RetrogeneDB ID: retro_hsap_1110

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 12:45566939..45568574(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000134297
• Aliases: PLEKHA8P1, PLEKHA9
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PLEKHA8
• Ensembl ID: ENSG00000106086
• Aliases: PLEKHA8, FAPP2
• Description: pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 8 [Source:HGNC Symbol;Acc:30037]

Sequence

>retro_hsap_1110
GCTGCTGGTGCTCCTCGCCTCCTGGGGCCTTGGGCAATGAGGGGGCCGGTGGGCGTGGGCTGAGTGGCCGTGGGCGCCAT
GGAGTGGGTGCTGTACAAGTGGACCAACTATCTGAGCAGTTGGCAGCCTTGATGGTTCTTTCTCTGTAGGGGAATATTGT
CCTATTATGATTCTCCTGAAGATGCCTGGAAAGGTTGCAAAGGGAGCATACAAATGGCAGTCTGTGAAATTGAAGTTCAT
TCTGTAGATAATACATGCATGGACCTGATAATCCCCGGGGAACAGTATTTCTACCTGAAGGCCAGAAGTGTGCCTGAAAG
ATAGCGGCGGCTGGTGGCCCTGGGATCAGCCAAGGCTTGCCTGACTGACAGTAGGACCCAGAAGGATAAAGAGTTTGCTG
AAAACACTGAAAACTTGAAAACCAAAATGTCAGAACTAAGACTCTGCTGTGACCTCCTTGTTCAGCAAGTAGATAAAACA
AAAGAAGTGACCACAACTGGTGTGTCCAATTCTGAGGAGGGAATTGATGTGGGAACTTTGCTGAAATCAACCTGTAATAC
TTTTCTGAAGACCTTGGAAGAATGCATGCAGATTGCAAATGCAGCCTTCACCTCTGAGCTGCTCTACCACACTCCACCAG
GATCACCACAGCTGGCCATGCTCAAGTCCAGCAAGATGAAACATCCTATTATACCAATTCATAATTCATTGGAAAGGCAA
ACGGAGTTGAGCACTTGTGAAAATGGATCTTTAAATATGGAAATAAATGGTGAGGAAGAAATCCTAATGAAAAATAAGAA
TTCCTTATATTTGAAATCTGCAGAGATAGACTGCAGCATATCAAGTGAGGAAAATACAGATGATAATATAACCGTCCAAG
GTGAAATAATGAAGGAAGATAGAATGGAAAACCTGAAAAATCATGACAATAACTTGTCTCAGTCTGGATCAGACTCAAGT
TGCTCTCCAGAATGCCTCTGGGAGGAAGGCAAAGAAGTTATCCCAACTTTCTTTAGTACCATGAACACAAGCTTTAGTGA
CATTGAACTTCTGGAAGACAGTGGCATTCCCACAGAAGCATTCTTGGCATCATGTTGTGCTGTGGTTCCAGTATTAGACA
AACTTGGCCCTACAGTGTTTGCTCCTGTTAAGATGGATCTTGTTGAAAATATTAAGAAAGTAAATCAGAAGTATATAACC
AACAAAGAAGAGTTTACCACTCTCCAGAAGATAGTGCTGCACGAAGTGGAGGCGGATGTAGCCCAGGTTAGGAACTCAGC
GACTGAAGCCCTCTTGTGGCTGAAGAGAGGTCTCAAATTTTTGAAGGGATTTTTGACAGAAGTGAAAAATGGGGAAAAGG
ATATCCAGACAGCCCTGAATAACGCATATGGTAAAACATTGCGGCAACACCATGGCTGGGTAGTTCGAGGGGTTTTTGCG
TTAGCTTTAAGGGCAACTCCATCCTATGAAGATTTTGTGGCCGCGTTAACCGTAAAGGAAGGTGACCACCGGAAAGAAGC
TTTCAGTATTGGGATGCAGAGGGACCTCAGCCTTTACCTCCCTGCCATGAAGAAGCAGATGGCCATACTGGACGCTTTAT
AAGAGGTCCATGGGCTGGAATCTGATGAGGTTGTA

Alignment

ORF - retro_hsap_1110 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.5 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AAGAPRLLGPGAVRGPAGVGRVAAGAMEGVLYKWTNYLSGWQPRWFLLCGGILSYYDSPEDAWKGCKGSI
          AAGAPRLLGP.A.RGP.GVG.VA.GAME.VLYKWTNYLS.WQP.WF.LC.GILSYYDSPEDAWKGCKGSI
Retrocopy AAGAPRLLGPWAMRGPVGVG*VAVGAMEWVLYKWTNYLSSWQP*WFFLCRGILSYYDSPEDAWKGCKGSI

Parental  QMAVCEIQVHSVDNTRMDLIIPGEQYFYLKARSVAERQRWLVALGSAKACLTDSRTQKEKEFAENTENLK
          QMAVCEI.VHSVDNT.MDLIIPGEQYFYLKARSV.ER.R.LVALGSAKACLTDSRTQK.KEFAENTENLK
Retrocopy QMAVCEIEVHSVDNTCMDLIIPGEQYFYLKARSVPER*RRLVALGSAKACLTDSRTQKDKEFAENTENLK

Parental  TKMSELRLYCDLLVQQVDKTKEVTTTGVSNSEEGIDVGTLLKSTCNTFLKTLEECMQIANAAFTSELLYR
          TKMSELRL.CDLLVQQVDKTKEVTTTGVSNSEEGIDVGTLLKSTCNTFLKTLEECMQIANAAFTSELLY.
Retrocopy TKMSELRLCCDLLVQQVDKTKEVTTTGVSNSEEGIDVGTLLKSTCNTFLKTLEECMQIANAAFTSELLYH

Parental  TPPGSPQLAMLKSSKMKHPIIPIHNSLERQMELSTCENGSLNMEINGEEEILMKNKNSLYLKSAEIDCSI
          TPPGSPQLAMLKSSKMKHPIIPIHNSLERQ.ELSTCENGSLNMEINGEEEILMKNKNSLYLKSAEIDCSI
Retrocopy TPPGSPQLAMLKSSKMKHPIIPIHNSLERQTELSTCENGSLNMEINGEEEILMKNKNSLYLKSAEIDCSI

Parental  SSEENTDDNITVQGEIRKEDGMENLKNHDNNLTQSGSDSSCSPECLWEEGKEVIPTFFSTMNTSFSDIEL
          SSEENTDDNITVQGEI.KED.MENLKNHDNNL.QSGSDSSCSPECLWEEGKEVIPTFFSTMNTSFSDIEL
Retrocopy SSEENTDDNITVQGEIMKEDRMENLKNHDNNLSQSGSDSSCSPECLWEEGKEVIPTFFSTMNTSFSDIEL

Parental  LEDSGIPTEAFLASCYAVVPVLDKLGPTVFAPVKMDLVGNIKKVNQKYITNKEEFTTLQKIVLHEVEADV
          LEDSGIPTEAFLASC.AVVPVLDKLGPTVFAPVKMDLV.NIKKVNQKYITNKEEFTTLQKIVLHEVEADV
Retrocopy LEDSGIPTEAFLASCCAVVPVLDKLGPTVFAPVKMDLVENIKKVNQKYITNKEEFTTLQKIVLHEVEADV

Parental  AQVRNSATEALLWLKRGLKFLKGFLTEVKNGEKDIQTALNNAYGKTLRQHHGWVVRGVFALALRAAPSYE
          AQVRNSATEALLWLKRGLKFLKGFLTEVKNGEKDIQTALNNAYGKTLRQHHGWVVRGVFALALRA.PSYE
Retrocopy AQVRNSATEALLWLKRGLKFLKGFLTEVKNGEKDIQTALNNAYGKTLRQHHGWVVRGVFALALRATPSYE

Parental  DFVAALTVKEGDHQKEAFSIGMQRDLSLYLPAMEKQLAILDTLYEVHGLESDEVV
          DFVAALTVKEGDH.KEAFSIGMQRDLSLYLPAM.KQ.AILD.L.EVHGLESDEVV
Retrocopy DFVAALTVKEGDHRKEAFSIGMQRDLSLYLPAMKKQMAILDAL*EVHGLESDEVV

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
bodymap2_adipose	1.79 RPM	24.69 RPM
bodymap2_adrenal	1.25 RPM	6.90 RPM
bodymap2_brain	0.45 RPM	19.76 RPM
bodymap2_breast	6.69 RPM	11.09 RPM
bodymap2_colon	1.88 RPM	11.08 RPM
bodymap2_heart	0.79 RPM	6.30 RPM
bodymap2_kidney	1.51 RPM	18.57 RPM
bodymap2_liver	0.68 RPM	4.73 RPM
bodymap2_lung	3.38 RPM	11.64 RPM
bodymap2_lymph_node	6.18 RPM	20.48 RPM
bodymap2_ovary	1.66 RPM	19.39 RPM
bodymap2_prostate	4.17 RPM	16.37 RPM
bodymap2_skeletal_muscle	0.15 RPM	4.18 RPM
bodymap2_testis	2.07 RPM	21.44 RPM
bodymap2_thyroid	1.71 RPM	7.57 RPM
bodymap2_white_blood_cells	6.36 RPM	20.87 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_1110 was not detected

EST

17 EST(s) were mapped to retro_hsap_1110 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AA449847	45566888	45567301	100	413	0	413
AA449903	45567156	45567658	99.9	501	1	500
AI989772	45566837	45567356	100	517	0	517
AU123031	45567050	45567660	97.7	607	1	598
BF969547	45567099	45567739	99.9	638	1	636
BG001226	45567468	45567927	99.8	439	1	436
BI962918	45566847	45567334	100	487	0	487
BI963739	45566890	45567251	100	361	0	361
BI964007	45566899	45567334	99.6	433	2	431
BI964918	45566846	45567334	99.4	485	3	482
BI966751	45566890	45567351	100	461	0	461
BI966840	45566888	45567224	100	336	0	336
BM727873	45566826	45567522	99.2	686	5	676
BQ941977	45566882	45567637	100	754	0	754
BU741550	45566816	45567522	99.9	703	0	699
CA489189	45566830	45567713	97.8	841	10	826
CK903702	45566887	45567350	100	463	0	463

TSS

No TSS is located nearby retro_hsap_1110 retrocopy 5' end.

Lab

retro_hsap_1110 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1110 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_688
Pongo abelii	retro_pabe_919

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000106086	1 retrocopy	retro_hsap_1110 ,
Homo sapiens	ENSG00000116095	1 retrocopy	retro_hsap_2060,
Homo sapiens	ENSG00000139433	1 retrocopy	retro_hsap_755,
Gorilla gorilla	ENSGGOG00000006031	1 retrocopy	retro_ggor_868,
Pongo abelii	ENSPPYG00000017682	1 retrocopy	retro_pabe_919,
Pan troglodytes	ENSPTRG00000019036	1 retrocopy	retro_ptro_688,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	1.99 RPM
CEU_NA11843	2.76 RPM
CEU_NA11930	2.25 RPM
CEU_NA12004	2.24 RPM
CEU_NA12400	2.10 RPM
CEU_NA12751	1.85 RPM
CEU_NA12760	1.98 RPM
CEU_NA12827	2.03 RPM
CEU_NA12872	1.58 RPM
CEU_NA12873	1.75 RPM
FIN_HG00183	2.94 RPM
FIN_HG00277	3.14 RPM
FIN_HG00315	2.07 RPM
FIN_HG00321	2.69 RPM
FIN_HG00328	1.89 RPM
FIN_HG00338	2.49 RPM
FIN_HG00349	2.08 RPM
FIN_HG00375	1.81 RPM
FIN_HG00377	1.99 RPM
FIN_HG00378	2.04 RPM
GBR_HG00099	3.31 RPM
GBR_HG00111	2.94 RPM
GBR_HG00114	2.21 RPM
GBR_HG00119	3.57 RPM
GBR_HG00131	2.24 RPM
GBR_HG00133	2.36 RPM
GBR_HG00134	2.45 RPM
GBR_HG00137	2.69 RPM
GBR_HG00142	2.47 RPM
GBR_HG00143	3.19 RPM
TSI_NA20512	2.85 RPM
TSI_NA20513	3.75 RPM
TSI_NA20518	2.50 RPM
TSI_NA20532	1.80 RPM
TSI_NA20538	2.21 RPM
TSI_NA20756	2.91 RPM
TSI_NA20765	2.34 RPM
TSI_NA20771	2.07 RPM
TSI_NA20786	1.96 RPM
TSI_NA20798	2.78 RPM
YRI_NA18870	1.93 RPM
YRI_NA18907	2.11 RPM
YRI_NA18916	1.89 RPM
YRI_NA19093	1.09 RPM
YRI_NA19099	1.78 RPM
YRI_NA19114	1.23 RPM
YRI_NA19118	1.74 RPM
YRI_NA19213	1.51 RPM
YRI_NA19214	2.07 RPM
YRI_NA19223	2.29 RPM

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Indel association:

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