RetrogeneDB ID: retro_ogar_1827

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873568.1:13169331..13170541(+)
• Located in intron of: ENSOGAG00000001670

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: MAPK6
• Ensembl ID: ENSOGAG00000030786
• Aliases: None
• Description: mitogen-activated protein kinase 6 [Source:HGNC Symbol;Acc:6879]

Sequence

>retro_ogar_1827
ATAACAGAGAAATTTGAAAGTCTCATGAACATTCATGGTTTTGATCTGGGCTCCAGGTATCTGGACTTAAAATGATTGGG
TTATGGAGGCAATGGCTTGGTTTTTTTCTGTCGTAGACAATGACTGTGACAAAAGAATAGCCATCAAGATAATTTTCCTA
ACTGATCTCCAGAGTGTCAAAGATGCTCTACGTGAAATCAAAATTATTAGAAGACTTGACCATGACAATATTGTGAAAAT
GTTTGAAATTTCTTGGTGTCAGTAGAAACCAATTAACAGATTTAACAGATGATGTGGTCTCTCTTACTGAACTTAACAGT
GTTTACATTGTTCAGGAGTACATGGAGACAGGCTTGGTTAATGTGCTGGAGCAGGGCCTTTTACTGCATGCCAAGCTATT
CATGTATCAGCTGCTATAGGGGCTCGAGTATATCACACTGCAAACATACTGCATAGAGATCTCAAACCAGCTAATCTAAT
CTTTTCGTTAACGCTGAAGGTAGGTGAACTCGGTTTTGCATGGATTATAGATCCTCATTATTCCTAAAAGAGTCGTCTTT
CTGAAGGATTGGTTACTAAATACTACAGATCTCCACATCTTTTGCTTTCTCCTAATAATTATACTAAAGCCATTGACATG
TAGGTTGCAGACTGCATCTTGGCTGAAATTTGACTTGTGAAACCCTTGTTGTGGGAGCACATGAAGAGATTCCGCTGATT
TTAGAATCTATACCTGTTGTACATGAGGAAGATTGTGAGGAGCTTCTTAGTGTAATTCCAGTTTACATTATAAATGACAT
GACTGAGCCACACAAACTTTTAACTCAGCTGCTTCTGGGGATTAGTGCAGAAGCACTGGATTTCCTGGAACCAATTTTGA
CATTTAGCCCCATGGATCCCTTGACAGTAGAAGAAGCGGTCTCCATGGTTCCATGAGCGTATTTTCTTTTCCAATGGATG
AACTAATTCAAGTCATCCTTTCCATATTGAAGATGAAGTTAATATTTTGCATATGGAAGAAAGTCACAGTCACATTTACA
ACCAGGAGATGTACAATGATTTTCAAATTTTAGAGAATGATAGGCCCATTCATAACAACTTTGACTCTGATGAATATCAA
CTTGACCCAAGAGGTCTGTCCAGTGTCTCTGATGAAGAGGAAGTATAAGTTGATCCTCAAAAATATTTGGATGGAGATCA
GGAAAAGTAT

Alignment

ORF - retro_ogar_1827 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.36 %
• Parental protein coverage: 56.65 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MAEKFESLMNIHGFDLGSRYMDLKPLGCGGNGLVF-SAVDNDCDKRVAIKKIVLTDPQSVKHALREIKII
          ..EKFESLMNIHGFDLGSRY.DLK.LG.GGNGLVF.S.VDNDCDKR.AIK.I.LTD.QSVK.ALREIKII
Retrocopy ITEKFESLMNIHGFDLGSRYLDLK*LGYGGNGLVF>SVVDNDCDKRIAIKIIFLTDLQSVKDALREIKII

Parental  RRLDHDNIVKVFEI-LGPSGSQ---LTDDVGSLTELNSVYIVQEYMETDLANVLEQGPLLEEHARLFMYQ
          RRLDHDNIVK.FEI.LG.S..Q...LTDDV.SLTELNSVYIVQEYMET.L.NVLEQG.LL..HA.LFMYQ
Retrocopy RRLDHDNIVKMFEI>LGVSRNQLTDLTDDVVSLTELNSVYIVQEYMETGLVNVLEQGLLL--HAKLFMYQ

Parental  LLRGLKYI-HSANVLHRDLKPANLFINTEDLVLKIGDFGLARIMDPHYSHKGHLSEGLVTKWYRSPRLLL
          LL.GL.YI.H.AN.LHRDLKPANL......L.LK.G..G.A.I.DPHYS.K..LSEGLVTK.YRSP.LLL
Retrocopy LL*GLEYI<HTANILHRDLKPANLIFS---LTLKVGELGFAWIIDPHYS*KSRLSEGLVTKYYRSPHLLL

Parental  SPNNYTKAIDMWAAGCIFAEM-LTGKTLFAGAHELEQMQLILESIPVVHEEDRQELLSVIPVYIRNDMTE
          SPNNYTKAIDM..A.CI.AE..LT..TL..GAHE.....LILESIPVVHEED..ELLSVIPVYI.NDMTE
Retrocopy SPNNYTKAIDM*VADCILAEI<LTCETLVVGAHE--EIPLILESIPVVHEEDCEELLSVIPVYIINDMTE

Parental  PHKPLTQLLPGISREALDFLEQILTFSPMDRLTAEEALS-HPYMSIYSFPMDEPI-SSHPFHIEDEVDDI
          PHK.LTQLL.GIS.EALDFLE.ILTFSPMD.LT.EEA.S.H..MS..SFPMDE.I.SSHPFHIEDEV..I
Retrocopy PHKLLTQLLLGISAEALDFLEPILTFSPMDPLTVEEAVS<HGSMSVFSFPMDELI<SSHPFHIEDEV-NI

Parental  LLMDETHSHIYNWERYHDCQFSEHDWPIHNNFDIDEVQLDPRALSDVTDEEEVQVDPRKYLDGDREKY
          L.M.E.HSHIYN.E.Y.D.Q..E.D.PIHNNFD.DE.QLDPR.LS.V.DEEEV.VDP.KYLDGD.EKY
Retrocopy LHMEESHSHIYNQEMYNDFQILENDRPIHNNFDSDEYQLDPRGLSSVSDEEEV*VDPQKYLDGDQEKY

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_1827 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 12 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000962	1 retrocopy	retro_cjac_2633,
Homo sapiens	ENSG00000069956	2 retrocopies	retro_hsap_1257, retro_hsap_2519,
Gorilla gorilla	ENSGGOG00000004003	1 retrocopy	retro_ggor_1571,
Monodelphis domestica	ENSMODG00000001962	2 retrocopies	retro_mdom_138, retro_mdom_63,
Nomascus leucogenys	ENSNLEG00000006476	2 retrocopies	retro_nleu_1441, retro_nleu_2095,
Otolemur garnettii	ENSOGAG00000030786	1 retrocopy	retro_ogar_1827 ,
Pongo abelii	ENSPPYG00000006482	2 retrocopies	retro_pabe_1853, retro_pabe_3322,
Pan troglodytes	ENSPTRG00000020224	3 retrocopies	retro_ptro_1464, retro_ptro_2743, retro_ptro_3045,
Sarcophilus harrisii	ENSSHAG00000017091	1 retrocopy	retro_shar_445,
Sus scrofa	ENSSSCG00000004624	1 retrocopy	retro_sscr_162,
Tupaia belangeri	ENSTBEG00000007876	2 retrocopies	retro_tbel_1879, retro_tbel_2946,
Tursiops truncatus	ENSTTRG00000016253	2 retrocopies	retro_ttru_322, retro_ttru_75,