RetrogeneDB ID: retro_ogar_227

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873570.1:8403487..8405380(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000026282
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: DDX43
• Ensembl ID: ENSOGAG00000013660
• Aliases: None
• Description: DEAD (Asp-Glu-Ala-Asp) box polypeptide 43 [Source:HGNC Symbol;Acc:18677]

Sequence

>retro_ogar_227
ACAGAGTGGAAGATGGGGGACTCTAAACCAAGAAATTTTAGGACCAGCTGGGATGACGGAGGTGGCGGAGGTGGCAGAGG
TGGCAGAGGCGGCAGAGGCAGCGGCAGGAGTGGCCCCTCTGACCAAATGGGGCCTAGGGCCCCAGGCTCACGTGAACCAC
CACTCTGCTTTAGATTGAGTAACAGCATGATTGGTGCGGTAATTGGTCGTAGTGGATCAAGAATAAATAATGTGCAACGT
TCGACAAACACTAAAATACAAATTATAGAGGGAGATTCCGAAGCAGAGGTAAAAATTTATGGCAGCAAGGACATGAAAGA
AAAGGCAAAAGCAGCTATAGAAACTTTGATTAAAAAACAAGAAAGCTATCAGTCAAAATATGATGTTGATAATGTAGCAT
CCCAACCCCCTGTTGGAAGAGACTTAACCAGAAATGAGAATGTTAGAGTACAGAAGCCAATGATAGATTGGGATCGAGTC
AAGGCGAAAGTTGCAGAATGGGAAAAAGCAAAATGGGCAGATTTACCACCAATTAAGAAAAACTTTTATATAGAATCGAA
AGCAACAACATCTATGTCGGAAATGCAGGTAGATAATTGGAGAAAGGAACATTTTAACATCACGTGTCAGGACTTGAAAG
ATGGTGAAAAGCGTCGCATCCCGAATCCTACGTGTAGATTCGAAGATGCTTTCCGACACTACTCTGGGCTCCTGGAAAGC
ATAACATCTTCAGGTTTCCAGAGCCCAACCCCAATTCAGTGTCAGGCGTGGCCCATTATTCTACAAGGATTAGATCTTAT
AGGAATCGCTCAAACGGGAACAGGCAAAACATTAGCCTATTTAATGCCTGGGTTTATACATCTTGACTCTCAACCAATAG
CAAGAGAACAAAGGAATGGACCTGGGATGCTGGTTCTTACACCAACTAGAGAATTAGCTCTTCAGGTGGAAGCTGAATGT
TCTAAGTATTTGTACAAAGATCTGAAAAGTGTTTGCATATATGGTGGTAAAGACAGAGACAAACAAATACAAGATGTTAA
GAAAGGTGTAGATATCATTATTGCAACTCCTGGTAGACTACACGATCTACAAATGAACAAGATGATCAACCTAAGAAGCA
TAACCTACTTAGTGTTGGATGAAGCAGATAAAATGCTGGATCTGGGATTTGAACCCCAGATAATGAAGATTTTATTAGAT
GTGCGCCCAGACCGGCAAACTGTAATGTTAAGTGCAACTTGGCCAGATACCATTCGTCGCCTTGCAAAGTCTTATTTGAA
AGATCCCATGATGGTTTATGTTGGTACTCTTGATCTGGTTGCTGTACATACAGTGACGCAAAATATAATTATTACCACTG
AAAGAAAAAAACGAGCACTTATCCAAGAATTCCTAGACAATATGTCACCCAACGACAAAGTCCTTGTGTTTGTCAACCGA
AAACTTGTTGCTGATGATTTATCAAGTGACTTTGGTATCCTAGGTATTCCTGTGCAGTCACTGCATGGTGACAGAGAACA
ATGTGATAGAGAACAAGCATTAGAAGACTTTAAAAGTGGAAGAGTGAAGATATTGATAGCAACTGATTTAGCATCTCGAG
GTCTCGACGTTAATGATATCACACACATATACAATTATGATTTTCCACGAAATGTTGAAGAATATGTACACAGAGTAGGA
CGTACTGGAAGAGCAGGAAAGACTGGCATATCAATTACCCTTATCACTCCAGAAAATTCGAAGATTGCCAGTGAATTGAT
TGAAATTCTGAAAAAAACAAATCAGAGCATCCCAGAAGATCTTGTAAAAATGGCTGAACAATACAAGTCACATCAACAAA
AAACGGAGGCAGAAAGACCAAGAAAATGTGGAAGAAAATCCAAGAAGTTTTAA

Alignment

ORF - retro_ogar_227 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.12 %
• Parental protein coverage: 93.22 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RGGRGGDETDYSDFLGSRAAGL-EPPICFELKNHFVGVVIETGPGGSTIKDIQSTTSTKIQIIKGPQESL
          RGGRG......SD..G.RA.G..EPP.CF.L.N...G.VI..G..GS.I...Q..T.TKIQII.G..E..
Retrocopy RGGRGSGRSGPSDQMGPRAPGSREPPLCFRLSNSMIGAVI--GRSGSRINNVQRSTNTKIQIIEGDSEAE

Parental  VKIFGNKAMQTKAKAVIDNFVKKQEEKYYSHRVDIVAFQPSVGRGRGTDNNVAAEDRPLIDWDQIREEGL
          VKI.G.K.M..KAKA.I....KKQE.......VD.VA.QP.VGR......NV.....P.IDWD.......
Retrocopy VKIYGSKDMKEKAKAAIETLIKKQESYQSKYDVDNVASQPPVGRDLTRNENVRVQ-KPMIDWDRVKAKVA

Parental  KWEKKKWADLPPIEKNFYKESTTTSSMTQVEVDSWRKENFNIVCDDLKEGEKRPIPNPTCAFADAFQCYP
          .WEK.KWADLPPI.KNFY.ES..T.SM....VD.WRKE.FNI.C.DLK.GEKR.IPNPTC.F.DAF..Y.
Retrocopy EWEKAKWADLPPIKKNFYIESKATTSMSEMQVDNWRKEHFNITCQDLKDGEKRRIPNPTCRFEDAFRHYS

Parental  EIMENIKKAGFQMPTPIQSQSWPIVLQGIDLIGVAQTGTGKTLSYLMPGFIHLDGQPKVGGKRNRPGMLV
          ...E.I...GFQ.PTPIQ.Q.WPI.LQG.DLIG.AQTGTGKTL.YLMPGFIHLD.QP.....RN.PGMLV
Retrocopy GLLESITSSGFQSPTPIQCQAWPIILQGLDLIGIAQTGTGKTLAYLMPGFIHLDSQPIAREQRNGPGMLV

Parental  LTPTRELAIQVEAECSKYSYKGLRSVCVYGGGDRDRQIEDLRKGVDVIIATPGRLNDLQMNNFVNLKSVT
          LTPTRELA.QVEAECSKY.YK.L.SVC.YGG.DRD.QI.D..KGVD.IIATPGRL.DLQMN...NL.S.T
Retrocopy LTPTRELALQVEAECSKYLYKDLKSVCIYGGKDRDKQIQDVKKGVDIIIATPGRLHDLQMNKMINLRSIT

Parental  YLVLDEADKMLDMGFEPQIMKILLDVRPDRQTIMTSATWPYAVRRLAQSYLKEPMIVYVGTLDLVAVSTV
          YLVLDEADKMLD.GFEPQIMKILLDVRPDRQT.M.SATWP...RRLA.SYLK.PM.VYVGTLDLVAV.TV
Retrocopy YLVLDEADKMLDLGFEPQIMKILLDVRPDRQTVMLSATWPDTIRRLAKSYLKDPMMVYVGTLDLVAVHTV

Parental  TQNVIVTTEEEKRAHIQTFLEHLSPNDKVIVFVCRKAVADHLSSDLILRHISVESLHGNREQRDREKALE
          TQN.I.TTE..KRA.IQ.FL...SPNDKV.VFV.RK.VAD.LSSD.....I.V.SLHG.REQ.DRE.ALE
Retrocopy TQNIIITTERKKRALIQEFLDNMSPNDKVLVFVNRKLVADDLSSDFGILGIPVQSLHGDREQCDREQALE

Parental  DFKTGKVRILIATDLASRGLDVHDITHVYNYDFPRNIEEYVHRIGRTGRAGRTGVAITLVTRNDWRVATE
          DFK.G.V.ILIATDLASRGLDV.DITH.YNYDFPRN.EEYVHR.GRTGRAG.TG..ITL.T......A.E
Retrocopy DFKSGRVKILIATDLASRGLDVNDITHIYNYDFPRNVEEYVHRVGRTGRAGKTGISITLITPENSKIASE

Parental  LIDILERANQSIPEELKAMSERYKAHQLKKQTE--RKMGRPQGKPKKF
          LI.IL...NQSIPE.L..M.E.YK.HQ.K...E..RK.GR...K.KKF
Retrocopy LIEILKKTNQSIPEDLVKMAEQYKSHQQKTEAERPRKCGR---KSKKF

Legend:

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

Expression

RNA-Seq

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq

Otolemur garnettii was not studied using ChIP-Seq data.

EST

Otolemur garnettii was not studied using EST data.

TSS

Otolemur garnettii was not studied using FANTOM5 data.

Lab

retro_ogar_227 was not experimentally validated.

Homology

Retrocopy orthology:

Otolemur garnettii 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 17 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007851	1 retrocopy	retro_amel_31,
Callithrix jacchus	ENSCJAG00000009966	2 retrocopies	retro_cjac_3639, retro_cjac_3640,
Equus caballus	ENSECAG00000017971	1 retrocopy	retro_ecab_7,
Felis catus	ENSFCAG00000031631	1 retrocopy	retro_fcat_583,
Homo sapiens	ENSG00000080007	1 retrocopy	retro_hsap_76,
Gorilla gorilla	ENSGGOG00000016092	1 retrocopy	retro_ggor_2889,
Microcebus murinus	ENSMICG00000017145	1 retrocopy	retro_mmur_1603,
Monodelphis domestica	ENSMODG00000018546	1 retrocopy	retro_mdom_14,
Mustela putorius furo	ENSMPUG00000004342	1 retrocopy	retro_mputfur_47,
Nomascus leucogenys	ENSNLEG00000001209	1 retrocopy	retro_nleu_1094,
Oryctolagus cuniculus	ENSOCUG00000006338	2 retrocopies	retro_ocun_1061, retro_ocun_227,
Otolemur garnettii	ENSOGAG00000001539	1 retrocopy	retro_ogar_3395,
Otolemur garnettii	ENSOGAG00000001844	2 retrocopies	retro_ogar_1492, retro_ogar_555,
Otolemur garnettii	ENSOGAG00000013660	1 retrocopy	retro_ogar_227 ,
Procavia capensis	ENSPCAG00000005962	1 retrocopy	retro_pcap_151,
Pongo abelii	ENSPPYG00000016774	1 retrocopy	retro_pabe_39,
Pan troglodytes	ENSPTRG00000018344	1 retrocopy	retro_ptro_35,