RetrogeneDB ID:

retro_ogar_1840

Retrocopy
location
Organism:Bushbaby (Otolemur garnettii)
Coordinates:GL873569.1:10299487..10300242(+)
Located in intron of:ENSOGAG00000006084
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSOGAG00000009152
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ogar_1840
AACCTTGACACAGTAGCATTTGTGCCAATTTCTGGCTGGAATGGTGACAACAATGTTGGAGCCAAGTGCTAATGTGCCTT
GGCTCAAGGGATAGAAAGTCACCCAGAAAGATGGCAATGGCAGTGGAACCACCCTGCTTGAAGCTCTGGATTGCATTATG
CCACTGACTTGTCCAACTGACAAGCCCCTACATCTGCCTCTCCAGGATGTCTTCAAAATTGGTGGCATTGGAACTGTCCC
TGTGGGCTGAGTGGAGACTGGTGCTCTCAAACAGGCATGGTGGTCACCTTTGCTGCAGGTAATGTTACAACTGAAGTAAA
GTCTGTTAAATGCACCATGTGACTTTGAGTGAAGCTCTCCCCGGGGACAATATGGGCTTCAATGTCAAGAATGTGTCTGT
CAAACATGTTAGTTGTGGCAACGCTGCTGGTGACAGCAAAAATGACTCACCAATGGAAGCAGCTGACTTCAATGCTCAGG
TGATTATCCTGAACCATACAGGCCAAATTAGTGCTGGCTACGCTCCTGTATGGGATTGTCACCTGGCTTACATTGCCTGC
AAGTTTGCTGAGCTAAAAGAAAAGATTGATTGCTGCTCTGGTAAGAAGCTGGAAGATGGCCCTAAATTCTTGAAATCTGC
TGATACTGCCATCGTTAGTATGGTTCCTGGCAAACCCACATGTATTCAGAGTTTCTCAGACTATCCTCCTCTGGGTCATT
TTGCTGGTTGTGAGATGAGACAGTTACTGTGGGTG

ORF - retro_ogar_1840 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.78 %
Parental protein coverage: 71.59 %
Number of stop codons detected: 2
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalNPDTVAFVPISGWNGDN-MLEPSANMPWFKGWKVTRKDGNASGTTLLEALDCILPPTRPTDKPLRLPLQD
N.DTVAFVPISGWNGDN.MLEPSAN.PW.KG.KVT.KDGN.SGTTLLEALDCI.P.T.PTDKPL.LPLQD
RetrocopyNLDTVAFVPISGWNGDN>MLEPSANVPWLKG*KVTQKDGNGSGTTLLEALDCIMPLTCPTDKPLHLPLQD
ParentalVYKIGGIGTVPVGRVETGVLKP-GMVVTFAPVNVTTEVKSVE-MHHEALSEALPGDNVGFNVKNVSVKDV
V.KIGGIGTVPVG.VETG.LK..GMVVTFA..NVTTEVKSV..MHH..LSEALPGDN.GFNVKNVSVK.V
RetrocopyVFKIGGIGTVPVG*VETGALKQ<GMVVTFAAGNVTTEVKSVK<MHHVTLSEALPGDNMGFNVKNVSVKHV
ParentalRRGNVAGDSKNDPPMEAAGFTAQVIILNHPGQISAGYAPVLDCHTAHIACKFAELKEKIDRRSGKKLEDG
..GN.AGDSKND.PMEAA.F.AQVIILNH.GQISAGYAPV.DCH.A.IACKFAELKEKID..SGKKLEDG
RetrocopySCGNAAGDSKNDSPMEAADFNAQVIILNHTGQISAGYAPVWDCHLAYIACKFAELKEKIDCCSGKKLEDG
ParentalPKFLKSGDAAIVDMVPGKPMCVESFSDYPPLGRFAVRDMRQTVAV
PKFLKS.D.AIV.MVPGKP.C..SFSDYPPLG.FA...MRQ...V
RetrocopyPKFLKSADTAIVSMVPGKPTCIQSFSDYPPLGHFAGCEMRQLLWV

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






RNA-Seq - click to see more details

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

ChIP-Seq - click to see more details

Otolemur garnettii was not studied using ChIP-Seq data.

EST - click to see more details

Otolemur garnettii was not studied using EST data.

TSS - click to see more details

Otolemur garnettii was not studied using FANTOM5 data.

Lab - click to see more details

retro_ogar_1840 was not experimentally validated.

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.
Parental genes homology:
Parental genes homology involve 15 parental genes, and 136 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000132491 retrocopy
retro_cfam_1007,
Dipodomys ordii ENSDORG000000096291 retrocopy
retro_dord_509,
Equus caballus ENSECAG000000222601 retrocopy
retro_ecab_802,
Erinaceus europaeus ENSEEUG000000003423 retrocopies
retro_eeur_407, retro_eeur_492, retro_eeur_625,
Echinops telfairi ENSETEG0000000423614 retrocopies
retro_etel_1189, retro_etel_1248, retro_etel_1260, retro_etel_1429, retro_etel_1436, retro_etel_1472, retro_etel_1578, retro_etel_1602, retro_etel_1682, retro_etel_1808, retro_etel_2135, retro_etel_366, retro_etel_411, retro_etel_830,
Loxodonta africana ENSLAFG000000280811 retrocopy
retro_lafr_651,
Microcebus murinus ENSMICG0000001531921 retrocopies
retro_mmur_1027, retro_mmur_1116, retro_mmur_1145, retro_mmur_1182, retro_mmur_1190, retro_mmur_12, retro_mmur_1282, retro_mmur_1316, retro_mmur_1339, retro_mmur_1343, retro_mmur_1350, retro_mmur_1568, retro_mmur_171, retro_mmur_26, retro_mmur_273, retro_mmur_49, retro_mmur_682, retro_mmur_729, retro_mmur_825, retro_mmur_877, retro_mmur_9,
Monodelphis domestica ENSMODG000000185334 retrocopies
retro_mdom_1053, retro_mdom_1146, retro_mdom_311, retro_mdom_792,
Mus musculus ENSMUSG0000003774215 retrocopies
retro_mmus_1349, retro_mmus_1518, retro_mmus_1667, retro_mmus_1783, retro_mmus_1816, retro_mmus_1849, retro_mmus_1850, retro_mmus_1864, retro_mmus_1909, retro_mmus_2363, retro_mmus_2583, retro_mmus_2902, retro_mmus_3249, retro_mmus_480, retro_mmus_483,
Otolemur garnettii ENSOGAG000000046308 retrocopies
retro_ogar_1067, retro_ogar_2034, retro_ogar_2329, retro_ogar_2497, retro_ogar_2583, retro_ogar_3191, retro_ogar_3270, retro_ogar_643,
Otolemur garnettii ENSOGAG00000009152 10 retrocopies
retro_ogar_1215, retro_ogar_1622, retro_ogar_1779, retro_ogar_1840 , retro_ogar_2281, retro_ogar_2526, retro_ogar_2557, retro_ogar_3013, retro_ogar_3046, retro_ogar_3271,
Pongo abelii ENSPPYG000000167771 retrocopy
retro_pabe_12,
Ictidomys tridecemlineatus ENSSTOG000000076874 retrocopies
retro_itri_1509, retro_itri_1740, retro_itri_1816, retro_itri_195,
Tupaia belangeri ENSTBEG0000001215151 retrocopies
retro_tbel_1084, retro_tbel_1330, retro_tbel_1373, retro_tbel_1452, retro_tbel_166, retro_tbel_1841, retro_tbel_1969, retro_tbel_1994, retro_tbel_2088, retro_tbel_2091, retro_tbel_2179, retro_tbel_2205, retro_tbel_2206, retro_tbel_2218, retro_tbel_2232, retro_tbel_2419, retro_tbel_2505, retro_tbel_259, retro_tbel_2627, retro_tbel_2718, retro_tbel_2738, retro_tbel_2758, retro_tbel_282, retro_tbel_2976, retro_tbel_3032, retro_tbel_3065, retro_tbel_3067, retro_tbel_3281, retro_tbel_3307, retro_tbel_3315, retro_tbel_338, retro_tbel_354, retro_tbel_360, retro_tbel_372, retro_tbel_3813, retro_tbel_3865, retro_tbel_3967, retro_tbel_4125, retro_tbel_4192, retro_tbel_4282, retro_tbel_4352, retro_tbel_4370, retro_tbel_4466, retro_tbel_4496, retro_tbel_4639, retro_tbel_4660, retro_tbel_4695, retro_tbel_473, retro_tbel_588, retro_tbel_620, retro_tbel_903,
Drosophila melanogaster FBgn00005571 retrocopy
retro_dmel_9,


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