13:25670336..25672232(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000151846
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:PABPC1
Ensembl ID:ENSG00000070756
Aliases:PABPC1, PAB1, PABP, PABP1, PABPC2, PABPL1
Description:poly(A) binding protein, cytoplasmic 1 [Source:HGNC Symbol;Acc:8554]


Retrocopy-Parental alignment summary:






>retro_hsap_88
ATGAACCCCAGCACCCCCAGCTACCCAACGGCCTCGCTCTACGTGGGGGACCTCCACCCCGACGTGACTGAGGCGATGCT
CTACGAGAAGTTCAGCCCGGCAGGGCCCATCCTCTCCATCCGGATCTGCAGGGACTTGATCACCAGCGGCTCCTCCAACT
ACGCGTATGTGAACTTCCAGCATACGAAGGACGCGGAGCATGCTCTGGACACCATGAATTTTGATGTTATAAAGGGCAAG
CCAGTACGCATCATGTGGTCTCAGCGTGATCCATCACTTCGAAAAAGTGGAGTGGGCAACATATTCGTTAAAAATCTGGA
TAAGTCCATTAATAATAAAGCACTGTATGATACAGTTTCTGCTTTTGGTAACATCCTTTCGTGTAACGTGGTTTGTGATG
AAAATGGTTCCAAGGGTTATGGATTTGTACACTTTGAGACACACGAAGCAGCTGAAAGAGCTATTAAAAAAATGAACGGA
ATGCTCCTAAATGGTCGCAAAGTATTTGTTGGACAATTTAAGTCTCGTAAAGAACGAGAAGCTGAACTTGGAGCTAGGGC
AAAAGAGTTCCCCAATGTTTACATCAAGAATTTTGGAGAAGACATGGATGATGAGCGCCTTAAGGATCTCTTTGGCAAGT
TCGGGCCCGCCTTAAGTGTGAAAGTAATGACCGATGAAAGTGGAAAATCCAAAGGATTTGGATTTGTAAGCTTTGAAAGG
CATGAAGATGCACAGAAAGCTGTAGATGAGATGAATGGAAAGGAGCTCAATGGAAAACAAATTTACGTTGGTCGAGCTCA
GAAAAAAGTGGAACGGCAGACGGAACTTAAGCGCACATTTGAACAGATGAAGCAAGATAGGATCACCAGATACCAGGTTG
TTAATCTTTATGTGAAAAATCTTGATGATGGTATTGATGATGAACGTCTCCGGAAAGCGTTTTCTCCATTTGGTACAATC
ACTAGTGCAAAGGTTATGATGGAAGGTGGTCGCAGCAAAGGGTTTGGTTTTGTATGTTTCTCCTCCCCAGAAGAAGCCAC
TAAAGCAGTTACAGAAATGAACGGTAGAATTGTGGCCACAAAGCCATTGTATGTAGCTTTAGCTCAGCGCAAAGAAGAGC
GCCAGGCTTACCTCACTAACGAGTATATGCAGAGAATGGCAAGTGTACGAGCTGTGCCCAACCAGCGAGCACCTCCTTCA
GGTTACTTCATGACAGCTGTCCCACAGACTCAGAACCATGCTGCATACTATCCTCCTAGCCAAATTGCTCGACTAAGACC
AAGTCCTCGCTGGACTGCTCAGGGTGCCAGACCTCATCCATTCCAAAATAAGCCCAGTGCTATCCGCCCAGGTGCTCCTA
GAGTACCATTTAGTACTATGAGACCAGCTTCTTCACAGGTTCCACGAGTCATGTCAACGCAGCGTGTTGCTAACACATCA
ACACAGACAGTGGGTCCACGTCCTGCAGCTGCTGCTGCTGCTGCAGCTACCCCTGCTGTGCGCACGGTTCCACGGTATAA
ATATGCTGCGGGAGTTCGCAATCCTCAGCAACATCGTAATGCACAGCCACAAGTTACAATGCAACAGCTTGCTGTTCATG
TACAAGGTCAGGAAACTTTGACTGCCTCCAGGTTGGCATCTGCCCCTCCTCAAAAGCAAAAGCAAATGTTAGGTGAACGG
CTCTTTCCTCTTATTCAAGCCATGCACCCTACTCTTGCTGGGAAAATCACTGGCATGTTGTTGGAGATTGATAATTCAGA
ACTTCTTTATATGCTCGAGTCTCCAGAGTCACTCCGTTCTAAGGTTGATGAAGCTGTAGCTGTACTACAAGCCCACCAAG
CTAAAGAGGCTACCCAGAAAGCAGTTAACAGTGCTACCGGTGTTCCAACTGTTTAA

ORF - retro_hsap_88 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 93.4 %
Parental protein coverage: 61.95 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD
MNPS.PSYP.ASLYVGDLHPDVTEAMLYEKFSPAGPILSIR.CRD.IT..S..YAYVNFQ...DAE.ALD
RetrocopyMNPSTPSYPTASLYVGDLHPDVTEAMLYEKFSPAGPILSIRICRDLITSGSSNYAYVNFQHTKDAEHALD
ParentalTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGY
TMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIF.KNLDKSI.NKALYDT.SAFGNILSC.VVCDENGSKGY
RetrocopyTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFVKNLDKSINNKALYDTVSAFGNILSCNVVCDENGSKGY
ParentalGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGEDMDDERLKDL
GFVHFET.EAAERAI.KMNGMLLN.RKVFVG.FKSRKEREAELGARAKEF.NVYIKNFGEDMDDERLKDL
RetrocopyGFVHFETHEAAERAIKKMNGMLLNGRKVFVGQFKSRKEREAELGARAKEFPNVYIKNFGEDMDDERLKDL
ParentalFGKFGPALSVKVMTDESGKSKGFGFVSFERHEDAQKAVDEMNGKELNGKQIYVGRAQKKVERQTELKRKF
FGKFGPALSVKVMTDESGKSKGFGFVSFERHEDAQKAVDEMNGKELNGKQIYVGRAQKKVERQTELKR.F
RetrocopyFGKFGPALSVKVMTDESGKSKGFGFVSFERHEDAQKAVDEMNGKELNGKQIYVGRAQKKVERQTELKRTF
ParentalEQMKQDRITRYQGVNLYVKNLDDGIDDERLRKEFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAV
EQMKQDRITRYQ.VNLYVKNLDDGIDDERLRK.FSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAV
RetrocopyEQMKQDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAV
ParentalTEMNGRIVATKPLYVALAQRKEERQAHLTNQYMQRMASVRAVPN
TEMNGRIVATKPLYVALAQRKEERQA.LTN.YMQRMASVRAVPN
RetrocopyTEMNGRIVATKPLYVALAQRKEERQAYLTNEYMQRMASVRAVPN

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 .26 RPM 940 .21 RPM
bodymap2_adrenal 0 .12 RPM 728 .94 RPM
bodymap2_brain 0 .33 RPM 156 .20 RPM
bodymap2_breast 0 .21 RPM 539 .93 RPM
bodymap2_colon 0 .08 RPM 1100 .11 RPM
bodymap2_heart 0 .04 RPM 176 .04 RPM
bodymap2_kidney 0 .17 RPM 326 .71 RPM
bodymap2_liver 0 .00 RPM 235 .61 RPM
bodymap2_lung 0 .12 RPM 1010 .44 RPM
bodymap2_lymph_node 0 .04 RPM 968 .43 RPM
bodymap2_ovary 0 .31 RPM 996 .65 RPM
bodymap2_prostate 0 .35 RPM 1375 .63 RPM
bodymap2_skeletal_muscle 0 .27 RPM 202 .12 RPM
bodymap2_testis 59 .29 RPM 1177 .43 RPM
bodymap2_thyroid 0 .32 RPM 400 .84 RPM
bodymap2_white_blood_cells 0 .33 RPM 2554 .91 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_88 was not detected

EST - click to see more details

15 EST(s) were mapped to retro_hsap_88 retrocopy
EST ID Start End Identity Match Mis-match Score
BG717008 25670297 25671008 99.1 707 3 701
BG718483 25670275 25671034 99.4 750 2 741
BI460001 25670162 25671090 98.5 791 8 776
BI464014 25670290 25670966 99.6 672 2 667
BI825788 25670331 25670947 99.7 613 1 610
BU567424 25670277 25670984 98.8 707 0 703
CD243801 25670318 25671120 97.7 796 5 783
CD358457 25670303 25671047 97.2 722 7 706
CD358574 25670199 25671120 99.2 818 0 808
CD358948 25670315 25671096 98.6 775 3 766
DB029258 25670309 25670915 100 606 0 606
DB032778 25670288 25670885 100 597 0 597
DB033450 25670410 25670980 100 570 0 570
DB039899 25670684 25671261 99.9 576 1 575
DB045095 25670387 25670943 99.5 556 0 555

TSS - click to see more details



TSS No. TSS Name TSS expression level (Expr) in TPM range:
no expression 0 < Expr ≤ 1 1 < Expr ≤ 5 5 < Expr ≤ 10 Expr > 10
TSS #1 TSS_321151660 libraries150 libraries15 libraries0 libraries4 libraries
TSS #2 TSS_321161825 libraries2 libraries2 libraries0 libraries0 libraries

The graphical summary, for retro_hsap_88 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Display detail expression values in each library
... or ...
Directly download all expression values

Lab - click to see more details

retro_hsap_88 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_88 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_8
Pongo abelii retro_pabe_68
Parental genes homology:
Parental genes homology involve 26 parental genes, and 51 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000003481 retrocopy
retro_amel_1650,
Choloepus hoffmanni ENSCHOG000000081781 retrocopy
retro_chof_2531,
Callithrix jacchus ENSCJAG000000158335 retrocopies
retro_cjac_1586, retro_cjac_2571, retro_cjac_3218, retro_cjac_4039, retro_cjac_41,
Cavia porcellus ENSCPOG000000129171 retrocopy
retro_cpor_1324,
Dasypus novemcinctus ENSDNOG000000087182 retrocopies
retro_dnov_1530, retro_dnov_2259,
Felis catus ENSFCAG000000018741 retrocopy
retro_fcat_1927,
Homo sapiens ENSG00000070756 1 retrocopy
retro_hsap_88 ,
Homo sapiens ENSG000000760671 retrocopy
retro_hsap_1143,
Homo sapiens ENSG000000906212 retrocopies
retro_hsap_109, retro_hsap_74,
Homo sapiens ENSG000001532501 retrocopy
retro_hsap_1131,
Gorilla gorilla ENSGGOG000000067851 retrocopy
retro_ggor_1986,
Myotis lucifugus ENSMLUG000000122451 retrocopy
retro_mluc_579,
Macaca mulatta ENSMMUG000000177862 retrocopies
retro_mmul_1462, retro_mmul_895,
Monodelphis domestica ENSMODG000000062224 retrocopies
retro_mdom_123, retro_mdom_1867, retro_mdom_216, retro_mdom_43,
Mus musculus ENSMUSG000000222832 retrocopies
retro_mmus_102, retro_mmus_2164,
Nomascus leucogenys ENSNLEG000000031423 retrocopies
retro_nleu_221, retro_nleu_2412, retro_nleu_611,
Oryctolagus cuniculus ENSOCUG000000043541 retrocopy
retro_ocun_13,
Pongo abelii ENSPPYG000000187903 retrocopies
retro_pabe_2373, retro_pabe_68, retro_pabe_854,
Pteropus vampyrus ENSPVAG000000166402 retrocopies
retro_pvam_10, retro_pvam_855,
Rattus norvegicus ENSRNOG000000086393 retrocopies
retro_rnor_1228, retro_rnor_2321, retro_rnor_265,
Sarcophilus harrisii ENSSHAG000000112671 retrocopy
retro_shar_24,
Sus scrofa ENSSSCG000000060632 retrocopies
retro_sscr_1153, retro_sscr_1205,
Ictidomys tridecemlineatus ENSSTOG000000163952 retrocopies
retro_itri_139, retro_itri_48,
Tarsius syrichta ENSTSYG000000042292 retrocopies
retro_tsyr_1743, retro_tsyr_273,
Tursiops truncatus ENSTTRG000000046892 retrocopies
retro_ttru_1050, retro_ttru_1812,
Vicugna pacos ENSVPAG000000038654 retrocopies
retro_vpac_14, retro_vpac_384, retro_vpac_620, retro_vpac_649,

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 = 1.39 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .26 RPM
CEU_NA11843 0 .45 RPM
CEU_NA11930 1 .04 RPM
CEU_NA12004 0 .27 RPM
CEU_NA12400 0 .60 RPM
CEU_NA12751 0 .51 RPM
CEU_NA12760 0 .85 RPM
CEU_NA12827 0 .75 RPM
CEU_NA12872 0 .41 RPM
CEU_NA12873 0 .41 RPM
FIN_HG00183 0 .63 RPM
FIN_HG00277 0 .41 RPM
FIN_HG00315 0 .52 RPM
FIN_HG00321 0 .60 RPM
FIN_HG00328 0 .40 RPM
FIN_HG00338 0 .38 RPM
FIN_HG00349 0 .46 RPM
FIN_HG00375 0 .56 RPM
FIN_HG00377 0 .45 RPM
FIN_HG00378 0 .28 RPM
GBR_HG00099 0 .58 RPM
GBR_HG00111 0 .19 RPM
GBR_HG00114 0 .50 RPM
GBR_HG00119 0 .50 RPM
GBR_HG00131 0 .49 RPM
GBR_HG00133 0 .36 RPM
GBR_HG00134 0 .35 RPM
GBR_HG00137 0 .36 RPM
GBR_HG00142 0 .64 RPM
GBR_HG00143 0 .26 RPM
TSI_NA20512 0 .34 RPM
TSI_NA20513 0 .24 RPM
TSI_NA20518 1 .39 RPM
TSI_NA20532 0 .41 RPM
TSI_NA20538 0 .64 RPM
TSI_NA20756 0 .64 RPM
TSI_NA20765 0 .52 RPM
TSI_NA20771 0 .77 RPM
TSI_NA20786 0 .34 RPM
TSI_NA20798 0 .50 RPM
YRI_NA18870 0 .54 RPM
YRI_NA18907 0 .59 RPM
YRI_NA18916 0 .32 RPM
YRI_NA19093 0 .23 RPM
YRI_NA19099 0 .37 RPM
YRI_NA19114 0 .29 RPM
YRI_NA19118 0 .54 RPM
YRI_NA19213 0 .45 RPM
YRI_NA19214 0 .20 RPM
YRI_NA19223 0 .38 RPM

Indel association:

The presence of retro_hsap_88 across human populations is associated with 1 indel. The percentage values indicate the frequencies of retro_hsap_88 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. 13:25671963..25673200 100 100 96.91 99.24 100 98.33 99.41 100 100 98.92 99.49 98.31 98.97 100

Indel #1, located at the genomic coordinates 13:25671963..25673200.

image/svg+xml Mexican Ancestryfrom Los Angeles USA MXL 99.24 % Puerto Ricansfrom Puerto Rico PUR 100 % Colombians fromMedellin, Colombia CLM 98.33 % Americans of AfricanAncestry in SW USA ASW 100 % Yoruba in Ibadan,Nigeria YRI 100 % Luhya in Webuye,Kenya LWK 96.91 % Utah Residents (CEPH)with Northern andWestern European Ancestry CEU 99.41 % Iberian Populationin Spain IBS 100 % British in Englandand Scotland GBR 100 % Finnish in Finland FIN 98.92 % Toscani in Italia TSI 99.49 % Han Chinese in Bejing,China CHB 98.97 % Japanese in Tokyo,Japan 98.31 % Southern Han Chinese CHS 100 % JPT EUROPE AMERICAS AFRICA EAST ASIA




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