RetrogeneDB ID:

retro_lafr_9

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_14:27385348..27386458(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSLAFG00000029932
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:TRAM1
Ensembl ID:ENSLAFG00000011625
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lafr_9
ATGGCGATCCGCAAGAAGAGCACCAAGAACCCCCCGGTCCTGAGTCACGAATTCATCCTGCAGAATCATGCGGACATTGC
CTCCTGTGTGGGCATGTTCTTCGTGCTGGGACTGATGTTCGAGGCGACTGCAGAAGCATCTATCGTTTTTATTACCCTTC
AGCACAGTGTTACCGTCCCCGCAGCGAAAGAACAAGCCACGGAATCCAGGTCCCTTTATAATTATGGTGTCAAAGATTTG
GCCACGGTGTTTTTCTACATGCTAGTGGCAATAATTATTCACGCCACAATTCAGGAGTATGTGTTGGATAAAATTAACAG
GCAAATGCAGTTTCCCAAGACGAAACAAAGCAAGTTTAATGAATCTGGTCAGCTTAGTGTATTTTACCTTGTTTCTTGTA
TTTGGGGCATAATCATTCTAATCTCTGAAAACTGCATTTCAGACGCTACTGTCTTGTGGAGGGCTCATCCCCATAACATG
ATGACATTTCAAATGAAGTTTTTTTACGTATCACAGTTGGCTTACTGGCTCCATGCTTTTCCTGAGCTCTACTTCCAGAA
AACCAAAAAACAGGACGTTCCCCGTCAACTCATCTACTTTGGTCTTCACCTCTTTCATGTCGCTGGGGCTTACCTTTTGT
ACTTGAATCATCTGGGACTTGTTCTCATGGTGTTGCATTATTTTGTTGAATTACTTTCCCACATGTGCGACCTGTTTTAT
ATGAGTGATGAAAAGTATGAGAAAGGGTTTTCTCTGTGGGCAATTGTGATTGTTTTGGGAAGACTGCTGATTTTAATTGT
TTCGGTACTCACTGTTGGCTTTCATCTTGCTGGATCTGAGACTCAGAAGCCGGATATCATTGCTGGAAATTTCAACGTGT
TGGCTGCGAAAATTGCTGTTCTGTCTTCCAGTTGCACGATCCAAGCATTCATAACATGGAATTTAATTACTGTCCAGCTC
CAGAGGTGGCGGGAACAATCTACTTTTGAGGCCCCCTGTGTGAAGAAGAAACGGACAACGACTAAAGGAAAATCTTCTAG
AAAAGGAACAGAAAATGGAGTGGAAACTTCAAATAGAGCAGACTCCCCCCGTAATAAGAAAGAGAAATGA

ORF - retro_lafr_9 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.94 %
Parental protein coverage: 99.1 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalTAKASIIFVTLQYNVTNSATEGQASESVSLYYYGVKDLATVFFYMLVAVIIHAIIQEYVLDKINRRMHFS
TA.ASI.F.TLQ..VT..A...QA.ES.SLY.YGVKDLATVFFYMLVA.IIHA.IQEYVLDKINR.M.F.
RetrocopyTAEASIVFITLQHSVTVPAAKEQATESRSLYNYGVKDLATVFFYMLVAIIIHATIQEYVLDKINRQMQFP
ParentalKTKHSKFNESGQLSAFYLFSCIWGTFILISENYISDPTILWRAYPHNLMTFQMKFFFISQLAYWLHAFPE
KTK.SKFNESGQLS.FYL.SCIWG..ILISEN.ISD.T.LWRA.PHN.MTFQMKFF..SQLAYWLHAFPE
RetrocopyKTKQSKFNESGQLSVFYLVSCIWGIIILISENCISDATVLWRAHPHNMMTFQMKFFYVSQLAYWLHAFPE
ParentalLYFQKTKKEDILRQLVYIGLYLFHIAGAYLLNLNHLGLVLLVLHYFVEFLFHISRLFYFSDEKYQKGFSL
LYFQKTKK.D..RQL.Y.GL.LFH.AGAYLL.LNHLGLVL.VLHYFVE.L.H...LFY.SDEKY.KGFSL
RetrocopyLYFQKTKKQDVPRQLIYFGLHLFHVAGAYLLYLNHLGLVLMVLHYFVELLSHMCDLFYMSDEKYEKGFSL
ParentalWAVLFVLGRLLTLILSVLTVGFGLARAENQKFDISTGNFNVLAVRIAVLASICITQAFMMWKFINFQLRR
WA...VLGRLL.LI.SVLTVGF.LA..E.QK.DI..GNFNVLA..IAVL.S.C..QAF..W..I..QL.R
RetrocopyWAIVIVLGRLLILIVSVLTVGFHLAGSETQKPDIIAGNFNVLAAKIAVLSSSCTIQAFITWNLITVQLQR
ParentalWREHSATQAPAVKKKPTVTKGRSSRKGTENGVNGTVTSNGADSPRNRKDK
WRE.S...AP.VKKK.T.TKG.SSRKGTENGV....TSN.ADSPRN.K.K
RetrocopyWREQSTFEAPCVKKKRTTTKGKSSRKGTENGVE---TSNRADSPRNKKEK

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_9 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 25 parental genes, and 26 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000063251 retrocopy
retro_amel_78,
Bos taurus ENSBTAG000000075621 retrocopy
retro_btau_24,
Canis familiaris ENSCAFG000000078661 retrocopy
retro_cfam_15,
Callithrix jacchus ENSCJAG000000078931 retrocopy
retro_cjac_168,
Dasypus novemcinctus ENSDNOG000000092962 retrocopies
retro_dnov_27, retro_dnov_906,
Dipodomys ordii ENSDORG000000019011 retrocopy
retro_dord_27,
Equus caballus ENSECAG000000183781 retrocopy
retro_ecab_506,
Echinops telfairi ENSETEG000000184471 retrocopy
retro_etel_674,
Felis catus ENSFCAG000000287751 retrocopy
retro_fcat_136,
Homo sapiens ENSG000000671671 retrocopy
retro_hsap_51,
Loxodonta africana ENSLAFG00000011625 1 retrocopy
retro_lafr_9 ,
Macaca mulatta ENSMMUG000000015161 retrocopy
retro_mmul_235,
Monodelphis domestica ENSMODG000000073161 retrocopy
retro_mdom_308,
Mustela putorius furoENSMPUG000000106161 retrocopy
retro_mputfur_558,
Mus musculus ENSMUSG000000259351 retrocopy
retro_mmus_117,
Nomascus leucogenys ENSNLEG000000113761 retrocopy
retro_nleu_73,
Oryctolagus cuniculus ENSOCUG000000087341 retrocopy
retro_ocun_52,
Otolemur garnettii ENSOGAG000000063791 retrocopy
retro_ogar_2932,
Pongo abelii ENSPPYG000000186601 retrocopy
retro_pabe_169,
Pan troglodytes ENSPTRG000000203341 retrocopy
retro_ptro_2081,
Rattus norvegicus ENSRNOG000000078921 retrocopy
retro_rnor_287,
Sus scrofa ENSSSCG000000061931 retrocopy
retro_sscr_980,
Ictidomys tridecemlineatus ENSSTOG000000055371 retrocopy
retro_itri_38,
Tarsius syrichta ENSTSYG000000138871 retrocopy
retro_tsyr_24,
Tursiops truncatus ENSTTRG000000003281 retrocopy
retro_ttru_24,


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