RetrogeneDB ID:

retro_hsap_4661

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:X:25047661..25048349(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000214111
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PAFAH1B2
Ensembl ID:ENSG00000168092
Aliases:PAFAH1B2, HEL-S-303
Description:platelet-activating factor acetylhydrolase 1b, catalytic subunit 2 (30kDa) [Source:HGNC Symbol;Acc:8575]


Retrocopy-Parental alignment summary:






>retro_hsap_4661
ATGAACCAAGGAGACTCAAACCCAGCAGCTACTCCGCATGCGGCAGAAGACATTCAAGGAGATGACAGATGGATGTGTCA
GCACAACAGATTTGTTTTGGACTGTAAAGACAAACAGCCTGATGTACCATTTGCGGGAGGCTCCGTGGTGCAGTTACTGC
AGCCATATGAGATATGGCGAGAGCTTTTTTCCCCACTTCATGCACTGAATTTTGGAACTGGGGGAGATACAACAAGACAT
GTTTTGTGGAGACTAAAGAGCGGAGAACTGGGGAATACTAAGCCTAAGGTCATTGTTTTCTGGCTAGGAAGAAACAACCA
TGAAAATATGGCAGAAGAGGTAGCAGGTGGTATGGCGGCCATCGTACAACTTATCAACACAAGGCAGCCACAGGCCAAAA
TCATTGTATTTGATCTGTTACCTCAAGGTGAGAAACCCAACCCTTTGAGGCAAAAGAACGCCAAGGTGAACCCACTCGTC
AAGATTTCGCTGCTGAAACTTAACCAACGTGCAGCTCCTGGATACTGACAGGGGTTTCGTGCACTCCGACCGTGCCATCT
CCTGCCACGACATGTTTGATTTTCTGCATTTGACAGGAGGTGGCTACTCAAAGGTCTGCAAACCCTTGAATGAACTGATC
ATGCAGTTGTTGGAGGAAACACCTGAGGAGAAACAAACCACCATTGCC

ORF - retro_hsap_4661 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.22 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMSQGDSNPAAIPHAAEDIQGDDRWMSQHNRFVLDCKDKEPDVLFVGDSMVQLMQQYEIWRELFSPLHALN
M.QGDSNPAA.PHAAEDIQGDDRWM.QHNRFVLDCKDK.PDV.F.G.S.VQL.Q.YEIWRELFSPLHALN
RetrocopyMNQGDSNPAATPHAAEDIQGDDRWMCQHNRFVLDCKDKQPDVPFAGGSVVQLLQPYEIWRELFSPLHALN
ParentalFGIGGDTTRHVLWRLKNGELENIKPKVIVVWVGTNNHENTAEEVAGGIEAIVQLINTRQPQAKIIVLGLL
FG.GGDTTRHVLWRLK.GEL.N.KPKVIV.W.G.NNHEN.AEEVAGG..AIVQLINTRQPQAKIIV..LL
RetrocopyFGTGGDTTRHVLWRLKSGELGNTKPKVIVFWLGRNNHENMAEEVAGGMAAIVQLINTRQPQAKIIVFDLL
ParentalPRGEKPNPLRQKNAKVNQLLKVSLPK-LANVQLLDTDGGFVHSDGAISCHDMFDFLHLTGGGYAKICKPL
P.GEKPNPLRQKNAKVN.L.K.SL.K.L.NVQLLDTD.GFVHSD.AISCHDMFDFLHLTGGGY.K.CKPL
RetrocopyPQGEKPNPLRQKNAKVNPLVKISLLK>LTNVQLLDTDRGFVHSDRAISCHDMFDFLHLTGGGYSKVCKPL
ParentalHELIMQLLEETPEEKQTTIA
.ELIMQLLEETPEEKQTTIA
RetrocopyNELIMQLLEETPEEKQTTIA

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 164 .51 RPM
bodymap2_adrenal 0 .00 RPM 108 .02 RPM
bodymap2_brain 0 .00 RPM 188 .39 RPM
bodymap2_breast 0 .00 RPM 128 .62 RPM
bodymap2_colon 0 .00 RPM 97 .51 RPM
bodymap2_heart 0 .00 RPM 66 .81 RPM
bodymap2_kidney 0 .00 RPM 123 .48 RPM
bodymap2_liver 0 .00 RPM 48 .61 RPM
bodymap2_lung 0 .00 RPM 112 .96 RPM
bodymap2_lymph_node 0 .00 RPM 126 .27 RPM
bodymap2_ovary 0 .02 RPM 163 .37 RPM
bodymap2_prostate 0 .00 RPM 101 .25 RPM
bodymap2_skeletal_muscle 0 .00 RPM 54 .73 RPM
bodymap2_testis 0 .04 RPM 204 .57 RPM
bodymap2_thyroid 0 .00 RPM 125 .87 RPM
bodymap2_white_blood_cells 0 .00 RPM 127 .56 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4661 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4661 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4661 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4661 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4661 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_3097
Gorilla gorilla retro_ggor_2893
Pongo abelii retro_pabe_3621
Macaca mulatta retro_mmul_2481
Parental genes homology:
Parental genes homology involve 14 parental genes, and 21 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000086282 retrocopies
retro_amel_1145, retro_amel_818,
Canis familiaris ENSCAFG000000132261 retrocopy
retro_cfam_1335,
Callithrix jacchus ENSCJAG000000126981 retrocopy
retro_cjac_3325,
Dipodomys ordii ENSDORG000000112741 retrocopy
retro_dord_560,
Felis catus ENSFCAG000000299451 retrocopy
retro_fcat_270,
Homo sapiens ENSG00000168092 2 retrocopies
retro_hsap_1148, retro_hsap_4661 ,
Gorilla gorilla ENSGGOG000000281972 retrocopies
retro_ggor_2893, retro_ggor_893,
Macaca mulatta ENSMMUG000000020502 retrocopies
retro_mmul_2481, retro_mmul_892,
Mustela putorius furoENSMPUG000000042461 retrocopy
retro_mputfur_898,
Nomascus leucogenys ENSNLEG000000073372 retrocopies
retro_nleu_1096, retro_nleu_946,
Pongo abelii ENSPPYG000000039072 retrocopies
retro_pabe_3621, retro_pabe_953,
Pan troglodytes ENSPTRG000000043182 retrocopies
retro_ptro_3097, retro_ptro_782,
Rattus norvegicus ENSRNOG000000180321 retrocopy
retro_rnor_2585,
Sarcophilus harrisii ENSSHAG000000114031 retrocopy
retro_shar_617,

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 = 0.02 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 .00 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 .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 .00 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .00 RPM

Indel association:

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



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