RetrogeneDB ID: retro_hsap_4131

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 9:11011748..11013089(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000234146
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: AKAP8
• Ensembl ID: ENSG00000105127
• Aliases: AKAP8, AKAP 95, AKAP-8, AKAP-95, AKAP95
• Description: A kinase (PRKA) anchor protein 8 [Source:HGNC Symbol;Acc:378]

Sequence

>retro_hsap_4131
GGCCCAGTCTCATAGGAGGCCACCAAGGCAAGCAAAGGTGGCCTGGTGGCCAGGGCCACTTCCATGCACATGGCCTCTTA
TGGCCCAGAGCGGGGCACCTACAATTGCAACTCCCTCACTGCCAAGATCAACCAGCTTTTGGACATGATGTCCAAGGAAG
AAGGCAGTGGGGGGAGCGGCCACGGTGGGGAGGGCATGCAGGACCAGGAGAGCTCCTTCCACTTGCAGACCTTGGAGTCC
TGTGACTCCATGGCCTGCCTGCCAGAGCACAGCCCCTACTGCCCCAGCTACAGCTACGACTATGACTTCGACCTGGGGTT
CCACCGCAATGGCAGCTTTCGGGGGCAGTACAGTGAATGTTGAGACCTGGCCCTGGAGTAGGGCTCCCTCAATGGCTTCA
TGCCGGGCGAGGCCAGGGCCATTTCCAGGACCAGAGCAATCCCGGCACCTTCATGTGCAACGACCCCTTCTAGCCACCCT
CAGCCTCCCCTGATCCTCTATCTACGCCCTAGAAAGAGCTGAACTACGTGAGTGGATGGGGTCTGGAAAGGCCCTCTCCC
CAGCCAATGGCCTCCTTGGCTCTTCTCCCCGTCCGTGGTTCCTGACTAAGGCTTGATGGGCATGCAGGAGGCGGGTGGCT
ATGACAGCGCTGGCCTTAAGGATGTGGTCACTCGCAGGGCCAGAAGCAGGATCAGGATCCACCCAGAAGGAGAGGGTTTG
ACCCGTTTGGGCTAGATGGCATGGGAAGGAAACAGAAGCAGTTCCAGAATTGTAAGGAGCCAGATGCCAAACTAGCCTGG
GTTGACAGTGAAGTAGATTTCTCAGAAAATGATAACAAAGCTGGTGACTTCCACTCAGAAGATGAAGAATTCAAAGGTGA
GGATGAATTCTGTGACTCTGGTAGGCAGAGAGAAGGACGACGAGGATGAGGAAGTGAAAAAGAGGAGGGAAAAATAAAGG
AGGAGAGACAGGATGCAGTACTGAGCAGCCGGAAGGATTCAGTTGGCCTCTTCTGTGTGCAATTTCTGTAGATTTGAAGA
CGAAGAGATCCAGAAGCATCTGCAAAGCGAATTTCACAAAGAGACGCTGCAGTTTATAAGCACCAAGCTGCCCAACAAGA
CAATGGAATTCATCCGGGAATACATTATAAACAGGAATAAAAAAATTGAGAAGAAGCATCAGGAATTGATGGAGAAAGAA
AGCACAAAACAAAAACCAGATCCTTTCAAAGAGATTGGCCAGGAGCACTTTAAGAAGATCCAGGCTGCTCACTGCCTGGC
CTGCGCCGTGCTGATCCCAGCGCAGCCACAGCTTCTCCAGCCACACCTGCACTTCCTTGAC

Alignment

ORF - retro_hsap_4131 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.15 %
• Parental protein coverage: 65.03 %
• Number of stop codons detected: 9
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GPASWEAAKANDGGLAAGAPAMHMASYGPEPCTDNSDSLIAKINQRLDMMSKEGGRGGSGGGGEGIQDRE
          GP.S.EA.KA..GGL.A.A..MHMASYGPE..T.N..SL.AKINQ.LDMMSKE.G.GGSG.GGEG.QD.E
Retrocopy GPVS*EATKASKGGLVARATSMHMASYGPERGTYNCNSLTAKINQLLDMMSKEEGSGGSGHGGEGMQDQE

Parental  SSFRFQPFESYDSRPCLPEHNPYRPSYSYDYEFDLGSDRNGSFGGQYSECRDPARERGSLDGFM-RGRGQ
          SSF..Q..ES.DS..CLPEH.PY.PSYSYDY.FDLG..RNGSF.GQYSEC.D.A.E.GSL.GFM..GRGQ
Retrocopy SSFHLQTLESCDSMACLPEHSPYCPSYSYDYDFDLGFHRNGSFRGQYSEC*DLALE*GSLNGFM<AGRGQ

Parental  GRFQDRSNPGTFMRSDPFVPPAASSEPLSTPWNELNYVGGRGL-GGPSPSRPPPSLFSQSMAPDYGVMGM
          G.FQD.SNPGTFM..DPF.PP.AS..PLSTP..ELNYV.G.GL..GP.PS..PP.LFS.S..PD.G.MGM
Retrocopy GHFQDQSNPGTFMCNDPF*PPSASPDPLSTP*KELNYVSGWGL>KGPLPSQWPPWLFSPSVVPD*GLMGM

Parental  QGAGGYDST-MPYGCGRSQPRMRDRDRPKRRGFDRFGPDGTGRKRKQFQLYEEPDTKLARVDSEGDFSEN
          Q.AGGYDS...P.GCG.SQ....D.D.P.RRGFD.FG.DG.GRK.KQFQ...EPD.KLA.VDSE.DFSEN
Retrocopy QEAGGYDSA<WP*GCGHSQGQKQDQDPPRRRGFDPFGLDGMGRKQKQFQNCKEPDAKLAWVDSEVDFSEN

Parental  DDAAGDFRSGDEEFKGEDELCDSGRQR-GEKEDEDEDVKKRREKQRRRDRTRDRAADRIQFACSVCKFRS
          D..AGDF.S.DEEFKGEDE.CDSGRQR....ED..E.VKKRREK.RRRDR....AA.RIQ.A.SVC.F..
Retrocopy DNKAGDFHSEDEEFKGEDEFCDSGRQR>KDDED--EEVKKRREK*RRRDRMQY*AAGRIQLASSVCNFCR

Parental  FDDEEIQKHLQSKFHKETLRFISTKLPDKTVEFLQEYIVNRNKKIEKRRQELMEKETAKPKPDPFKGIGQ
          F.DEEIQKHLQS.FHKETL.FISTKLP.KT.EF..EYI.NRNKKIEK..QELMEKE..K.KPDPFK.IGQ
Retrocopy FEDEEIQKHLQSEFHKETLQFISTKLPNKTMEFIREYIINRNKKIEKKHQELMEKESTKQKPDPFKEIGQ

Parental  EHFFKKIEAAHCLACDMLIPAQPQLLQRHLHSVD
          EH.FKKI.AAHCLAC..LIPAQPQLLQ.HLH..D
Retrocopy EH-FKKIQAAHCLACAVLIPAQPQLLQPHLHFLD

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	0.00 RPM	33.32 RPM
bodymap2_adrenal	0.00 RPM	56.93 RPM
bodymap2_brain	0.00 RPM	22.17 RPM
bodymap2_breast	0.00 RPM	22.57 RPM
bodymap2_colon	0.00 RPM	18.49 RPM
bodymap2_heart	0.00 RPM	17.35 RPM
bodymap2_kidney	0.00 RPM	31.50 RPM
bodymap2_liver	0.00 RPM	10.03 RPM
bodymap2_lung	0.00 RPM	28.15 RPM
bodymap2_lymph_node	0.00 RPM	35.85 RPM
bodymap2_ovary	0.00 RPM	34.20 RPM
bodymap2_prostate	0.00 RPM	38.49 RPM
bodymap2_skeletal_muscle	0.00 RPM	43.54 RPM
bodymap2_testis	0.02 RPM	27.39 RPM
bodymap2_thyroid	0.00 RPM	36.91 RPM
bodymap2_white_blood_cells	0.00 RPM	22.74 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_4131 was not detected

EST

No EST(s) were mapped for retro_hsap_4131 retrocopy.

TSS

No TSS is located nearby retro_hsap_4131 retrocopy 5' end.

Lab

retro_hsap_4131 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4131 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_2776
Pongo abelii	retro_pabe_3472

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000105127	1 retrocopy	retro_hsap_4131 ,
Gorilla gorilla	ENSGGOG00000013427	1 retrocopy	retro_ggor_2776,
Pongo abelii	ENSPPYG00000009671	1 retrocopy	retro_pabe_3472,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.00 RPM
CEU_NA11843	0.03 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	0.00 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

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Indel association:

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