RetrogeneDB ID: retro_ptro_49

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 9:6080403..6083721(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000029349
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: IPO5
• Ensembl ID: ENSPTRG00000005984
• Aliases: IPO5, RANBP5
• Description: importin 5 [Source:HGNC Symbol;Acc:6402]

Sequence

>retro_ptro_49
ATGGCGGCGACCGCGTCTGCAGGGGTGCCGGCGACCGTGTCAGAAAAGCAAGAGTTTTACCAGCTTCTGAAGAACCTGAT
CAATCCAAGCTGTATGGTGCGGAGGCAAGCAGAGGAAATCTATGAAAATATCCCAGGTCTGTGTAAGACTACCTTCCTCT
TAGATGCCGTCAGAAATAGAAGAGCAGGTTATGAGGTGAGACAAATGGCTGCCGCACTGCTACGACGGCTTTTGTCCTCT
GGGTTTGAGGAGGTTTATCCAAGTCTGCCTGCTGATGTTCAGAGGGATGTCAAGATTGAACTGATTCTGGCTGTTAAGTT
AGAAACACATGCTAGCATGAGGAAAAAACTTTGTGATATTTTTGCAGTGCTGGCCAGGAATTTGATAGATGAGGATGGCA
CTAACCACTGGCCGGAAGGTCTGAAGTTTCTTATTGATTCAATCTACTCCAAAAATGTGGTTCTATGGGAAGTTGCACTT
CACGTTTTCTGGCACTTTCCTGGGATTTTTGGGACCCAAGAGCGGCATGATTTGGATATCATCAAACGGTTGTTGGACCA
GTGTATTCAAGATCAAGAACATCCAGCAATCAGGACATTATCCGCTAGAGCTGCAGCTGCATTTGTACTTGCTAATGAGA
ATAATATTGCTCTTTTCAAAGACTTTGCAGACTTGCTTCCTGGAATCTTACAGGCTGTGAATGACTCATGCTACCAGGAT
GATGATTCAGTGCTAGAATCCCTTGTTGAGATTGCAGATACCGTACCTAAGTACTTGGGTCCTTATTTAGAAGATACTCT
ACAGTTGAGTTTGAAGTTATGTGGAGACTCTAGGCTTAGTAATCTGCAGCGCCAGCTGGCCCTCGAAGTTATAGTGACCT
TATCTGAAACTGCCACTCCGATGTTGAAAAAACATACAAATATTATTGCACAGGCAGTTCCTCATATATTAGCAATGATG
GTTGATCTACAAGATGATGAGGACTGGGTAAATGCTGATGAAATGGAAGAAGATGATTTTGACAGCAATGCAGTTGCTGC
GGAGAGTGCACTAGACAGACTGGCTTGTGGGCTTGGTGGAAAAGTTGTTTTACCAATGACCAAGGAGCATATCATGCAGA
TGCTTCAGAGCCCTGACTGGAAGTATCGACATGCTGGATTAATGGCCTTATCTGCCATTGGAGAAGGATGCCATCAACAA
ATGGAATCAATTCTAGATGAAACAGTTAACTCCGTTTTGCTTTTTCTTCAGGATCCTCATCCAAGGGTGAGGGCTGCAGC
CTGTACTACACTTGGACAGATGGCTACAGATTTTGCACCTAATTTCCAAAAGAAATTTCATGAAACAGTGATTGCAGCTC
TGTTACGTACCATGGAAAATCAAGGTAATCAGCGTGTGCAATCACATGCAGCTTCTGCTCTTATTATTTTTATTGAAGAC
TGCCCTAAATCATTGCTAGTTCTATATGTGGATAGTATGGTGAAAAATCTACATTCCATCTTGGTGATTAAACTTCAAGA
GTTGATTCGGAATGGAACTAAGTTGGCTTTGGAACAACTTGTGACAACCATTGCATCAGTTGCAGATACAATAGAAGAAA
AATTTGTCCCATATTATGATATATTCATGCCCTCACTAAAGCACATTGTTGAGCTTGCTGTTCAGAAGGAACTCAAGCTT
CTGAGAGGAAAAACTATCGAGTGCATTAGCCATATTGGTCTTGCTGTTGGGAAGGAAAAATTTATGCAAGATGCATCAAA
TGTGATGCAGCTGTTGTTGAAGACACAATCAGACTTAAATAATATGGAAGATGATGACCCTCAGACCTCTTACATGGTTT
CAGCATGGGCTAGAATGTGTAAAATTCTTGGAAAAGATTTTCAACAGTACCTTCCACTGGTTATCGAGCCTCTTATTAAG
ACTGCTTCAGCTAAACCTGATGTTGCTCTCTTAGACACACAGGATGTGGAAAATATGAGTGACGATGATGGCTGGCAATT
TGTAAATCTTGGAGACCAGCAGAGTTTTGGAATTAAAACTTCAGGACTTGAAGCAAAAGCAACTGCTTGCCAAATGTTGG
TTTACTATGCTAAGGAGTTAAGGGAAGGGTTTGTGGAATATACAGAACAAGTTGTGAAGCTGATGGTTCCTTTACTGAAA
TTTTATTTCCATGACAATGTTCGAGTGGCAGCAGCAGAGTCCATGCCTTTTCTCCTGGAATGTGCAAGAATTCGTGGCCC
AGAGTATCTTGCACAGATGTGGCAATTCATATGTGACCCCTTAATCAAGGCTATTGGTACTGAACCAGATACAGATGTGC
TCTCAGAAATAATGAATTCTTTTGCAAAGTCCATTGAAGTTATGGGAGATGGTTGCCTTAATGATGAACACTTGGAAGAA
CTGGGAGGAATACTGAAAGCAAAACTTGAAGGGCACTTTAAAAACCAAGAATTGAGACAGGTGAAAAGACAGGAAGAAAA
CTATGATCAACAGGTTGAGATGTCTCTGCAAGATGAGGATGAATGTGATGTTTATATTCTGACCAAAGTATCAGATATTT
TGCACTCATTATTTAGTACTTATAAGGAAAAGATTTTACCATGGTTTGAACAACTACTTCCATTAATTGTAAATCTAATT
TGTTCAAGTAGGCCATGGCCAGACAGACAGTGGGGATTGTGCATATTTGATGACATCATAGAGCACTGCAGTCCAACTTC
ATTTAAATATGTAGAATATTTTCGGTGGCCAATGCTACTAAATATGCGAGATAACAACCCTGAAGTCAGGCAAGCTGCTG
CTTATGGCCTGGGTGTCATGGCACAGTTTGGTGGAGATGATTATCGTTCTTTATGTTCAGAAGCTGTTCCACTGCTGGTA
AAAGTTATTAAGTGTGCAAATTCCAAAACCAAAAAAAATGTCATTGCTACAGAGAACTGTATCTCAGCAATAGGGAAGAT
TTTGAAGTTTAAGCCTAACTGTGTAAATGTAGATGAAGTTCTTCCACACTGGTTATCATGGCTTCCACTGCATGAAGATA
AAGAGGAAGCTATTCAGACTTTGAGTTTTCTCTGTGACCTAATTGAAAGTAACCACCCAGTTGTAATTGGTCCAAATAAT
TCCAATCTTCCCAAAATAATCAGTATAATTGCAGAAGGAAAAATTAATGAGACTATTAACTATGAAGATCCTTGTGCCAA
ACGCCTAGCTAATGTCGTGCGTCAGGTACAGACTTCTGAAGATTTATGGTTGGAATGTGTATCACAACTTGATGATGAAC
AGCAGGAAGCCTTACAGGAGTTGCTAAATTTTGCTTGA

Alignment

ORF - retro_ptro_49 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.06 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QETYENIPGQSKITFLLQAIRNTTAAEEARQMAAVLLRRLLSSAFDEVYPALPSDVQTAIKSELLMIIQM
          .E.YENIPG..K.TFLL.A.RN..A..E.RQMAA.LLRRLLSS.F.EVYP.LP.DVQ...K.EL......
Retrocopy EEIYENIPGLCKTTFLLDAVRNRRAGYEVRQMAAALLRRLLSSGFEEVYPSLPADVQRDVKIELILAVKL

Parental  ETQSSMRKKVCDIAAELARNLIDEDGNNQWPEGLKFLFDSVSSQNVGLREAALHIFWNFPGIFGNQQQHY
          ET..SMRKK.CDI.A.LARNLIDEDG.N.WPEGLKFL.DS..S.NV.L.E.ALH.FW.FPGIFG.Q..H.
Retrocopy ETHASMRKKLCDIFAVLARNLIDEDGTNHWPEGLKFLIDSIYSKNVVLWEVALHVFWHFPGIFGTQERHD

Parental  LDVIKRMLVQCMQDQEHPSIRTLSARATAAFILANEHNVALFKHFADLLPGFLQAVNDSCYQNDDSVLKS
          LD.IKR.L.QC.QDQEHP.IRTLSARA.AAF.LANE.N.ALFK.FADLLPG.LQAVNDSCYQ.DDSVL.S
Retrocopy LDIIKRLLDQCIQDQEHPAIRTLSARAAAAFVLANENNIALFKDFADLLPGILQAVNDSCYQDDDSVLES

Parental  LVEIADTVPKYLRPHLEATLQLSLKLCGDTSLNNMQRQLALEVIVTLSETAAAMLRKHTNIVAQTIPQML
          LVEIADTVPKYL.P.LE.TLQLSLKLCGD..L.N.QRQLALEVIVTLSETA..ML.KHTNI.AQ..P..L
Retrocopy LVEIADTVPKYLGPYLEDTLQLSLKLCGDSRLSNLQRQLALEVIVTLSETATPMLKKHTNIIAQAVPHIL

Parental  AMMVDLEEDEDWANADELEDDDFDSNAVAGESALDRMACGLGGKLVLPMIKEHIMQMLQNPDWKYRHAGL
          AMMVDL..DEDW.NADE.E.DDFDSNAVA.ESALDR.ACGLGGK.VLPM.KEHIMQMLQ.PDWKYRHAGL
Retrocopy AMMVDLQDDEDWVNADEMEEDDFDSNAVAAESALDRLACGLGGKVVLPMTKEHIMQMLQSPDWKYRHAGL

Parental  MALSAIGEGCHQQMEGILNEIVNFVLLFLQDPHPRVRYAACNAVGQMATDFAPGFQKKFHEKVIAALLQT
          MALSAIGEGCHQQME.IL.E.VN.VLLFLQDPHPRVR.AAC...GQMATDFAP.FQKKFHE.VIAALL.T
Retrocopy MALSAIGEGCHQQMESILDETVNSVLLFLQDPHPRVRAAACTTLGQMATDFAPNFQKKFHETVIAALLRT

Parental  MEDQGNQRVQAHAAAALINFTEDCPKSLLIPYLDNLVKHLHSIMVLKLQELIQKGTKLVLEQVVTSIASV
          ME.QGNQRVQ.HAA.ALI.F.EDCPKSLL..Y.D..VK.LHSI.V.KLQELI..GTKL.LEQ.VT.IASV
Retrocopy MENQGNQRVQSHAASALIIFIEDCPKSLLVLYVDSMVKNLHSILVIKLQELIRNGTKLALEQLVTTIASV

Parental  ADTAEEKFVPYYDLFMPSLKHIVENAVQKELRLLRGKTIECISLIGLAVGKEKFMQDASDVMQLLLKTQT
          ADT.EEKFVPYYD.FMPSLKHIVE.AVQKEL.LLRGKTIECIS.IGLAVGKEKFMQDAS.VMQLLLKTQ.
Retrocopy ADTIEEKFVPYYDIFMPSLKHIVELAVQKELKLLRGKTIECISHIGLAVGKEKFMQDASNVMQLLLKTQS

Parental  DFNDMEDDDPQISYMISAWARMCKILGKEFQQYLPVVMGPLMKTASIKPEVALLDTQDMENMSDDDGWEF
          D.N.MEDDDPQ.SYM.SAWARMCKILGK.FQQYLP.V..PL.KTAS.KP.VALLDTQD.ENMSDDDGW.F
Retrocopy DLNNMEDDDPQTSYMVSAWARMCKILGKDFQQYLPLVIEPLIKTASAKPDVALLDTQDVENMSDDDGWQF

Parental  VNLGDQQSFGIKTAGLEEKSTACQMLVCYAKELKEGFVEYTEQVVKLMVPLLKFYFHDGVRVAAAESMPL
          VNLGDQQSFGIKT.GLE.K.TACQMLV.YAKEL.EGFVEYTEQVVKLMVPLLKFYFHD.VRVAAAESMP.
Retrocopy VNLGDQQSFGIKTSGLEAKATACQMLVYYAKELREGFVEYTEQVVKLMVPLLKFYFHDNVRVAAAESMPF

Parental  LLECARVRGPEYLTQMWHFMCDALIKAIGTEPDSDVLSEIMHSFAKCIEVMGDGCLNNEHFEELGGILKA
          LLECAR.RGPEYL.QMW.F.CD.LIKAIGTEPD.DVLSEIM.SFAK.IEVMGDGCLN.EH.EELGGILKA
Retrocopy LLECARIRGPEYLAQMWQFICDPLIKAIGTEPDTDVLSEIMNSFAKSIEVMGDGCLNDEHLEELGGILKA

Parental  KLEEHFKNQELRQVKRQDEDYDEQVEESLQDEDDNDVYILTKVSDILHSIFSSYKEKVLPWFEQLLPLIV
          KLE.HFKNQELRQVKRQ.E.YD.QVE.SLQDED..DVYILTKVSDILHS.FS.YKEK.LPWFEQLLPLIV
Retrocopy KLEGHFKNQELRQVKRQEENYDQQVEMSLQDEDECDVYILTKVSDILHSLFSTYKEKILPWFEQLLPLIV

Parental  NLICPHRPWPDRQWGLCIFDDVIEHCSPASFKYAEYFLRPMLQYVCDNSPEVRQAAAYGLGVMAQYGGDN
          NLIC..RPWPDRQWGLCIFDD.IEHCSP.SFKY.EYF..PML....DN.PEVRQAAAYGLGVMAQ.GGD.
Retrocopy NLICSSRPWPDRQWGLCIFDDIIEHCSPTSFKYVEYFRWPMLLNMRDNNPEVRQAAAYGLGVMAQFGGDD

Parental  YRPFCTEALPLLVRVIQSADSKTKENVNATENCISAVGKIMKFKPDCVNVEEVLPHWLSWLPLHEDKEEA
          YR..C.EA.PLLV.VI..A.SKTK.NV.ATENCISA.GKI.KFKP.CVNV.EVLPHWLSWLPLHEDKEEA
Retrocopy YRSLCSEAVPLLVKVIKCANSKTKKNVIATENCISAIGKILKFKPNCVNVDEVLPHWLSWLPLHEDKEEA

Parental  VQTFNYLCDLIESNHPIVLGPNNTNLPKIFSIIAEGEMHEAIKHEDPCAKRLANVVRQVQTSGGLWTECI
          .QT...LCDLIESNHP.V.GPNN.NLPKI.SIIAEG...E.I..EDPCAKRLANVVRQVQTS..LW.EC.
Retrocopy IQTLSFLCDLIESNHPVVIGPNNSNLPKIISIIAEGKINETINYEDPCAKRLANVVRQVQTSEDLWLECV

Parental  AQLSPEQQAAIQELLNSA
          .QL..EQQ.A.QELLN.A
Retrocopy SQLDDEQQEALQELLNFA

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	17.48 RPM	43.85 RPM
SRP007412_cerebellum	24.56 RPM	56.00 RPM
SRP007412_heart	19.64 RPM	51.50 RPM
SRP007412_kidney	16.08 RPM	49.58 RPM
SRP007412_liver	8.45 RPM	21.64 RPM
SRP007412_testis	9.06 RPM	435.34 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_49 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_49 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_49 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_57
Gorilla gorilla	retro_ggor_47
Mus musculus	retro_mmus_251
Rattus norvegicus	retro_rnor_240

---

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,