RetrogeneDB ID:

retro_lafr_745

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_34:24071247..24072013(-)
Located in intron of:ENSLAFG00000000426
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSLAFG00000000867
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lafr_745
ATGGCTGAAAATGGTGATAGTGAAAAAATGGCTGCGCTAGAGGCCAAAATCTGTCATCAAGCTGAATATTATTTTGGTGA
CTTTAATTTGCCACAGGACAAATTTTTAAAGGAACAGATCAAACTGGATGAAGGCTGGGTACCTTCAGAGATAATGAAAA
AAACTGACAGGCTAAACCACCTAACAGACTTTAATGTAATAGTAGAAGCAATGAGCAAGTAAAAGGTAGAACTCATGGAA
ATGAGTGAAGATAAAACTAAAATCAGAAGTTCTCCAAGCAAACCCCTCCCTGAAGTACTGACAAGTATAAAAATGATGTA
AAAAACAGATCTGTTTATATTAAAGTCTTCCCAACTGATGGAACCCTTGATGACATAAAGAATGGTTAGAAGACAAAGGT
CAAGTACTGACTATTCTGATGACAAGAACACTGCACAAAGCATTTAAGGGATCAATATTTGTTGTGTTTGGTAGCACTGA
ATCCGCTAGTAAGTTTGTAAAGATCCCTGGTCAGAAGTACAAAGACTCAGACCTGCTAATAGTTTTCAAGGAATATTAGT
TTGCAAAAAAGAATGAAGAAAGCAAAATAAACTGGAAGCTAAATTATGAGCTAAACAAGAACAAGATGAAAAACAGAAGT
TAGCAGAAGGTGTTGAAATGAAATCTCTAGAAGAAAAGATGGGCTGTTTGCTGAAATTTTCAAATGACTTAGATGATCAG
ACCTACAGAGAAAATTTGCACAACCTTTTTCTCATATCACGGTGAA

ORF - retro_lafr_745 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.61 %
Parental protein coverage: 61.14 %
Number of stop codons detected: 2
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalMAENGDSEKMAALEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLEIMIKFNRLNRLTTDFNVIVE
MAENGDSEKMAALEAKICHQ.EYYFGDFNLP.DKFLKEQIKLDEGWVP.EIM.K..RLN.LT.DFNVIVE
RetrocopyMAENGDSEKMAALEAKICHQAEYYFGDFNLPQDKFLKEQIKLDEGWVPSEIMKKTDRLNHLT-DFNVIVE
ParentalALSKSKVELMEISEDKTKIRRSPSKPLPEV-TDEYKNDVKNRSVYIKGFPTDATLDDIK-EWLEDKGQVL
A.SK.KVELME.SEDKTKIR.SPSKPLPEV.TD.YKNDVKNRSVYIK.FPTD.TLDDIK.EWLEDKGQVL
RetrocopyAMSK*KVELMEMSEDKTKIRSSPSKPLPEV<TDKYKNDVKNRSVYIKVFPTDGTLDDIK<EWLEDKGQVL
ParentalNILMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQKYKDTDLLILFKEDYFAKKNEERKQN-KLEAKL-R
.ILM.RTLHKAFKGSIFVVF.S.ESA.KFV..PGQKYKD.DLLI.FKE..FAKKNEE.K.N.KL...L..
RetrocopyTILMTRTLHKAFKGSIFVVFGSTESASKFVKIPGQKYKDSDLLIVFKEY*FAKKNEESKINWKLNYEL<K
ParentalAKQEQEEKQKLAEDAEMKSLEEKMGCLLKFSGDLDDQTCREDLQDL-FSSHGE
..Q....KQKLAE..EMKSLEEKMGCLLKFS.DLDDQT.RE.L..L.FS.HGE
RetrocopyQEQDE--KQKLAEGVEMKSLEEKMGCLLKFSNDLDDQTYRENLHNL>FSYHGE

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






Loxodonta africana was not studied using RNA-Seq expression data.
Loxodonta africana was not studied using ChIP-Seq data.
Loxodonta africana was not studied using EST data.
Loxodonta africana was not studied using FANTOM5 data.
retro_lafr_745 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 18 parental genes, and 38 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000077635 retrocopies
Dasypus novemcinctus ENSDNOG000000134501 retrocopy
Echinops telfairi ENSETEG000000046141 retrocopy
Homo sapiens ENSG000001383851 retrocopy
Gorilla gorilla ENSGGOG000000115073 retrocopies
Gorilla gorilla ENSGGOG000000234714 retrocopies
Loxodonta africana ENSLAFG00000000867 3 retrocopies
retro_lafr_698, retro_lafr_745 , retro_lafr_982,
Macropus eugenii ENSMEUG000000016501 retrocopy
Myotis lucifugus ENSMLUG000000163161 retrocopy
Macaca mulatta ENSMMUG000000230512 retrocopies
Monodelphis domestica ENSMODG000000082271 retrocopy
Nomascus leucogenys ENSNLEG000000049583 retrocopies
Otolemur garnettii ENSOGAG000000297681 retrocopy
Pongo abelii ENSPPYG000000129193 retrocopies
Pan troglodytes ENSPTRG000000126201 retrocopy
Rattus norvegicus ENSRNOG000000079981 retrocopy
Tupaia belangeri ENSTBEG000000090564 retrocopies
Tursiops truncatus ENSTTRG000000021522 retrocopies



Copyright © RetrogeneDB 2014-2017