RetrogeneDB ID: retro_pabe_3472

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 9:51610933..51612269(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: AKAP8
• Ensembl ID: ENSPPYG00000009671
• Aliases: None
• Description: A kinase (PRKA) anchor protein 8 [Source:HGNC Symbol;Acc:378]

Sequence

>retro_pabe_3472
CCAGTCTCATAGGAGGCCACCAAGGCAAGCAAAGGTGGCCTGGTGGCCAGGGCCACTTCCGTGCACATGGCCTCTTATGG
CCCAGAGCGGGGTACCTACAATTGCAACTCCCTCACTGCCAAGATCAACCAGCTTTGGACATGATGTCCAAGGAAGAAGG
CAGTGGGGGAAGCGGCCACGGTGGGGAAGGCATCCAGGACCGGAAGAGCTCCTTCCACTTGCAGACCTTGGAGTCCTGTG
ACTCCATGGCCTGCCTGCCAGAGCACAGCCCCTACTGCCCCAGCTACAGCTATGACTATGACTTCGACCTGGGGTTCCAC
CCCAATGGCAGCTTTTGGGGGCAGTACAGTGAATGTTGAGACCTGGCCCTGGAGTAGGGCTCCCTCAATGGCTTCATGCC
GGGTGGGGCCAGGGCCATTTCCAGGACCAGAGCAATCCCGGCACCTTCATGTGGAGCGACCCCGTCAAGCCACCCTCGGC
CTCCCCTGATCCTCTATCCACGCCCTAGAAAGAGCTGAACTACATGAGGGGATGGGGTCTGGGAAGGCCCTCTCCCCAGC
CAGCGGCCTCCTTGGCTCTTCTCCCCATCCATGGCTACTGACTAAGGCTTGATGGGCACGCAGGGGTCACGTGGCTATGA
CAGCACTGGCCTTAAGGATGTGGTCACTAGCAGGGCCAGATGCAGGATCGGGATCCACCCAGAAGGAGAGGGTTTGACCC
CTTTGGGCTAGATGGCATGGGAAGGAAACAGAAGCAGTTCCAGATTTGTAAGGAGCCGACGCAAAACTAGCCTGGGTTGA
CAGCAAAGGAGATTACTCAGAAAATGATAACAAAGCTGATGACTTCCACTCAAGAGATGAAGAATTCAAAGGTGAGGATG
AATTCTGTGACTCTGGTAGGCAGAGAGAAGGATGACGAGGATGAGGAAGTGAAAAAGAGAAGGGAAAAGTAAAGGAGACG
AGACAGGATGCAGGACTGCGCAGCCAACAGGATTCAGTTGGCCTCTTCTGTGGGCAATTTCTGTAGATTTGAAGACAAAG
AGATCCAGAAGCATCTGCAAAGTGAATTTCACAAAGAGACGCTGCAGTTTATAAGCACCAAGCTGCCCAACAAGACAATG
GAATTCATCCAGGAATACATTATAAACAGGAATAAAAAAATTGAGAAGAAGCGTCAGGAATTGATGGAGAAAGAAAGCAC
AAAACCAAAACCAGATCCTTTCAGAGAGATTGGCCAGGAGCACTTTAAGAAGATCCAGGCTGCTCACTGCCTGGCCTGTG
CTGTGCTGATCCAAGCGCAGCCACAGCTTCTCCAGCCACACCTGCACTTCATTGAC

Alignment

ORF - retro_pabe_3472 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.33 %
• Parental protein coverage: 64.88 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  PASWEAAKANDGGLAAGAPAMHMASYGPEPCTDNSDSLIAKINQ-RLDMMSKEGGRGGSGGGGEGMQDRE
          P.S.EA.KA..GGL.A.A...HMASYGPE..T.N..SL.AKINQ..LDMMSKE.G.GGSG.GGEG.QDR.
Retrocopy PVS*EATKASKGGLVARATSVHMASYGPERGTYNCNSLTAKINQ<ALDMMSKEEGSGGSGHGGEGIQDRK

Parental  SSFRFQPFESYDSRPCLPEHNPYRPSYSYDYDFDLGSDRNGSFGGQYSECRDPARERGSLDGFM-RGRGQ
          SSF..Q..ES.DS..CLPEH.PY.PSYSYDYDFDLG...NGSF.GQYSEC.D.A.E.GSL.GFM..G.GQ
Retrocopy SSFHLQTLESCDSMACLPEHSPYCPSYSYDYDFDLGFHPNGSFWGQYSEC*DLALE*GSLNGFM<AGWGQ

Parental  GRFQDRSNPGTFMRSDPFVPPAASSEPLSTPWNELNYVGGRGLG-GPSPSRPPPSLFSQSMAPDYGVMGM
          G.FQD.SNPGTFM.SDP..PP.AS..PLSTP..ELNY..G.GLG.GP.PS..PP.LFS.SMA.D.G.MG.
Retrocopy GHFQDQSNPGTFMWSDPVKPPSASPDPLSTP*KELNYMRGWGLG>GPLPSQRPPWLFSPSMATD*GLMGT

Parental  QGAGGYDST-MPYGCGRSQPRMRDRDRPKRRGFEHFGPDGTGRKRKQFQLYEEP-DTKLARVDSEGDFSE
          QG..GYDST..P.GCG..Q..M.DRD.P.RRGF..FG.DG.GRK.KQFQ...EP.D.KLA.VDS.GD.SE
Retrocopy QGSRGYDST<WP*GCGH*QGQMQDRDPPRRRGFDPFGLDGMGRKQKQFQICKEP<DAKLAWVDSKGDYSE

Parental  NDDAAGDFRSGDEEFKGEDEFCDSGRQR-GEKEDEEEDVKKRREKQRRRDRTRDRAADRIQFACSVCKFR
          ND..A.DF.S.DEEFKGEDEFCDSGRQR....EDEE..VKKRREK.RRRDR..D.AA.RIQ.A.SV..F.
Retrocopy NDNKADDFHSRDEEFKGEDEFCDSGRQR>KDDEDEE--VKKRREK*RRRDRMQDCAANRIQLASSVGNFC

Parental  SFDDEEIQKHLQSKFHKETLRFISTKLPDKTVEFLQEYIVNRNKKIEKRRQELMEKETAKPKPDPFKGIG
          .F.D.EIQKHLQS.FHKETL.FISTKLP.KT.EF.QEYI.NRNKKIEK.RQELMEKE..KPKPDPF..IG
Retrocopy RFEDKEIQKHLQSEFHKETLQFISTKLPNKTMEFIQEYIINRNKKIEKKRQELMEKESTKPKPDPFREIG

Parental  QEHFFKKIEAAHCLACDMLIPAQPQLLQRHLHSVD
          QEH.FKKI.AAHCLAC..LI.AQPQLLQ.HLH..D
Retrocopy QEH-FKKIQAAHCLACAVLIQAQPQLLQPHLHFID

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
SRP007412_brain_prefrontal_cortex	0.00 RPM	14.15 RPM
SRP007412_cerebellum	0.00 RPM	21.28 RPM
SRP007412_heart	0.00 RPM	6.68 RPM
SRP007412_kidney	0.00 RPM	17.04 RPM
SRP007412_liver	0.00 RPM	8.35 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3472 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3472 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3472 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4131
Gorilla gorilla	retro_ggor_2776

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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 ,