RetrogeneDB ID: retro_pabe_1449

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 17:31183743..31186822(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDZD8
• Ensembl ID: ENSPPYG00000002691
• Aliases: None
• Description: PDZ domain containing 8 [Source:HGNC Symbol;Acc:26974]

Sequence

>retro_pabe_1449
TTCGAAAAGCTGCTGCAGACCAAGACGGCCGGGCGCCTGCTGGAGGGGCTGAGCCTGCGGGACGTGTTCCTGGGCGAGAC
GGTGCCCTTCATCGAGACCATCCGGCTCGTCCGGCCTGTCGTGCCCTCGGCCACCGGGGAGCCCGACGGCCCCGAAGGGG
AGGCGCTGCCCGCCGCCTGCCCCGAGGAGCTGGCCTTCGAGGCGGAGGTGGAGTACAACGGGGGCTTCCACCTGGCCATC
CACGTGGACCTGGTCTTAGGCAAGTCCGCCTACTTGTTTGTCAAGCTGTCCCGCGTGGTGGGGAGGCTGCGCTTGGTCTT
CACGCGCGTGCCCTTCACCCACTGGTTCTTCTCCTTCGTGGAGGACCCGCTGATGGACTTCAAAGTGCGCTCCCAGTTTG
AAGGGCGGCCCATGCCCCAGCTCACCTCCATCATCGTCAACCAGCTCAAGAAGATCATCAAGCGCAAACACATCCTCCCG
AATTACAAGATCAGGTTCAAGCCGTTTTTTCCATACCAGACCTTGCAAGGATTTGAAGAAGGTGAAGAGCATATCCATAT
ACAACAACGGGCACTTACTGAAGGCCGTCTTAAAGTTACATTGTTAGAATGTAGCAGGTTACTCATTTTTGGATCCTGTG
ACAGAGAGGCAAATGTTCATTGCACACTTGAATTAAGCATTAGTGTTTGGGAAGAAAAACAGAGGAGTTCTATTAAGACG
GTTGAATTAATAAAAGGGAATTTACAAAGTGTTGGACTTACACTTCGTTTTGTCCAGTCAACTGTTGGGTATGCTGGACA
CGTCATCATTGAAACTGTGGCTCCAAACTCGCCTGCTGCAATTGCAGATCTTCAGCAGGGAGATCGACTTATTGCCATTG
GAGGTGTGAAAATCACATCAACACTGCAAGTGTTGAAGCTTATCAAGCAGGCTGGTGACCGAGTCCTGGTGTACTATGAA
AGGCCTGTTGGCCAGAGTAATCAAGGTACAGTGCTGCAAGATAACTTTGGCCAGTTGGAAGAAAACATTTTGTGAAGCTC
ATGCCAATCAGGTTATGAAGAGGAAGCTGCCGGGTTGACAGTAGATACTGAAAGTAAAGAGCTGGATTCTGAATTTGAAG
ACTTGGCAAGTGATGTCAGAGCACAAAACGAATTCAAAGATGAGGCACAATCATTAAGTCATAGTGCCAAATGTGCTCCA
ACAACACTTTCTATTAAACCCCTTGGAGCTGTATCACCAGTTTTAAACCATAAATTAGCTGTAAGAAGTCACCCACTACC
ACCAAAATTTCAGTCCAAAGGTGGAAATAAACCTCCACCCCTAAAAACTTCTGAGATAACAGACCAGGCACAAGTGTGAA
AACCCATCCAGGGATCTACTTTCAAACCACCTGTGCCACCACGACCACAAGTGAAAGTTCCTTTGCTTTCCACTGATGCC
CCAAATCAGGCAGAACCAGATGTTCTTGATGAAAAGCCAGAGGTGCTGCCACCTCCTCTTGTAGATAAATCTGCTGAAAA
GCAAGCAAAAAATGTGGATCCCATAGACGATGCAGCTGCGTCTAAGCAGTTTTTAGCAAAGCAAGAAGTGGCCAAAGATG
TCACTTCAGAAACTTCGTGCCCTACTAGGGACAGTTGGGATGACCGTCAAACATGGGAATCATCAGAAATTCTTTATCGT
AATAAGCTAGGAAAATGGACAAGAACCAGAGCATCCTGTTTGTTTGACATAGAAGCCTGTCACAAGTACTTAAACATTGC
ATTGTGGTGCAGGGATCCTTTTAAGTTGGGAGGTCTCATCTGTTTGGGGCATGTTAGTTTAAAACTTCAAGATGTGGCTT
TAGGATGCCTAGCTACATCAAACATGGAATACCTTTCCAAATTGAGACTGGAAGCCCCCTCACCTAAGGCTATAGTCACT
AGAACTGCACTACACAATCTGAGTATGCAAAAGGGATTCAATGACAAATTTTGTTATGGTGACATTACTATTCACTTCAA
ATATTTGAAAGAAGGAGAATCAGACCACCATGTAGTTACTAACATAGAGAAAGAGAAAGAACCCCATTTGGTTGAAGAAG
TTTCTGTTCTCCCTAAAGAGGAGCAATTTGTTGGACAGATGGGTTTAACAGAAAACAAACACAGTTTCCAGGATACTCAG
TTCCAGAACCCAACATGGTGTGACTACTGTAAGAAAAAAGTTTGGACTAAAGCAGCTTCCCAGTGTATGTTTTGTGCTTA
TGTTTGCCATAAAAAATGTCAAGAAAAGTGTCTAGCTGAGACTTCTGTTTGTGGAGCAACTGATAGGCGAATAGACGGGA
CCCTGAAAAACCTTAGCTGGAAGGACAGGAAACCCTCTTAGGCCTGCCTCCTCATGCTGATGCTGAAGCTAGCAAGTCAG
TCAATAAAACAACAGGTTTGACAAAGCATATTATCAATACTAGTTCTTGTTTATTAAATTTCCGTCAAGTCTCTAAAACT
TGCCTTTCTGAACCAGGAACCAATCTCATAGAACCTTCACCAAAACACACACCCAACACGTCAGACAATGAAGGCAGTGA
TACGGAGGTCTGTGGTCCAAACAGTCCTTCTAAATGGGGAAACAGCGTAGGAATAAAGTTAGTGAGAAAAGAGGGTGGTC
TGGATGACAGTGTTTTCATTGCAGTTAAAGAAATTGGTCATGATATGTACAGGGGCTTGCCTACAGAGGAAAGGATCCAG
AAACTCGAGTTCACGTTGGATAAGCTACAGAATGAAATTGATCAGGAGTTGGAACACAATAATTCCCTTGTTAGAGAAGA
AAAAGAGACAACTGATACAAGGAAGAAATCACTTCTTTCTGCTGCTTTAGCTAAATCAGTGAAAGCCTACAAGCTCTAAC
ACTTCTTATGATCCACTTCAGAGCAGGCACTGAAAATATAGAAATTTTAGAAAGTCTGTCTTTAGACCAGCACTCCAAAA
ATATAAGCAAGTACACAGATGATACAGAAGAAGACCTTGATAATGAAATAAGCCAACTAATAGACTCTCAGCCATTCAGC
AGCATATCAGATGACTTATTTGGCCCATCTGAGTCTGTG

Alignment

ORF - retro_pabe_1449 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.3 %
• Parental protein coverage: 89.08 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FEELLQTKTAGRLLEGLSLRDVFLGETVPFIKTIRLVRPVVPSATGEPDGPEGEALPAACPEELAFEAEV
          FE.LLQTKTAGRLLEGLSLRDVFLGETVPFI.TIRLVRPVVPSATGEPDGPEGEALPAACPEELAFEAEV
Retrocopy FEKLLQTKTAGRLLEGLSLRDVFLGETVPFIETIRLVRPVVPSATGEPDGPEGEALPAACPEELAFEAEV

Parental  EYNGGFHLAIDVDLVFGKSAYLFVKLSRVVGRLRLVFTRVPFTHWFFSFVEDPLIDFEVRSQFEGRPMPQ
          EYNGGFHLAI.VDLV.GKSAYLFVKLSRVVGRLRLVFTRVPFTHWFFSFVEDPL.DF.VRSQFEGRPMPQ
Retrocopy EYNGGFHLAIHVDLVLGKSAYLFVKLSRVVGRLRLVFTRVPFTHWFFSFVEDPLMDFKVRSQFEGRPMPQ

Parental  LTSIIVNQLKKIIKRKHTLPNYKIRFKPFFPYQTLQGFEEDEEHIHIQQWALTEGRLKVTLLECNRLLIF
          LTSIIVNQLKKIIKRKH.LPNYKIRFKPFFPYQTLQGFEE.EEHIHIQQ.ALTEGRLKVTLLEC.RLLIF
Retrocopy LTSIIVNQLKKIIKRKHILPNYKIRFKPFFPYQTLQGFEEGEEHIHIQQRALTEGRLKVTLLECSRLLIF

Parental  GSYDREANVHCTLELSSSVWEEKQRSSIKTVELIKGNLQSVGLTLRLVQSTDGYAGHVIIETVAPNSPAA
          GS.DREANVHCTLELS.SVWEEKQRSSIKTVELIKGNLQSVGLTLR.VQST.GYAGHVIIETVAPNSPAA
Retrocopy GSCDREANVHCTLELSISVWEEKQRSSIKTVELIKGNLQSVGLTLRFVQSTVGYAGHVIIETVAPNSPAA

Parental  IADLQRGDRLIAIGGVKITSTLQVLKLIKQAGDRVLVYYERPVGQSNQGAVLPDNFGQLEENFLSSSCQS
          IADLQ.GDRLIAIGGVKITSTLQVLKLIKQAGDRVLVYYERPVGQSNQG.VL.DNFGQLEEN.L.SSCQS
Retrocopy IADLQQGDRLIAIGGVKITSTLQVLKLIKQAGDRVLVYYERPVGQSNQGTVLQDNFGQLEENIL*SSCQS

Parental  SYEEEAAGLTVDTESRELDSEFEDLASDVRAQNEFKDEAQSLSHSPKRAPTTLSIKPLGAISPVLNRKLA
          .YEEEAAGLTVDTES.ELDSEFEDLASDVRAQNEFKDEAQSLSHS.K.APTTLSIKPLGA.SPVLN.KLA
Retrocopy GYEEEAAGLTVDTESKELDSEFEDLASDVRAQNEFKDEAQSLSHSAKCAPTTLSIKPLGAVSPVLNHKLA

Parental  VGSHPLPPKIQSKDGNKPPPLKTSEITDPAQVSKPTQGSAFKPPVPPRPQVKVPLPSADAPNQAEPDVLV
          V.SHPLPPK.QSK.GNKPPPLKTSEITD.AQV.KP.QGS.FKPPVPPRPQVKVPL.S.DAPNQAEPDVL.
Retrocopy VRSHPLPPKFQSKGGNKPPPLKTSEITDQAQV*KPIQGSTFKPPVPPRPQVKVPLLSTDAPNQAEPDVLD

Parental  EKPEKVPPPPLVDKSAEKQAKNVDPVDDAAASKQFLAKQEVAKDVISETSCPTKDSSDDRQTWESSEILY
          EKPE.V.PPPLVDKSAEKQAKNVDP.DDAAASKQFLAKQEVAKDV.SETSCPT.DS.DDRQTWESSEILY
Retrocopy EKPE-VLPPPLVDKSAEKQAKNVDPIDDAAASKQFLAKQEVAKDVTSETSCPTRDSWDDRQTWESSEILY

Parental  RNKLGKWTRTRASCLFDIEACHRYLNIALWCRDPFKLGGLICLGHVSLKLEDVALGCLATSNMEYLSKLR
          RNKLGKWTRTRASCLFDIEACH.YLNIALWCRDPFKLGGLICLGHVSLKL.DVALGCLATSNMEYLSKLR
Retrocopy RNKLGKWTRTRASCLFDIEACHKYLNIALWCRDPFKLGGLICLGHVSLKLQDVALGCLATSNMEYLSKLR

Parental  LEAPSPKAIVTRTALRNLSMQKGFNDKFCYGDITIHFKYLKEGESDHHVVTNVEKEKEPHLVEEVSVLPK
          LEAPSPKAIVTRTAL.NLSMQKGFNDKFCYGDITIHFKYLKEGESDHHVVTN.EKEKEPHLVEEVSVLPK
Retrocopy LEAPSPKAIVTRTALHNLSMQKGFNDKFCYGDITIHFKYLKEGESDHHVVTNIEKEKEPHLVEEVSVLPK

Parental  EEQFVGQMGLTENKHSFQDTQFQNPTWCDYCKKKVWTKAASQCMFCAYVCHKKCQEKCLAETSVCGATDR
          EEQFVGQMGLTENKHSFQDTQFQNPTWCDYCKKKVWTKAASQCMFCAYVCHKKCQEKCLAETSVCGATDR
Retrocopy EEQFVGQMGLTENKHSFQDTQFQNPTWCDYCKKKVWTKAASQCMFCAYVCHKKCQEKCLAETSVCGATDR

Parental  RIDRTLKNLR-LEGQETLLGLPPRVDAEASKSVNKTTGLTRHIINTSSRLLNLRQVSKTRLSEPGTDLVE
          RID.TLKNL..LEGQETLLGLPP..DAEASKSVNKTTGLT.HIINTSS.LLN.RQVSKT.LSEPGT.L.E
Retrocopy RIDGTLKNLS<LEGQETLLGLPPHADAEASKSVNKTTGLTKHIINTSSCLLNFRQVSKTCLSEPGTNLIE

Parental  PSPKHTPNTSDNEGSDTEVCGPNSPSKRGNSTGIKLVRKEGGLDDSVFIAVKEIGRDLYRGLPTEERIQK
          PSPKHTPNTSDNEGSDTEVCGPNSPSK.GNS.GIKLVRKEGGLDDSVFIAVKEIG.D.YRGLPTEERIQK
Retrocopy PSPKHTPNTSDNEGSDTEVCGPNSPSKWGNSVGIKLVRKEGGLDDSVFIAVKEIGHDMYRGLPTEERIQK

Parental  LEFMLDKLQNEIDQELEHNNSLVREEKETTDTRKKSLLSAALAKS-GERLQALTLLMIHYRAGIEDIETL
          LEF.LDKLQNEIDQELEHNNSLVREEKETTDTRKKSLLSAALAKS..E.LQALTLLMIH.RAG.E.IE.L
Retrocopy LEFTLDKLQNEIDQELEHNNSLVREEKETTDTRKKSLLSAALAKS<SESLQALTLLMIHFRAGTENIEIL

Parental  ESLSLDQHSKKISKYTDDTEEDLDNEISQLIDSQPFSSISDDLFGPSESV
          ESLSLDQHSK.ISKYTDDTEEDLDNEISQLIDSQPFSSISDDLFGPSESV
Retrocopy ESLSLDQHSKNISKYTDDTEEDLDNEISQLIDSQPFSSISDDLFGPSESV

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	16.09 RPM
SRP007412_cerebellum	0.36 RPM	24.44 RPM
SRP007412_heart	0.00 RPM	6.68 RPM
SRP007412_kidney	0.00 RPM	13.52 RPM
SRP007412_liver	0.00 RPM	17.69 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1449 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1449 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1449 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Pongo abelii	ENSPPYG00000002691	1 retrocopy	retro_pabe_1449 ,
Sus scrofa	ENSSSCG00000010669	1 retrocopy	retro_sscr_234,