RetrogeneDB ID: retro_ogar_2637

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873642.1:6169663..6170422(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000027486
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOGAG00000008348
• Aliases: None
• Description: None

Sequence

>retro_ogar_2637
GTGGATGACAATATTGCTGCGCTCATGCTTGACAACAGCTCCAGCATGTGCAAGGCCAGTTTCATGGGTGACGATGCCCC
CCCAGGCTGTCTTCCCTTCCCTCATCAGGCTCCCGCAGCACCAGAGCATGATCGTAGGCTTGGGCCAGGACTCGTATGTG
GGCAATGAGGTCCAGAGCAAGAGAGGCACGCTGACCCTGAGGTACCTCATTGAGCACAGCATTGTCACCAACTGGGATGA
GATGGAGCAAATACGGCACCACACTTTCTACAACGAGTTCTGTCTGACCACAGAGAAGCACACTGTGCTGCTGACTGAAG
CCCCCCTGAACCCCAAGGCCAACCATGAGAAGATGATGCAGATTATGTTGGAGACCTTCAACACTCCAGCAGTGTGTATG
GCCGTCCAGGTTATGCTGTCCCTGTATGCCTCTGGCCACACCACTGGCATCGTGATGGACTCGGGTGATGGGTCACCCAC
ATTGTGCCCATCTATAGGGGTATACCCTCCCCCAGGCCCTCTTATGTCTGGACCTGGTTGGCTGGGACCTTAAAGACTAC
CTCATGAAGACCCTCACAGAGTGTGGCTACAGCTTCACCACCATGGCCAGTGGGAAATTGTGCCTGACATCAAGGAGAAG
CTGTGTTATATCACCCTGAACTTCAAGCAAGAGATGGCCACAGCAGCCTCCAGCTCCTCCCTGGAGAAGAGCTATGAGCT
CCCGATGGCCAGGTGATCACCATCAGAAATGAGCAGTTC

Alignment

ORF - retro_ogar_2637 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.31 %
• Parental protein coverage: 68. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MDDDIAALVVDNGSGMCKAGFAGDDAP-RAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKY
          .DD.IAAL..DN.S.MCKA.F.GDDAP..AVFPS....P.HQ...VG.GQ.DSYVG.E.QSKRG.LTL.Y
Retrocopy VDDNIAALMLDNSSSMCKASFMGDDAP>QAVFPSLIRLPQHQSMIVGLGQ-DSYVGNEVQSKRGTLTLRY

Parental  PIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAV
          .IEH.IVTNWD.ME.I.HHTFYNE.....E.H.VLLTEAPLNPKAN.EKM.QIM.ETFNTPA...A.Q..
Retrocopy LIEHSIVTNWDEMEQIRHHTFYNEFCLTTEKHTVLLTEAPLNPKANHEKMMQIMLETFNTPAVCMAVQVM

Parental  LSLYASGRTTGIVMDSGDG-VTHTVPIYE-GYALPHAILRLDLAGRDLTDYLMKILTQRGYSFTTTA-ER
          LSLYASG.TTGIVMDSGDG.VTH.VPIY..GY.LP.A.L.LDL.G.DL.DYLMK.LT..GYSFTT.A...
Retrocopy LSLYASGHTTGIVMDSGDG<VTHIVPIYR<GYTLPQALLCLDLVGWDLKDYLMKTLTECGYSFTTMA<QW

Parental  EIVRDIKEKLCYVALDFEQEMATAASSSSLEKSYEL-PDGQVITIGNERF
          EIV.DIKEKLCY..L.F.QEMATAASSSSLEKSYEL.PDGQVITI.NE.F
Retrocopy EIVPDIKEKLCYITLNFKQEMATAASSSSLEKSYEL<PDGQVITIRNEQF

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_2637 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 28 parental genes, and 128 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006601	1 retrocopy	retro_amel_11,
Anas platyrhynchos	ENSAPLG00000010147	1 retrocopy	retro_apla_2,
Canis familiaris	ENSCAFG00000016020	3 retrocopies	retro_cfam_120, retro_cfam_260, retro_cfam_934,
Callithrix jacchus	ENSCJAG00000000008	2 retrocopies	retro_cjac_243, retro_cjac_56,
Cavia porcellus	ENSCPOG00000013467	1 retrocopy	retro_cpor_60,
Dipodomys ordii	ENSDORG00000010079	1 retrocopy	retro_dord_11,
Equus caballus	ENSECAG00000015935	2 retrocopies	retro_ecab_271, retro_ecab_994,
Felis catus	ENSFCAG00000006788	1 retrocopy	retro_fcat_1613,
Homo sapiens	ENSG00000075624	6 retrocopies	retro_hsap_1563, retro_hsap_1894, retro_hsap_3386, retro_hsap_38, retro_hsap_4204, retro_hsap_518,
Gallus gallus	ENSGALG00000009621	1 retrocopy	retro_ggal_4,
Gorilla gorilla	ENSGGOG00000001133	18 retrocopies	retro_ggor_1177, retro_ggor_1188, retro_ggor_1211, retro_ggor_1266, retro_ggor_1297, retro_ggor_1332, retro_ggor_1387, retro_ggor_1622, retro_ggor_1825, retro_ggor_1890, retro_ggor_2292, retro_ggor_2774, retro_ggor_2817, retro_ggor_3002, retro_ggor_352, retro_ggor_405, retro_ggor_44, retro_ggor_477,
Loxodonta africana	ENSLAFG00000009167	1 retrocopy	retro_lafr_116,
Meleagris gallopavo	ENSMGAG00000003960	2 retrocopies	retro_mgal_5, retro_mgal_6,
Macaca mulatta	ENSMMUG00000011153	1 retrocopy	retro_mmul_135,
Mustela putorius furo	ENSMPUG00000016612	2 retrocopies	retro_mputfur_440, retro_mputfur_461,
Mus musculus	ENSMUSG00000029580	7 retrocopies	retro_mmus_1613, retro_mmus_1677, retro_mmus_283, retro_mmus_2880, retro_mmus_3411, retro_mmus_3532, retro_mmus_761,
Ornithorhynchus anatinus	ENSOANG00000007716	2 retrocopies	retro_oana_4, retro_oana_8,
Otolemur garnettii	ENSOGAG00000008040	3 retrocopies	retro_ogar_148, retro_ogar_1808, retro_ogar_2430,
Otolemur garnettii	ENSOGAG00000008348	1 retrocopy	retro_ogar_2637 ,
Petromyzon marinus	ENSPMAG00000004161	1 retrocopy	retro_pmar_4,
Pongo abelii	ENSPPYG00000017336	23 retrocopies	retro_pabe_1281, retro_pabe_1292, retro_pabe_1575, retro_pabe_1610, retro_pabe_1772, retro_pabe_1816, retro_pabe_1911, retro_pabe_2042, retro_pabe_2168, retro_pabe_2175, retro_pabe_2188, retro_pabe_227, retro_pabe_2754, retro_pabe_2811, retro_pabe_2824, retro_pabe_2862, retro_pabe_2978, retro_pabe_309, retro_pabe_3563, retro_pabe_3567, retro_pabe_3746, retro_pabe_745, retro_pabe_86,
Pan troglodytes	ENSPTRG00000018890	27 retrocopies	retro_ptro_1042, retro_ptro_1051, retro_ptro_1076, retro_ptro_1143, retro_ptro_1272, retro_ptro_1515, retro_ptro_1756, retro_ptro_178, retro_ptro_2122, retro_ptro_2173, retro_ptro_2349, retro_ptro_2454, retro_ptro_263, retro_ptro_2805, retro_ptro_2854, retro_ptro_314, retro_ptro_3207, retro_ptro_3219, retro_ptro_3282, retro_ptro_3287, retro_ptro_3292, retro_ptro_3302, retro_ptro_3307, retro_ptro_387, retro_ptro_432, retro_ptro_53, retro_ptro_584,
Rattus norvegicus	ENSRNOG00000034254	10 retrocopies	retro_rnor_1324, retro_rnor_1386, retro_rnor_1799, retro_rnor_2371, retro_rnor_2714, retro_rnor_2856, retro_rnor_2978, retro_rnor_351, retro_rnor_459, retro_rnor_935,
Sarcophilus harrisii	ENSSHAG00000012694	4 retrocopies	retro_shar_120, retro_shar_370, retro_shar_62, retro_shar_93,
Sus scrofa	ENSSSCG00000007585	1 retrocopy	retro_sscr_548,
Ictidomys tridecemlineatus	ENSSTOG00000006868	2 retrocopies	retro_itri_1675, retro_itri_531,
Ictidomys tridecemlineatus	ENSSTOG00000014797	3 retrocopies	retro_itri_149, retro_itri_1881, retro_itri_4,
Xenopus tropicalis	ENSXETG00000025116	1 retrocopy	retro_xtro_6,