RetrogeneDB ID:

retro_lafr_627

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_264:214122..215058(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:EI24
Ensembl ID:ENSLAFG00000010888
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lafr_627
GTAGTTGATGGTTTGGGCGGTGAAGAGATGGCCGGTGGTGTCAAAACATTTCTCCAGGGCCTTGCCAGGGGAATCAAGGA
CTCCATCTGGGGTATCTACACCATTTCGAAGCTGGGCGCTCCAATACTGTAAAAGAGGGAGGAAAAGCATAGAACAAGGC
TAGTAGCGACCTGACACAGAAAGGACCCCAGAGTACAGAGCCTAAACAAGACAAGTGAGCCACGTGTTGCTGGTAGAATT
TTCCAGTGCTGCGCTTGGAATGGAGGAATATTCTGCTTGAGTCTCCTCTTGTTTCATCAAGTGTTTATTCCTGTGATTCA
GTCAGTAACAGCACAAATTATTGGTGATCTTTTCTTCTATCACTATGGAGATGTTTGATCGTGGCTGGAATTCTTCCTCA
CGTCAATTTTCAGTGCTCTTTGGGTGCTCCCCTGTTCTTGCTTAGCAAAGTTGTCAATGTCATTTGGTTCCAAAATATAG
CTGGCCAGGCATTTGAGGTATCAGGGAGAAACCCTCACCCATTCCCTAGTGTCAGGAAAGCAACTGCTGATATGCTCTTC
AACCTCTGCCTCAGGCTCTTTTCCTTCTCCAGGGGAAGTTTGGGAGTCTCTTCATCCATCCTGTTGGTCAGCTGGTTTGT
CTCCTGCATATGTCCCTTCTATATTCACTACACTGCTTTGGATAATACTGATTCATTAAAGGAATTGAAGTGCACTAGTT
GTTGTCAGACATAGAAAGGAACTGGCCCTCCTACTTTGGATTTGGTTTGCCCTTGGCTTTGCTCACAGCAACGCAGTTCT
CATACATCATCAGTGGCTGCCTTTTCTCCATCCTCTTTCCTTTATTCATTTATCAGCACCAATGGAGCAAAGGCCCCTGG
CAAAGTGTATTATTTTTAAGTTAAGCCTCTTCTCTCTGGTGGTCTTATTAACAGAC

ORF - retro_lafr_627 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 74.29 %
Parental protein coverage: 87.61 %
Number of stop codons detected: 5
Number of frameshifts detected 6


Retrocopy - Parental Gene Alignment:

ParentalVVDRWGGEEMADSVKTFLQDLARGIKDSIWGICTISKLDARIQQKREEQRRRR-ASSVLAQRRAQSIERK
VVD..GGEEMA..VKTFLQ.LARGIKDSIWGI.TISKL.A.I..KREE..R.R.ASS.L.Q...QS.E.K
RetrocopyVVDGLGGEEMAGGVKTFLQGLARGIKDSIWGIYTISKLGAPIL*KREEKHRTR<ASSDLTQKGPQSTEPK
ParentalQE-SEPRIVSRIFQCCAWNGGVFWLSLLLFYRVFIPGLQSVTAQIIGDPSL--HGDVWSWLEFFLTSIFS
Q..SEPR...RIFQCCAWNGG.F.LSLLLF..VFIP..QSVTAQIIGD......GDV.SWLEFFLTSIFS
RetrocopyQD>SEPRVAGRIFQCCAWNGGIFCLSLLLFHQVFIPVIQSVTAQIIGDLFFYHYGDV*SWLEFFLTSIFS
ParentalALWVL-PLFVLSKVVNAIWFQDIADLAFEVSGRKPHPFPSVSKIIADMLFNLLL-QALFLLQGMFVSLFP
ALWVL.PLF.LSKVVN.IWFQ.IA..AFEVSGR.PHPFPSV.K..ADMLFNL.L.QALFLLQG.F.SLF.
RetrocopyALWVL<PLFLLSKVVNVIWFQNIAGQAFEVSGRNPHPFPSVRKATADMLFNLCL<QALFLLQGKFGSLF-
ParentalIHLVGQLVSLLHMSLLYSLYCFEYRWFNKGIEMHQRLSNIERNWPYYFGFGLPLAFLTAMQSSYIISGCL
IH.VGQLV.LLHMSLLYSL.CF....F.KGIE.H..LS.IERNWP.YFGFGLPLA.LTA.Q.SYIISGCL
RetrocopyIHPVGQLVCLLHMSLLYSLHCFG*Y*FIKGIEVH*LLSDIERNWPSYFGFGLPLALLTATQFSYIISGCL
ParentalFSILFPLFI-ISANEAKTPGKAY-LFQLRLFSLVVFLSN
FSILFPLFI.IS.N.AK.PGK.Y..F.L.LFSLVV.L..
RetrocopyFSILFPLFI>ISTNGAKAPGKVY>IFKLSLFSLVVLLTD

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_627 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 26 parental genes, and 69 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000009902 retrocopies
retro_amel_1449, retro_amel_1681,
Bos taurus ENSBTAG000000072022 retrocopies
retro_btau_1242, retro_btau_443,
Canis familiaris ENSCAFG000000108981 retrocopy
retro_cfam_1829,
Choloepus hoffmanni ENSCHOG000000126693 retrocopies
retro_chof_1433, retro_chof_1994, retro_chof_804,
Cavia porcellus ENSCPOG000000072722 retrocopies
retro_cpor_132, retro_cpor_929,
Dasypus novemcinctus ENSDNOG000000023624 retrocopies
retro_dnov_1083, retro_dnov_1421, retro_dnov_2143, retro_dnov_2345,
Equus caballus ENSECAG000000158611 retrocopy
retro_ecab_1022,
Erinaceus europaeus ENSEEUG000000032741 retrocopy
retro_eeur_435,
Felis catus ENSFCAG000000151001 retrocopy
retro_fcat_1754,
Homo sapiens ENSG000001495473 retrocopies
retro_hsap_236, retro_hsap_2782, retro_hsap_3804,
Loxodonta africana ENSLAFG00000010888 15 retrocopies
retro_lafr_262, retro_lafr_263, retro_lafr_264, retro_lafr_265, retro_lafr_394, retro_lafr_395, retro_lafr_396, retro_lafr_397, retro_lafr_398, retro_lafr_399, retro_lafr_566, retro_lafr_589, retro_lafr_626, retro_lafr_627 , retro_lafr_999,
Microcebus murinus ENSMICG000000030233 retrocopies
retro_mmur_398, retro_mmur_498, retro_mmur_632,
Myotis lucifugus ENSMLUG000000015831 retrocopy
retro_mluc_1249,
Macaca mulatta ENSMMUG000000100093 retrocopies
retro_mmul_1443, retro_mmul_1653, retro_mmul_2244,
Nomascus leucogenys ENSNLEG000000074513 retrocopies
retro_nleu_2149, retro_nleu_684, retro_nleu_853,
Oryctolagus cuniculus ENSOCUG000000146701 retrocopy
retro_ocun_1578,
Otolemur garnettii ENSOGAG000000018386 retrocopies
retro_ogar_1055, retro_ogar_1379, retro_ogar_2700, retro_ogar_2701, retro_ogar_659, retro_ogar_799,
Ochotona princeps ENSOPRG000000134912 retrocopies
retro_opri_106, retro_opri_1130,
Procavia capensis ENSPCAG000000127621 retrocopy
retro_pcap_452,
Pongo abelii ENSPPYG000000040333 retrocopies
retro_pabe_2234, retro_pabe_3107, retro_pabe_416,
Pan troglodytes ENSPTRG000000044444 retrocopies
retro_ptro_1202, retro_ptro_1883, retro_ptro_206, retro_ptro_2581,
Pteropus vampyrus ENSPVAG000000045321 retrocopy
retro_pvam_1124,
Rattus norvegicus ENSRNOG000000303911 retrocopy
retro_rnor_2605,
Sarcophilus harrisii ENSSHAG000000173331 retrocopy
retro_shar_433,
Ictidomys tridecemlineatus ENSSTOG000000042992 retrocopies
retro_itri_1343, retro_itri_1373,
Tarsius syrichta ENSTSYG000000047472 retrocopies
retro_tsyr_1238, retro_tsyr_1423,


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