RetrogeneDB ID: retro_pabe_172

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 9:56800043..56803361(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000019232
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: IPO5
• Ensembl ID: ENSPPYG00000005458
• Aliases: None
• Description: importin 5 [Source:HGNC Symbol;Acc:6402]

Sequence

>retro_pabe_172
ATGGCGGCGACCGCGTCTGCGGGGGTGCCGGCGACCGTGTCAGAAAAGCAAGAGTTTTACCAGCTTCTGAAGAACCTGAT
CAATCCAAGCTGTATGGTGCGGAGGCAAGCAGAGGAAATCTATGAAAATATCCCAGGTCTGTGTAAGACTACCTTCCTCT
TAGATGCCGTCAGAAATAGAAGAGCAGGTTATGAGGTGAGACAAATGGCTGCCGCACTGCTACGACGGCTTTTGTCCTCT
GGGTTTGAGGAGGTTTATCCAAATCTGCCTGCTGATGTTCAGAGGGATGTCAAGATTGAACTGATTCTGGCTGTTAAGTT
AGAAACACATGCTAGCATGAGGAAAAAACTTTGTGATATTTTTGCAGTGCTGGCCAGGAATTTGATAGATGAGGATGGCA
CTAACCACTGGCCGGAAGGTCTGAAGTTTCTTATTGATTCAATCTACTCCAAAAATGTGGTTCTATGGGAAGTTGCACTT
CACGTTTTCTGGCACTTTCCTGGGATTTTTGGGACCCAAGAGCGGCATGATTTGGATATCATCAAACGGTTGTTGGACCA
GTGTATTCAAGATCAAGAACATCCAGCAATCAGGACATTATCCGCTAGAGCTGCAGCTGCATTTGTACTTGCTAATGAGA
ATAATATTGCTCTTTTCAAAGACTTTGCAGACTTGCTTCCTGGAATCTTACAGGCTGTGAATGACTCATGCTACCAGGAT
GATGATTCAGTGCTAGAATCCCTTGTTGAGATTGCAGATACCGTACCTAAGTACTTGGGTCCTTATTTAGAAGATACTCT
ACAGTTGAGTTTGAAGTTATGTGGAGACTCTAGGCTTAGTAATCTGCAGCGCCAGCTGGCCCTCGAAGTTATAGTGACCT
TGTCTGAAACTGCCACTCCGATGTTGAAAAAACATACAAATATTATTGCACAGGCAGTTCCTCATATATTAGCAATGATG
GTTGATCTACAAGATGATGAGGACTGGGTAAATGCTGATGAAATGGAAGAAGATGATTTTGACAGCAATGCAGTTGCTGC
AGAGAGTGCACTAGACAGACTGGCTTGTGGGCTTGGTGGAAAAGTTGTTTTACCAATGACCAAGGAGCATATCATGCAGA
TGCTTCAGAGCCCTGACTGGAAGTATCGACATGCTGGATTAATGGCCTTATCTGCCATTGGAGAAGGATGCCATCAACAA
ATGGAATCAATTCTAGATGAAACAGTTAACTCCGTTTTGCTTTTTCTTCAGGATCCTCATCCAAGGGTGAGGGCTGCAGC
CTGTACTACACTTGGACAGATGGCTACAGATTTTGCACCTAATTTCCAAAAGAAATTTCATGAAACAGTGATTGCAGCTC
TGTTACGTACCATGGAAAATCAAGGTAATCAGCGTGTGCAATCACATGCAGCTTCTGCTCTTATTATTTTTATTGAAGAC
TGCCCTAAATCATTGCTAGTTCTGTATGTGGATAGTATGGTGAAAAATCTACATTCCATCTTGGTGATTAAACTTCAAGA
GTTGATTCGGAATGGAACTAAGTTGGCTTTGGAACAACTTGTGACAACCATTGCATCAGTTGCAGATACAATAGAAGAAA
AATTTGTCCCATATTATGATATATTCATGCCCTCGCTAAAGCACATCATTGAGCTTGCTGTTCAGAAGGAACTCAAGCTT
CTGAGAGGAAAAACTATCGAGTGCATTAGCCATATTGGTCTTGCTGTTGGGAAGGAAAAATTTATGCAAGATGCATCAAA
TGTGATGCAGCTGTTGTTGAAGACACAATCAGACTTAAATAATATGGAAGATGATGACCCTCAGACCTCTTACATGGTTT
CAGCATGGGCTAGAATGTGTAAAATTCTTGGAAAAGATTTTCAACAGTACCTTCCACTGGTTATCGAGCCTCTTATTAAG
ACTGCTTCAGCTAAACCTGATGTTGCTCTCTTAGACACACAGGATGTGGAAAATATGAGTGACGATGATGGCTGGCAATT
TGTAAATCTTGGAGACCAGCAGAGTTTTGGAATTAAAACTTCAGGACTTGAAGCAAAAGCAACTGCTTGCCAAATGTTGG
TTTACTATGCTAAGGAGTTAAGGGAAGGGTTTGTGGAATATACAGAACAAGTTGTGAAGCTGATGGTTCCTTTACTGAAA
TTTTATTTCCATGACAATGTTCGAGTGGCAGCAGCAGAGTCCATGCCTTTTCTCCTGGAATGTGCAAGAATTCGTGGCCC
AGAGTATCTTGCACAGATGTGGCAATTCATATGTGACCCCTTAATCAAGGCTATTGGTACTGAACCGGATACAGATGTGC
TCTCAGAAATAATGAATTCTTTTGCAAAGTCCATTGAAGTTATGGGAGATGGTTGCCTTAATGATGAACACTTGGAAGAA
CTGGGAGGAATACTGAAAGCAAAACTTGAAGGGCACTTTAAAAACCAAGAATTGAGACAGGTGAAAAGACAGGAAGAAAA
CTATGATCAACAGGTTGAGATGTCTCTGCAAGATGAGGATGAATGTGATGTTTATATTCTGACCAAAGTATCAGATATTT
TGCACTCATTATTTAGTACTTATAAGGAAAAGATTTTACCATGGTTTGAACAACTACTTCCATTAATTGTAAATCTAATT
TGTTCAAGTAGGCCATGGCCAGACAGACAGTGGGGATTGTGCATATTTGATGACATCATAGAGCACTGCAGTCCAACTTC
ATTTAAATATGTAGAATATTTTCGGTGGCCAATGCTACTAAATATGCGAGATAACAACCCTGAAGTCAGGCAAGCTGCTG
CTTATGGCCTGGGTGTCATGGCACAGTTTGGTGGAGATGATTATCGTTCTTTATGTTCAGAAGCTGTTCCACTGCTGGTA
AAAGTTATTAAGTGTGCAAATTCCAAAACCAAAAAAAATGTCATTGCTACAGAGAACTGTATCTCAGCAATAGGGAAGAT
TTTGAAGTTTAAGCCTAACTGTGTAAATGTAGATGAAGTTCTTCCACACTGGTTATCATGGCTTCCACTGCATGAAGATA
AGGAGGAAGCTATTCAGACTTTGAGTTTTCTCTGTGACCTAATTGAAAGTAACCACCCAGTTGTAATTGGTCCAAATAAT
TCCAATCTTCCCAAAATAATCAGTATAATTGCAGAAGGAAAAATTAATGAGACTATTAACTATGAAGATCCTTGTGCCAA
ACGCCTAGCTAACGTCGTGCGTCAGGTACAGACTTCTGAAGATTTATGGTTGGAATGTGTATCGCAACTTGATGACGAAC
AGCAGGAAGCCTTACAGGAGTTGCTAAATTTTGCTTGA

Alignment

ORF - retro_pabe_172 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.27 %
• Parental protein coverage: 99.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AAAAEQQQFYLLLGNLLSPDNVVRKQAEETYENIPGQSKITFLLQAIRNTTAAEEARQMAAVLLRRLLSS
          A...E.Q.FY.LL.NL..P...VR.QAEE.YENIPG..K.TFLL.A.RN..A..E.RQMAA.LLRRLLSS
Retrocopy ATVSEKQEFYQLLKNLINPSCMVRRQAEEIYENIPGLCKTTFLLDAVRNRRAGYEVRQMAAALLRRLLSS

Parental  AFDEVYPALPSDVQTAIKSELLMIIQMETQSSMRKKVCDIAAELARNLIDEDGNNQWPEGLKFLFDSVSS
          .F.EVYP.LP.DVQ...K.EL......ET..SMRKK.CDI.A.LARNLIDEDG.N.WPEGLKFL.DS..S
Retrocopy GFEEVYPNLPADVQRDVKIELILAVKLETHASMRKKLCDIFAVLARNLIDEDGTNHWPEGLKFLIDSIYS

Parental  QNVGLREAALHIFWNFPGIFGNQQQHYLDVIKRMLVQCMQDQEHPSIRTLSARATAAFILANEHNVALFK
          .NV.L.E.ALH.FW.FPGIFG.Q..H.LD.IKR.L.QC.QDQEHP.IRTLSARA.AAF.LANE.N.ALFK
Retrocopy KNVVLWEVALHVFWHFPGIFGTQERHDLDIIKRLLDQCIQDQEHPAIRTLSARAAAAFVLANENNIALFK

Parental  HFADLLPGFLQAVNDSCYQNDDSVLKSLVEIADTVPKYLRPHLEATLQLSLKLCGDTSLNNMQRQLALEV
          .FADLLPG.LQAVNDSCYQ.DDSVL.SLVEIADTVPKYL.P.LE.TLQLSLKLCGD..L.N.QRQLALEV
Retrocopy DFADLLPGILQAVNDSCYQDDDSVLESLVEIADTVPKYLGPYLEDTLQLSLKLCGDSRLSNLQRQLALEV

Parental  IVTLSETAAAMLRKHTNIVAQTIPQMLAMMVDLEEDEDWANADELEDDDFDSNAVAGESALDRMACGLGG
          IVTLSETA..ML.KHTNI.AQ..P..LAMMVDL..DEDW.NADE.E.DDFDSNAVA.ESALDR.ACGLGG
Retrocopy IVTLSETATPMLKKHTNIIAQAVPHILAMMVDLQDDEDWVNADEMEEDDFDSNAVAAESALDRLACGLGG

Parental  KLVLPMIKEHIMQMLQNPDWKYRHAGLMALSAIGEGCHQQMEGILNEIVNFVLLFLQDPHPRVRYAACNA
          K.VLPM.KEHIMQMLQ.PDWKYRHAGLMALSAIGEGCHQQME.IL.E.VN.VLLFLQDPHPRVR.AAC..
Retrocopy KVVLPMTKEHIMQMLQSPDWKYRHAGLMALSAIGEGCHQQMESILDETVNSVLLFLQDPHPRVRAAACTT

Parental  VGQMATDFAPGFQKKFHEKVIAALLQTMEDQGNQRVQAHAAAALINFTEDCPKSLLIPYLDNLVKHLHSI
          .GQMATDFAP.FQKKFHE.VIAALL.TME.QGNQRVQ.HAA.ALI.F.EDCPKSLL..Y.D..VK.LHSI
Retrocopy LGQMATDFAPNFQKKFHETVIAALLRTMENQGNQRVQSHAASALIIFIEDCPKSLLVLYVDSMVKNLHSI

Parental  MVLKLQELIQKGTKLVLEQVVTSIASVADTAEEKFVPYYDLFMPSLKHIVENAVQKELRLLRGKTIECIS
          .V.KLQELI..GTKL.LEQ.VT.IASVADT.EEKFVPYYD.FMPSLKHI.E.AVQKEL.LLRGKTIECIS
Retrocopy LVIKLQELIRNGTKLALEQLVTTIASVADTIEEKFVPYYDIFMPSLKHIIELAVQKELKLLRGKTIECIS

Parental  LIGLAVGKEKFMQDASDVMQLLLKTQTDFNDMEDDDPQISYMISAWARMCKILGKEFQQYLPVVMGPLMK
          .IGLAVGKEKFMQDAS.VMQLLLKTQ.D.N.MEDDDPQ.SYM.SAWARMCKILGK.FQQYLP.V..PL.K
Retrocopy HIGLAVGKEKFMQDASNVMQLLLKTQSDLNNMEDDDPQTSYMVSAWARMCKILGKDFQQYLPLVIEPLIK

Parental  TASIKPEVALLDTQDMENMSDDDGWEFVNLGDQQSFGIKTAGLEEKSTACQMLVCYAKELKEGFVEYTEQ
          TAS.KP.VALLDTQD.ENMSDDDGW.FVNLGDQQSFGIKT.GLE.K.TACQMLV.YAKEL.EGFVEYTEQ
Retrocopy TASAKPDVALLDTQDVENMSDDDGWQFVNLGDQQSFGIKTSGLEAKATACQMLVYYAKELREGFVEYTEQ

Parental  VVKLMVPLLKFYFHDGVRVAAAESMPLLLECARVRGPEYLTQMWHFMCDALIKAIGTEPDSDVLSEIMHS
          VVKLMVPLLKFYFHD.VRVAAAESMP.LLECAR.RGPEYL.QMW.F.CD.LIKAIGTEPD.DVLSEIM.S
Retrocopy VVKLMVPLLKFYFHDNVRVAAAESMPFLLECARIRGPEYLAQMWQFICDPLIKAIGTEPDTDVLSEIMNS

Parental  FAKCIEVMGDGCLNNEHFEELGGILKAKLEEHFKNQELRQVKRQDEDYDEQVEESLQDEDDNDVYILTKV
          FAK.IEVMGDGCLN.EH.EELGGILKAKLE.HFKNQELRQVKRQ.E.YD.QVE.SLQDED..DVYILTKV
Retrocopy FAKSIEVMGDGCLNDEHLEELGGILKAKLEGHFKNQELRQVKRQEENYDQQVEMSLQDEDECDVYILTKV

Parental  SDILHSIFSSYKEKVLPWFEQLLPLIVNLICPHRPWPDRQWGLCIFDDVIEHCSPASFKYAEYFLRPMLQ
          SDILHS.FS.YKEK.LPWFEQLLPLIVNLIC..RPWPDRQWGLCIFDD.IEHCSP.SFKY.EYF..PML.
Retrocopy SDILHSLFSTYKEKILPWFEQLLPLIVNLICSSRPWPDRQWGLCIFDDIIEHCSPTSFKYVEYFRWPMLL

Parental  YVCDNSPEVRQAAAYGLGVMAQYGGDNYRPFCTEALPLLVRVIQSADSKTKENVNATENCISAVGKMMKF
          ...DN.PEVRQAAAYGLGVMAQ.GGD.YR..C.EA.PLLV.VI..A.SKTK.NV.ATENCISA.GK..KF
Retrocopy NMRDNNPEVRQAAAYGLGVMAQFGGDDYRSLCSEAVPLLVKVIKCANSKTKKNVIATENCISAIGKILKF

Parental  KPDCVNVEEVLPHWLSWLPLHEDKEEAVQTFNYLCDLIESNHPIVLGPNNTNLPKIFSIIAEGEMHEAIK
          KP.CVNV.EVLPHWLSWLPLHEDKEEA.QT...LCDLIESNHP.V.GPNN.NLPKI.SIIAEG...E.I.
Retrocopy KPNCVNVDEVLPHWLSWLPLHEDKEEAIQTLSFLCDLIESNHPVVIGPNNSNLPKIISIIAEGKINETIN

Parental  HEDPCAKRLANVVRQVQTSGGLWTECIAQLSPEQQAAIQELLNSA
          .EDPCAKRLANVVRQVQTS..LW.EC..QL..EQQ.A.QELLN.A
Retrocopy YEDPCAKRLANVVRQVQTSEDLWLECVSQLDDEQQEALQELLNFA

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	23.66 RPM	176.43 RPM
SRP007412_cerebellum	29.91 RPM	128.65 RPM
SRP007412_heart	12.58 RPM	91.42 RPM
SRP007412_kidney	13.89 RPM	101.23 RPM
SRP007412_liver	14.11 RPM	56.80 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

6 EST(s) were mapped to retro_pabe_172 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
CR536996	56800555	56801096	99.5	538	3	535
CR554958	56800429	56800826	99.8	396	1	395
CR559894	56801833	56802596	100	763	0	763
CR765273	56800223	56800993	99.9	767	1	766
CR766614	56800035	56800727	99.6	689	3	686
CR856138	56800035	56800786	99.9	750	1	749

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_172 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_172 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003784	1 retrocopy	retro_amel_3,
Bos taurus	ENSBTAG00000039374	1 retrocopy	retro_btau_104,
Canis familiaris	ENSCAFG00000005561	1 retrocopy	retro_cfam_452,
Choloepus hoffmanni	ENSCHOG00000006061	1 retrocopy	retro_chof_11,
Cavia porcellus	ENSCPOG00000004827	2 retrocopies	retro_cpor_265, retro_cpor_57,
Equus caballus	ENSECAG00000014808	1 retrocopy	retro_ecab_37,
Felis catus	ENSFCAG00000025657	1 retrocopy	retro_fcat_24,
Homo sapiens	ENSG00000065150	1 retrocopy	retro_hsap_57,
Gorilla gorilla	ENSGGOG00000008742	1 retrocopy	retro_ggor_47,
Loxodonta africana	ENSLAFG00000016190	1 retrocopy	retro_lafr_22,
Myotis lucifugus	ENSMLUG00000006500	1 retrocopy	retro_mluc_295,
Mus musculus	ENSMUSG00000030662	2 retrocopies	retro_mmus_251, retro_mmus_3683,
Nomascus leucogenys	ENSNLEG00000007831	2 retrocopies	retro_nleu_1610, retro_nleu_2482,
Oryctolagus cuniculus	ENSOCUG00000003898	1 retrocopy	retro_ocun_143,
Otolemur garnettii	ENSOGAG00000007570	1 retrocopy	retro_ogar_169,
Pongo abelii	ENSPPYG00000005458	1 retrocopy	retro_pabe_172 ,
Pan troglodytes	ENSPTRG00000005984	2 retrocopies	retro_ptro_49, retro_ptro_745,
Pteropus vampyrus	ENSPVAG00000004516	1 retrocopy	retro_pvam_8,
Rattus norvegicus	ENSRNOG00000010989	1 retrocopy	retro_rnor_240,
Sus scrofa	ENSSSCG00000009509	1 retrocopy	retro_sscr_24,
Ictidomys tridecemlineatus	ENSSTOG00000011164	1 retrocopy	retro_itri_32,