RetrogeneDB ID: retro_dmel_1

Retrocopy location

• Organism: Fruit fly (Drosophila melanogaster)
• Coordinates: 2R:19029688..19031878(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: FBgn0034827
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Klp10A
• Ensembl ID: FBgn0030268
• Aliases: None
• Description: Klp10A [Source:FlyBase gene name;Acc:FBgn0030268]

Sequence

>retro_dmel_1
ATGGATCGCATCAAAATTGGCGAGCAGCTCCTCTTCCAGAGGAGTGACGGGCGTGTCCATCAGGTGGTCTGCACTGCCAA
GAACCTGGAACGGGATTCCATCACGGGCGAATGGACCGAGGGCACGGTGGTGAAGGGTAAGGAAGTGCCATTGAGCACGC
TGATTGGCATCAACCATCATATATTCGCGGAGAATCAACCGCCGATATCGAAGCCACCGAGCTCCTTGCTGCCGAAGCCT
CGAGGCTCGAGTCCGACCGGAGGACCTAAGACCCACACTGGAAATCCGTATGCAGAGCGCATGAGAGTACAGGACGGTCG
CAGTAAAATTGCCACCAGAAAGACGGATCCTGCAGCGGTCGGAGCGGGAAATCATGAGCTGGGTAGAGCGCACACCCCTC
GTGTGCCAGCCGGTAGGCCGGACCGGGATGCCAGCCCCACCCAAGGTCGCAAGTCACAGGGTGGCAACAATAGCAACCAA
CGCTTTTCCAGTGTAGTGAGGGAGGTGAATCGCATGAAGGAGCAGAGGGAGAAGCGAAGGGCTCGCCAGGCGGAACAGCT
CCAGGAGAAGGATGCACTGCGTCGCAATAATCCGGGGAATCCCAACTGGGAGGTGTCGGTGATGCTGCGCCAATACCGCT
CCACCTTGATCTTTTCTCCACTTCGATGCCTGGATCCCAATGGAGGCACTGTTCAGCAAATTACGGTGTGTGTGCGAAAA
CGACCCATGAGTCGCAAGGAGGAGAACTCCAAGAACCTGGACATCATCACAGTTCCCAGTGCCGACAGCCTGATCGTCCA
TGAGTTGCGCCTCAAGGTGGATCTCACCAAGTTCCTGGAGCACCACAAATTCCGTTTCGACTACACGTTCGACGAGGAGT
GCTCCAATGCGCTGGTCTACGATCACACTGCTCGTCCGTTGATCAGAACCATGTTCGAGGGCGGCAATGCCACTTGTTTC
GCTTACGGACAAACTGGCAGCGGAAAAACGCACACCATGGGCGGAGAATTCTTCGGAAAGGTTCAGGATTGCGGTACCGG
GATCTACGCCATGGCAGCTCGCGATGTCTTCGAGGAGGTATCGCGCCCGGAGTACCGGCAAATGGGTGCCAAGATTACGT
GCAGCTTCTTCGAAATCTATGGCACCAAGGTGTTCGATCTCTTGCTACCCAACAAGCCCATGCTGCGGGTCCTAGAGGAT
GCCAGGCAGCAGGTCGTGGTGGTGGGCCTAACGGAGATGCCGGTGACCAAAGTGGAGGATGTCCTGAGACTGATTGAGCA
CGGCAGCAAAGAGCGCACTTCCGGCCAAACATCGGCGAACGCCAAGTCATCGCGTTCCCACGCCGTCTTTCAAATAGCAC
TCCACTTTCCCGATTCCTGGGGCCCACACGGCAAGTGCTCCTTTGTGGACTTGGCGGGCAATGAACGCGGGGCGGATACG
CAATCCGCCGATCGTCAAACTCGCATCGAGGGAGCCGAGATCAATAAATCTCTGCTGGCCCTCAAGGAGTGCATTCGAGC
CCTCAGCCGGCAGTCGAGTCACCTTCCCTTCCGTGGCTCCAAGTTGACCCAAGTGCTGCGCGACTCCTTTGTCGGCGGCA
AGAAGAACAAGACCTGCATGATTGCCATGATATCGCCATCCATGAGCTGCGTGGAGAATACGCTCAACACTCTACGTTAC
GCAGACAGGGTTAAGGAGCTCATAGCCAAGGAAGACGAACACTTGCAGTCCGTGGAAGGGGATGGAGAGAAGTCTCCCGA
TCTCAACGAGGAATCAGAGCCAGAAATGATGGCCGACGAGGAGGGCGATGAGGAGCCGGAGGATGAGGACAATCAGCATC
TAACCATATCCTCGGAGGAGGCAAGCTCCTACAACAACATGAGTTATGACATGAGCTTTAACCACACCCTCAACATTCTG
GGTCCCTCAAGGAACGTGGATATCCAAGAGGTGGCCGAGCAGCACGCACTTTTGGTAGAGAATCTAGAGACTTACGCTCA
CAATTTCCGGCAACTGAAAACGGATAAGGAAATAGAGCAGTACACGCAAAATTCAGAAAGCGCATTGATGAAACTGCTAG
CAATGGTGAATAGAACGCGGGATGTAACGCACAATTACAACACTCAGAAATTATTGAAGGAAGAAAACCAAAATGCATAT
AAGAAGGGCGAGCTGGATGAATCCGAGTAG

Alignment

ORF - retro_dmel_1 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.1 %
• Parental protein coverage: 51.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TQGAGGASTRRSHALKEVERLKENREKRRARQAEMKEEKVALMNQDPGNPNWETAQMIREYQSTLEFVPL
          .QG......R.S....EV.R.KE.REKRRARQAE...EK.AL....PGNPNWE...M.R.Y.STL.F.PL
Retrocopy SQGGNNSNQRFSSVVREVNRMKEQREKRRARQAEQLQEKDALRRNNPGNPNWEVSVMLRQYRSTLIFSPL

Parental  --LDGQAVDDHQITVCVRKRPISRKEVNRKEIDVISVPRKDMLIVHEPRSKVDLTKFLENHKFRFDYAFN
          ..LD.......QITVCVRKRP.SRKE.N.K..D.I.VP..D.LIVHE.R.KVDLTKFLE.HKFRFDY.F.
Retrocopy RCLDPNGGTVQQITVCVRKRPMSRKEENSKNLDIITVPSADSLIVHELRLKVDLTKFLEHHKFRFDYTFD

Parental  DTCDNAMVYKYTAKPLVKTIFEGGMATCFAYGQTGSGKTHTMGGEFNGKVQDCKNGIYAMAAKDVFVTLN
          ..C.NA.VY..TA.PL..T.FEGG.ATCFAYGQTGSGKTHTMGGEF.GKVQDC..GIYAMAA.DVF....
Retrocopy EECSNALVYDHTARPLIRTMFEGGNATCFAYGQTGSGKTHTMGGEFFGKVQDCGTGIYAMAARDVFEEVS

Parental  MPRYRAMNLVVSASFFEIYSGKVFD-LLSDKQKLRVLEDGKQQVQVVGLTEKVVDGVEEVLKLIQHGNAA
          .P.YR.M......SFFEIY..KVFD.LL..K..LRVLED..QQV.VVGLTE..V..VE.VL.LI.HG...
Retrocopy RPEYRQMGAKITCSFFEIYGTKVFDLLLPNKPMLRVLEDARQQVVVVGLTEMPVTKVEDVLRLIEHGSKE

Parental  RTSGQTSANSNSSRSHAVFQIVLRPQGSTKIHGKFSFIDLAGNERGVDTSSADRQTRMEGAEINKSLLAL
          RTSGQTSAN..SSRSHAVFQI.L....S...HGK.SF.DLAGNERG.DT.SADRQTR.EGAEINKSLLAL
Retrocopy RTSGQTSANAKSSRSHAVFQIALHFPDSWGPHGKCSFVDLAGNERGADTQSADRQTRIEGAEINKSLLAL

Parental  KECIRALGKQSAHLPFRVSKLTQVLRDSFI-GEKSKTCMIAMISPGLSSCEHTLNTLRYADRVKELVVKD
          KECIRAL..QS.HLPFR.SKLTQVLRDSF..G.K.KTCMIAMISP..S..E.TLNTLRYADRVKEL..K.
Retrocopy KECIRALSRQSSHLPFRGSKLTQVLRDSFVGGKKNKTCMIAMISPSMSCVENTLNTLRYADRVKELIAKE

Legend:

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

Expression

RNA-Seq

Drosophila melanogaster was not studied using RNA-Seq expression data.

ChIP-Seq

Drosophila melanogaster was not studied using ChIP-Seq data.

EST

8 EST(s) were mapped to retro_dmel_1 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BF488127	19029675	19029908	100	233	0	233
BF491581	19030010	19030545	99.1	529	5	524
BF492043	19029567	19030245	99.5	674	4	670
BF498093	19030004	19030670	99.3	661	5	656
BF498183	19029566	19030297	99.4	724	4	717
BF502759	19029675	19030364	99.3	683	5	678
BF506692	19029853	19030532	99.3	674	5	669
BG634281	19029989	19030597	99.6	605	3	602

TSS

Drosophila melanogaster was not studied using FANTOM5 data.

Lab

retro_dmel_1 was not experimentally validated.

Homology

Retrocopy orthology:

Drosophila melanogaster 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 30 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Anas platyrhynchos	ENSAPLG00000009519	1 retrocopy	retro_apla_3,
Bos taurus	ENSBTAG00000015022	1 retrocopy	retro_btau_180,
Choloepus hoffmanni	ENSCHOG00000007888	1 retrocopy	retro_chof_1348,
Cavia porcellus	ENSCPOG00000009393	1 retrocopy	retro_cpor_72,
Dipodomys ordii	ENSDORG00000006335	1 retrocopy	retro_dord_763,
Equus caballus	ENSECAG00000019810	1 retrocopy	retro_ecab_32,
Homo sapiens	ENSG00000068796	1 retrocopy	retro_hsap_69,
Gorilla gorilla	ENSGGOG00000004774	1 retrocopy	retro_ggor_68,
Macaca mulatta	ENSMMUG00000000399	1 retrocopy	retro_mmul_145,
Monodelphis domestica	ENSMODG00000019605	1 retrocopy	retro_mdom_242,
Mus musculus	ENSMUSG00000021693	1 retrocopy	retro_mmus_68,
Mus musculus	ENSMUSG00000028678	1 retrocopy	retro_mmus_1251,
Nomascus leucogenys	ENSNLEG00000002865	1 retrocopy	retro_nleu_2329,
Oryctolagus cuniculus	ENSOCUG00000010466	1 retrocopy	retro_ocun_156,
Otolemur garnettii	ENSOGAG00000000527	5 retrocopies	retro_ogar_126, retro_ogar_3166, retro_ogar_3498, retro_ogar_3501, retro_ogar_672,
Otolemur garnettii	ENSOGAG00000006916	1 retrocopy	retro_ogar_1892,
Ochotona princeps	ENSOPRG00000011768	1 retrocopy	retro_opri_815,
Procavia capensis	ENSPCAG00000005089	1 retrocopy	retro_pcap_22,
Pongo abelii	ENSPPYG00000001427	1 retrocopy	retro_pabe_88,
Pteropus vampyrus	ENSPVAG00000009856	1 retrocopy	retro_pvam_3,
Rattus norvegicus	ENSRNOG00000014000	2 retrocopies	retro_rnor_1284, retro_rnor_47,
Sorex araneus	ENSSARG00000007768	1 retrocopy	retro_sara_457,
Sarcophilus harrisii	ENSSHAG00000001950	1 retrocopy	retro_shar_30,
Sus scrofa	ENSSSCG00000003931	1 retrocopy	retro_sscr_25,
Ictidomys tridecemlineatus	ENSSTOG00000012710	1 retrocopy	retro_itri_40,
Tupaia belangeri	ENSTBEG00000009396	1 retrocopy	retro_tbel_761,
Tarsius syrichta	ENSTSYG00000002115	1 retrocopy	retro_tsyr_1791,
Tursiops truncatus	ENSTTRG00000000748	1 retrocopy	retro_ttru_1318,
Vicugna pacos	ENSVPAG00000008864	1 retrocopy	retro_vpac_572,
Drosophila melanogaster	FBgn0030268	2 retrocopies	retro_dmel_1 , retro_dmel_2,