RetrogeneDB ID: retro_amel_3

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL194955.1:60273..63591(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSAMEG00000019264
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: IPO5
• Ensembl ID: ENSAMEG00000003784
• Aliases: None
• Description: importin 5 [Source:HGNC Symbol;Acc:6402]

Sequence

>retro_amel_3
ATGGCGGCGGCCGGGTCTGCAGGGGTACCGGCCGCCGTGTCGGGAAAGCAAGAGTTTTACCAGCTTCTGAAGAACCTGAT
CAATCCAAGCTGTATGGTGCGGAGACAGGCAGAGGAAATCTATGAAAATATCCCAGGTCTGTGTAAGACTACATTCCTCT
TAGATGCTGTCAGGAATAGAAGAGCAGGTTATGAGGTGAGACAAATGGCTGCCGCACTGCTACGACGGCTTTTGTCCTCT
GGGTTTGAGGAAGTCTATCCAAATCTGCCTTCTGATGTTCAGAGGGACGTCAAGATTGAACTGATACTGGCTGTTAAGTT
AGAAACACATGCTAGCATGAGGAAAAAACTTTGTGATATTTTTGCAGTGCTGGCCAGGAATCTGATAGATGAGGATGGCA
CTAACCACTGGCCCGAAGGTTTGAAGTTCCTTATTGATTCAATCTACTCTAAAAATGTAGTTTTATGGGAAGTCGCACTT
CATGTTTTCTGGCACTTTCCTGGGATTTTTGGGAACCAAGAGCGGCATGATTTGGATATCATCAAACGGTTGTTGGACCA
GTGCATTCAAGATCAAGAGCATCCAGCAATCAGGACATTGTCTGCTAGAGCTGCAGCTGCATTTGTACTTGCTAATGAGA
ATAATATTGCTCTTTTCAAAGACTTTGCAGACTTGCTTCCTGGAATCTTACAGGCTGTGAATGACTCATGTTACCAGGAT
GATGATTCAGTGCTAGAATCCCTTGTTGAGATTGCAGATACTGTACCTAAATACCTGGGTCCTTATTTAGAAGATACTCT
GCAGTTGAGTCTGAAGTTATGTGGAGACTCTAGACTTAGTAATCTGCAGCGCCAGCTGGCCCTTGAAATAATAGTGACCT
TGTCTGAAACTGCAACCCCAATGTTGAAAAAACATACAAATATAATTGCACAGGCAGTTCCTCATATATTAGCAATGATG
GTTGATCTACAAGATGATGAGGACTGGGTAAATGCTGATGAAATGGAAGAAGATGATTTTGACAGCAATGCAGTTGCTGC
TGAGAGTGCACTAGACAGGCTGGCTTGTGGGCTCGGTGGAAAACTTGTTTTACCAATGACTAAGGAGCACATCATGCAGA
TGCTTCAGAGCCCTGACTGGAAATATCGACATGCTGGATTAATGGCCTTATCTGCCATTGGAGAAGGATGCCATCAGCAA
ATGGAATCAATTCTAGATGAAACAGTTAACTCTGTTTTGCTTTTTCTTCAGGATCCTCACCCAAGAGTGAGGGCTGCAGC
CTGTACTACACTTGGACAGATGGCTACAGATTTTGCACCTAACTTCCAAAAGAAATTCCATGAAACAGTGATTGCAGCTC
TGTTGCGTACCATGGAAAATCAAGGTAATCAGCGTGTGCAATCACATGCAGCTTCAGCACTTATTATTTTTATTGAAGAC
TGCCCCAAAGCATTGCTAGTTCTATATTTGGATAGTATGGTGAGAAATCTACATTCCATCTTGGTGATTAAACTTCAAGA
GTTGATTCGAAATGGAACTAAATTGGCCTTGGAACAGCTTGTGACAACCATTGCCTCAGTTGCAGATACAATAGAAGAAA
AATTTCTTCCATATTATGATATATTTATGCCATCACTAAAGCACATTGTTGAACTTGCTGTTCAAAAGGAGCTCAAGCTT
CTGAAAGGAAAAACTATTGAATGCATTAGCCATGTCGGTCTTGCTGTTGGGAAGGAAAAATTTATGCAAGATTCATCAAA
TGTTATGCAGCTGTTGTTGAAGACACAATCAGACTTAAGTAATATGGAAGATGATGACCCTCAGACATCTTACATGGTTT
CAGCATGGGCTAGAATGTGTAAAATTCTTGGAAATGATTTTCAACAATACCTTCCACTAGTTATTGAGCCTCTTATTAAG
ACTGCTTCAGCTAAACCTGATGTTGCGCTCTTAGACACACAAGATGTGGAAAATATGAGTGATGATGATGGATGGCAATT
TGTAAATCTTGGAGACCAGCAAAGTTTTGGAATTAAAACTTCAGGACTTGAAGCAAAAGCAACTGCTTGCCAGATGTTGG
TTTACTATGCTAAGGAGTTAAGGGAAGGATTTGTGGAATATACAGAACAAGTTGTAAAGCTTATGGTTCCTTTATTGAAA
TTTTATTTCCATGACAATGTTCGAGTGGCAGCAGCAGAGTCAATGCCTTTTCTCCTGGAATGTGCAAGAATTCATGGCCC
AGAGTATCTTGCACAGATGTGGCAATTCATATGTGATCCCTTAATCAAGGCTATTGGGACTGAACCTGATACAGATGTAC
TCTCAGAAATAATGAATTCTTTTGCAAAGTCCATTGAAGTAATGGGAGATGGGTGCCTTAATGATGAACACTTGGAAGAA
CTAGGAGAAATATTGAAAGCAAAACTTGAGGGGCACTTTAAAAACCAAGAATTGAGACAGGTTAAAAGACAGGAAGAAAA
CTATGACCAACAGGTTGAAATGTCTCTCCAAGATGAGGATGAATGTGATGTTTATATTCTGACCAAAGTATCAGATATTT
TGCACTCATTATTTAGTACTTATAAGGAAAAGATTTTACCGTGGTTTGAACAGCTGCTTCCATTAATTGTAAATCTGATT
TGTTCAAGTAGGCCATGGCCAGACAGGCAGTGGGGATTGTGCATTTTTGATGATATTATAGAGCACTGCAGTCCAACCTC
CTTTAAATACGTAGAATATTTTCGGTGGCCAATGCTACTAAATATGCGAGACAATAACCCTGAAGTCAGGCAAGCTGCCG
CTTATGGCCTGGGTGTTATGGCACAGTTTGGTGGAGATGATTATCGTTCTTTATGTTCAGAAGCTGTTCCACTGCTGGTA
AAAGTTATTAAGTGTGCAAATTCCAAAACAAAAAAAAATGTCATTGCTACAGAGAACTGTATCTCAGCAGTTGGGAAGAT
TTTGAGGTTTAAGCCTAACTGTGTAAATGTAGATGAAGTTCTTCCACACTGGTTATCATGGCTTCCACTGCATGAGGATA
AAGAGGAAGCTATTCAGACTTTGAGTTTTCTCTGTGACTTAATCGAAAGTAACCATCCAGTTGTACTTGGTCCAAATAAT
TCCAATCTTCCCCAAATAATCAGTATAATTGCAGAAGGAAAAATTAATGAGACTGTTAACTATGGAGATCCTTGTGCCAA
ACGCCTAGCTAATGTTGTGCGTCAGGTACAGACTTCTGAAGAATTATGGTTGGAATGCATATCCCAACTTGATGATGTGC
AGCAGGAAGCTTTACAGGGGTTGCTAAATTTTGCTTGA

Alignment

ORF - retro_amel_3 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.55 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VIGVVALRRQDFLLLTNLLS-FYIIHGEAEETYENIPGQSKITFLLQAIRNTTAAEEARQMAAVLLRRLL
          V...V........LL.NL..........AEE.YENIPG..K.TFLL.A.RN..A..E.RQMAA.LLRRLL
Retrocopy VPAAVSGKQEFYQLLKNLINPSCMVRRQAEEIYENIPGLCKTTFLLDAVRNRRAGYEVRQMAAALLRRLL

Parental  SSAFDEVYPTLPSDVQTAIKSELLMIIQMETQSSMRKKICDIAAELARNLIDEDGNNQWPEGLKFLFDSV
          SS.F.EVYP.LPSDVQ...K.EL......ET..SMRKK.CDI.A.LARNLIDEDG.N.WPEGLKFL.DS.
Retrocopy SSGFEEVYPNLPSDVQRDVKIELILAVKLETHASMRKKLCDIFAVLARNLIDEDGTNHWPEGLKFLIDSI

Parental  SSQNMGLREAALHIFWNFPGIFGNQQQHYLDVIKRMLVQCMQDQEHPSIRTLSARATAAFILANEHNVAL
          .S.N..L.E.ALH.FW.FPGIFGNQ..H.LD.IKR.L.QC.QDQEHP.IRTLSARA.AAF.LANE.N.AL
Retrocopy YSKNVVLWEVALHVFWHFPGIFGNQERHDLDIIKRLLDQCIQDQEHPAIRTLSARAAAAFVLANENNIAL

Parental  FKHFADLLPGFLQAVNDSCYQNDDSVLKSLVEIADTVPKYLRPHLEATLQLSLKLCGDTSLNNMQRQLAL
          FK.FADLLPG.LQAVNDSCYQ.DDSVL.SLVEIADTVPKYL.P.LE.TLQLSLKLCGD..L.N.QRQLAL
Retrocopy FKDFADLLPGILQAVNDSCYQDDDSVLESLVEIADTVPKYLGPYLEDTLQLSLKLCGDSRLSNLQRQLAL

Parental  EVIVTLSETAAAMLRKHTNIVAQTIPQMLAMMVDLEEDEDWANADELEDDDFDSNAVAGESALDRMACGL
          E.IVTLSETA..ML.KHTNI.AQ..P..LAMMVDL..DEDW.NADE.E.DDFDSNAVA.ESALDR.ACGL
Retrocopy EIIVTLSETATPMLKKHTNIIAQAVPHILAMMVDLQDDEDWVNADEMEEDDFDSNAVAAESALDRLACGL

Parental  GGKLVLPMIKEHIMQMLQNPDWKYRHAGLMALSAIGEGCHQQMEGILNEIVNFVLLFLQDPHPRVRYAAC
          GGKLVLPM.KEHIMQMLQ.PDWKYRHAGLMALSAIGEGCHQQME.IL.E.VN.VLLFLQDPHPRVR.AAC
Retrocopy GGKLVLPMTKEHIMQMLQSPDWKYRHAGLMALSAIGEGCHQQMESILDETVNSVLLFLQDPHPRVRAAAC

Parental  NAVGQMATDFAPGFQKKFHEKVIAALLQTMEDQGNQRVQAHAAAALINFTEDCPKSLLIPYLDNLVKHLH
          ...GQMATDFAP.FQKKFHE.VIAALL.TME.QGNQRVQ.HAA.ALI.F.EDCPK.LL..YLD..V..LH
Retrocopy TTLGQMATDFAPNFQKKFHETVIAALLRTMENQGNQRVQSHAASALIIFIEDCPKALLVLYLDSMVRNLH

Parental  SIMVLKLQELIQKGTKLVLEQVVTSIASVADTAEEKFVPYYDLFMPSLKHIVENAVQKELRLLRGKTIEC
          SI.V.KLQELI..GTKL.LEQ.VT.IASVADT.EEKF.PYYD.FMPSLKHIVE.AVQKEL.LL.GKTIEC
Retrocopy SILVIKLQELIRNGTKLALEQLVTTIASVADTIEEKFLPYYDIFMPSLKHIVELAVQKELKLLKGKTIEC

Parental  ISLIGLAVGKEKFMQDASDVMQLLLKTQTDFSDMEDDDPQISYMISAWARMCKILGKEFQQYLPVVMGPL
          IS..GLAVGKEKFMQD.S.VMQLLLKTQ.D.S.MEDDDPQ.SYM.SAWARMCKILG..FQQYLP.V..PL
Retrocopy ISHVGLAVGKEKFMQDSSNVMQLLLKTQSDLSNMEDDDPQTSYMVSAWARMCKILGNDFQQYLPLVIEPL

Parental  MKTASIKPEVALLDTQDMENMSDDDGWEFVNLGDQQSFGIKTAGLEEKSTACQMLVCYAKELKEGFVEYT
          .KTAS.KP.VALLDTQD.ENMSDDDGW.FVNLGDQQSFGIKT.GLE.K.TACQMLV.YAKEL.EGFVEYT
Retrocopy IKTASAKPDVALLDTQDVENMSDDDGWQFVNLGDQQSFGIKTSGLEAKATACQMLVYYAKELREGFVEYT

Parental  EQVVKLMVPLLKFYFHDEIKRVRVAAAESMPLLLECARVRGPEYLTQMWHFMCDALIKAIGTEPDSDVLS
          EQVVKLMVPLLKFYFHD....VRVAAAESMP.LLECAR..GPEYL.QMW.F.CD.LIKAIGTEPD.DVLS
Retrocopy EQVVKLMVPLLKFYFHD---NVRVAAAESMPFLLECARIHGPEYLAQMWQFICDPLIKAIGTEPDTDVLS

Parental  EIMHSFAKCIEVMGDGCLNNEHFEELGGILKAKLEEHFKNQELRQVKRQDEDYDEQVEESLQDEDDNDVY
          EIM.SFAK.IEVMGDGCLN.EH.EELG.ILKAKLE.HFKNQELRQVKRQ.E.YD.QVE.SLQDED..DVY
Retrocopy EIMNSFAKSIEVMGDGCLNDEHLEELGEILKAKLEGHFKNQELRQVKRQEENYDQQVEMSLQDEDECDVY

Parental  ILTKVSDILHSIFSSYKEKVLPWFEQLLPLIVNLICPHRPWPDRQWGLCIFDDVIEHCSPASFKYAEYFL
          ILTKVSDILHS.FS.YKEK.LPWFEQLLPLIVNLIC..RPWPDRQWGLCIFDD.IEHCSP.SFKY.EYF.
Retrocopy ILTKVSDILHSLFSTYKEKILPWFEQLLPLIVNLICSSRPWPDRQWGLCIFDDIIEHCSPTSFKYVEYFR

Parental  RPMLQYVCDNSPEVRQAAAYGLGVMAQYGGDNYRPFCTEALPLLVRVIQSADSKTKENVNATENCISAVG
          .PML....DN.PEVRQAAAYGLGVMAQ.GGD.YR..C.EA.PLLV.VI..A.SKTK.NV.ATENCISAVG
Retrocopy WPMLLNMRDNNPEVRQAAAYGLGVMAQFGGDDYRSLCSEAVPLLVKVIKCANSKTKKNVIATENCISAVG

Parental  KIMKFKPDCVNVEEVLPHWLSWLPLHEDKEEAVQTFNYLCDLIESNHPIVLGPNNTNLPKIFSIIAEGEM
          KI..FKP.CVNV.EVLPHWLSWLPLHEDKEEA.QT...LCDLIESNHP.VLGPNN.NLP.I.SIIAEG..
Retrocopy KILRFKPNCVNVDEVLPHWLSWLPLHEDKEEAIQTLSFLCDLIESNHPVVLGPNNSNLPQIISIIAEGKI

Parental  HEAIKHEDPCAKRLANVVRQVQTSGGLWTECIAQLSPEQQAAIQELLNSA
          .E.....DPCAKRLANVVRQVQTS..LW.ECI.QL...QQ.A.Q.LLN.A
Retrocopy NETVNYGDPCAKRLANVVRQVQTSEELWLECISQLDDVQQEALQGLLNFA

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ailuropoda melanoleuca was not studied using RNA-Seq expression data.

ChIP-Seq

Ailuropoda melanoleuca was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_amel_3 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_3 was not experimentally validated.

Homology

Retrocopy orthology:

Ailuropoda melanoleuca does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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,