RetrogeneDB ID:

retro_lafr_504

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_2:34371904..34373316(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:GLUD1
Ensembl ID:ENSLAFG00000012059
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lafr_504
ATAATGGAATTCATCAAGACCCAGGACAGTGAGGAGCAGAAGCGGAAATGAGTGCTCGGGATTCTGTGAATCATCAAGCC
CTGCAACCGTGTGCTGAGTCTCTCCTTCCCCATCCGGCTCACAGCGGCTCCTGGGAGGCCATTCATGGCTACTGAGCCCA
GCACAGTCAGCACTGCACTCCCTGCAAGGCTGGTATCTGTTAAAGCGCAAATGTGAGTATAAATGAAGTAAAAGCTTTGG
CTGCTTTGATGACATAGAAATGTGCTGTGGTTGATGTGCTCTCTGGGGGTGCTAAAGCTGGTGTTAAGATCAATCCCAAG
AATTATACCCATAATGAATTTGAAAAGATCACAAGGAGGTTCCATGGAATTAGCAAAGAAGGGCTTTATTGGTCCTAGCG
TTGATGTGCTTGCCCCCAGATATGGGCACTGGTGAGCGTGAGATGTCCTGGATTGCTGACACCTATGCCAGCACCATAGG
GTAGTATGATATTAATTCACATGCCTGTGTTACAGGTAAACCCATCAGTCAGGGTGGTATCCATGGACATATCTCTGCTA
CTGGCCATGGTGTTTTCCTTGGTATTGAAAACTTTATCAGTGAAGCTTCTTACATGAACATTTTAGTGTTGACATCAAGA
GTTCAAAATAAAACACTTGTTCAGGGATTTGGTAATATGGGCCATTATACTATAAGATATTTACGTCATTTTGGTGCTAA
ATGTGTTGGTGTTAGTGACTCTCACAGGGGCATATGGAATTCAGATGGTATTGATCCAAAGGAACTGGAGGACTTCAAAT
TGCAACGTGGATCAGTCATGGGTTTCACCAAGGCAAAACCCTATAAAGGAAGCATCTTGGAAGCTGACTGTGACATACTG
ATTCCTGCCGCCAAGGAGAAGCAGTTGACCAAATTCAGTGCACAGAAAGTCAAAGCCAAGACCATTGCTGAAGGTGCCAA
TGAACAGACAACGCCAGAAGTTCATAAGATTTTCCTGGCGAAGAAGATTCTAGTAATCCTTGATCTCTGCTTGAATGCTG
GAGGACTGACAGTATCTTACTTTGAGCGGCTGAAGAATATAAGTCATGTCAGCTATGGCCATTTGACTTTCAAATATGAA
AGGGATTCTACTACCATTTGCTCAGGTCTGCTTAAAAGAGTTTAGAAAGAACATTTGGAAGCTCAGTGGAACTCTTCCCA
TTTTACCCACAGCAGGATTCCAAGATAGACTATCAGGTGCATCTGAGAAAGACATCGTGCACTCTGGCTTAGCTTATACC
ATGGAGTATCCTGCTAGGCAAACCATGAGCACAGCCAGGAAGTATAAACTGGGAATGGATGTGAGAATGGCTGCCTACGT
CATTGCCATTGAGAAAATTGTCAGGGTGTACAATGAAGCTGGTTTGACCTTC

ORF - retro_lafr_504 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 72.8 %
Parental protein coverage: 84.77 %
Number of stop codons detected: 7
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalLVEDLRTRESEEQKRNRVRGILRIIKPCNHVLSVSFPIR-RDDGSWEVIEGYRAQHSQHRTPCKGGIRYS
..E...T..SEEQKR..V.GIL.IIKPCN.VLS.SFPIR....GSWE.I.GY.AQHSQH.TPCK.GI..S
RetrocopyIMEFIKTQDSEEQKRK*VLGIL*IIKPCNRVLSLSFPIR<AHSGSWEAIHGY*AQHSQHCTPCKAGIC*S
ParentalTDVSVDEVKALASLMTYKCAVVDVPFGGAKAGVKINPKNYTDSELEKITRRFTMELAKKG-FIGPGIDVP
..VS..EVKALA.LMT.KCAVVDV..GGAKAGVKINPKNYT..E.EKITRRF.....K.G.FIGP..DV.
RetrocopyANVSINEVKALAALMT*KCAVVDVLSGGAKAGVKINPKNYTHNEFEKITRRF-HGISKEG>FIGPSVDVL
ParentalA-PDMSTGEREMSWIADTYASTIGHYDINAHACVTGKPISQGGIHGRISATGRGLFHGIENFINEASYMS
A.PDM.TGEREMSWIADTYASTIG.YDIN.HACVTGKPISQGGIHG.ISATG.G.F.GIENFI.EASYM.
RetrocopyA>PDMGTGEREMSWIADTYASTIG*YDINSHACVTGKPISQGGIHGHISATGHGVFLGIENFISEASYMN
ParentalILGMTPGFGDKTFVVQGFGNVGLHSMRYLHRFGAKCVGVAESEGSIWNPDGIDPKELEDFKLQHGSIMGF
IL..T.....KT..VQGFGN.G....RYL..FGAKCVGV..S...IWN.DGIDPKELEDFKLQ.GS.MGF
RetrocopyILVLTSRVQNKT-LVQGFGNMGHYTIRYLRHFGAKCVGVSDSHRGIWNSDGIDPKELEDFKLQRGSVMGF
ParentalPKAKPYEGSILEADCDILIPAASEKQLTKSNAPRVKAKIIAEGANGPTTPEADKIFLERNIMVIPDLYLN
.KAKPY.GSILEADCDILIPAA.EKQLTK..A..VKAK.IAEGAN..TTPE..KIFL...I.VI.DL.LN
RetrocopyTKAKPYKGSILEADCDILIPAAKEKQLTKFSAQKVKAKTIAEGANEQTTPEVHKIFLAKKILVILDLCLN
ParentalAGGVTVSYFEWLKNLNHVSYGRLTFKYERDSN-YHLLMSVQESLERKFG-KHGGTIPIVPTAEFQDRISG
AGG.TVSYFE.LKN..HVSYG.LTFKYERDS..YHLL.S...SLER.FG.K..GT.PI.PTA.FQDR.SG
RetrocopyAGGLTVSYFERLKNISHVSYGHLTFKYERDST<YHLLRSA*KSLERTFG<KLSGTLPILPTAGFQDRLSG
ParentalASEKDIVHSGLAYTMERSARQIMRTAMKYNLGLDLRTAAYVNAIEKVFKVYNEAGVTF
ASEKDIVHSGLAYTME..ARQ.M.TA.KY.LG.D.R.AAYV.AIEK...VYNEAG.TF
RetrocopyASEKDIVHSGLAYTMEYPARQTMSTARKYKLGMDVRMAAYVIAIEKIVRVYNEAGLTF

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






RNA-Seq - click to see more details

Loxodonta africana was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Loxodonta africana was not studied using ChIP-Seq data.

EST - click to see more details

Loxodonta africana was not studied using EST data.

TSS - click to see more details

Loxodonta africana was not studied using FANTOM5 data.

Lab - click to see more details

retro_lafr_504 was not experimentally validated.

Retrocopy orthology:
Loxodonta africana 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 20 parental genes, and 28 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000075402 retrocopies
retro_btau_1413, retro_btau_1741,
Canis familiaris ENSCAFG000000160951 retrocopy
retro_cfam_747,
Choloepus hoffmanni ENSCHOG000000011011 retrocopy
retro_chof_2002,
Callithrix jacchus ENSCJAG000000116331 retrocopy
retro_cjac_2830,
Dipodomys ordii ENSDORG000000097671 retrocopy
retro_dord_400,
Equus caballus ENSECAG000000073712 retrocopies
retro_ecab_886, retro_ecab_919,
Echinops telfairi ENSETEG000000196382 retrocopies
retro_etel_141, retro_etel_2024,
Homo sapiens ENSG000001486721 retrocopy
retro_hsap_31,
Gorilla gorilla ENSGGOG000000157701 retrocopy
retro_ggor_2954,
Loxodonta africana ENSLAFG00000012059 1 retrocopy
retro_lafr_504 ,
Microcebus murinus ENSMICG000000165261 retrocopy
retro_mmur_524,
Monodelphis domestica ENSMODG000000027561 retrocopy
retro_mdom_124,
Nomascus leucogenys ENSNLEG000000116581 retrocopy
retro_nleu_36,
Otolemur garnettii ENSOGAG000000036411 retrocopy
retro_ogar_2757,
Procavia capensis ENSPCAG000000086621 retrocopy
retro_pcap_11,
Pongo abelii ENSPPYG000000028273 retrocopies
retro_pabe_3109, retro_pabe_3213, retro_pabe_79,
Pan troglodytes ENSPTRG000000027114 retrocopies
retro_ptro_3162, retro_ptro_3283, retro_ptro_3285, retro_ptro_3290,
Ictidomys tridecemlineatus ENSSTOG000000128431 retrocopy
retro_itri_737,
Tarsius syrichta ENSTSYG000000015781 retrocopy
retro_tsyr_313,
Tursiops truncatus ENSTTRG000000081451 retrocopy
retro_ttru_950,


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