RetrogeneDB ID:

retro_lafr_62

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_32:28394447..28395314(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSLAFG00000028673
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:MORF4L1
Ensembl ID:ENSLAFG00000009851
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lafr_62
ATGAGTTCCAGAAAGCAGGGTTCTCAAACTCGTGGACAACAATCTGCAGAAGAAGACAACTTCAAAAAGCCAACTAGAAG
CAACATGCAGAGAAGTAAGATGAGAGGGGCCTCCTCAGGAAAGAAGACAGCTGGTCCTCAGCAGAAGAATCTGGAGCCAG
CTCTCCCAGGCAGATGGGGGGGTCGATCTGCAGAGAACCCCCCTTCAGGATCCGTGAGGAAGACAAGAAAGAACAAACAG
AAGACTCCCGGAAACGGAGATGGTGGCAGTACCAGTGAAGCCCCTCAGCCACCTCGGAAGAAAAGGGCCCGGGCGGATCC
TACTGTTGAAAGCGAGGAGGCATTTAAGAATAGAGTGGAGGTGAAGGTGAAGATTCCTGAAGAGTTAAAACCATGGCTTG
TTGAGGACTGGGACTTGGTTACCAGGCAGAAGCAGCTGTTTCAGCTCCCAGCTAAGAAAAATGTAGATGCCATCCTGGAA
GAGTACGCAAATTGCAAGAGATCTCAAGGAAACGTCGACAATAAGGAATACGCAGTTAACGAAGTTGTGGCAGGAATAAA
AGAGTATTTCAATGTGATGTTGGGCACTCAGCTGCTCTACAAATTTGAGAGGCCCCAGTATGCTGAGATCCTGATGGCTC
ACCCTGATGCGCCCATGTCCCAGGTTTATGGAGCGCCACACCTACTGAGATTATTTGTAAGAATCGGAGCAATGTTGGCC
TATACGCCCCTTGATGAGAAGAGCCTTGCATTATTGTTGGGCTATTTGCATGATTTCCTAAAATACCTGGCAAAGAATTC
TGCAGCCCTGTTTACTGCCAGTGATTACAAAGTGGCTTCAGCTGAGTACCATCGCAAAGCCCTGTGA

ORF - retro_lafr_62 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.66 %
Parental protein coverage: 75.23 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalQEQYAEGKMRGAAPGKKTSGLQQKNVEVKTKKNKQKTPGNGDGGSTSETPQPPRKKRARVDPTVENEETF
Q....E....G...G..........V..KT.KNKQKTPGNGDGGSTSE.PQPPRKKRAR.DPTVE.EE.F
RetrocopyQQKNLEPALPGRWGGRSAENPPSGSVR-KTRKNKQKTPGNGDGGSTSEAPQPPRKKRARADPTVESEEAF
ParentalMNRVEVKVKIPEELKPWLVDDWDLITRQKQLFYLPAKKNVDSILEDYANYKKSRGNTDNKEYAVNEVVAG
.NRVEVKVKIPEELKPWLV.DWDL.TRQKQLF.LPAKKNVD.ILE.YAN.K.S.GN.DNKEYAVNEVVAG
RetrocopyKNRVEVKVKIPEELKPWLVEDWDLVTRQKQLFQLPAKKNVDAILEEYANCKRSQGNVDNKEYAVNEVVAG
ParentalIKEYFNVMLGTQLLYKFERPQYAEILADHPDAPMSQVYGAPHLLRLFVRIGAMLAYTPLDEKSLALLLNY
IKEYFNVMLGTQLLYKFERPQYAEIL..HPDAPMSQVYGAPHLLRLFVRIGAMLAYTPLDEKSLALLL.Y
RetrocopyIKEYFNVMLGTQLLYKFERPQYAEILMAHPDAPMSQVYGAPHLLRLFVRIGAMLAYTPLDEKSLALLLGY
ParentalLHDFLKYLAKNSATLFSASDYEVAPPEYHRKAV
LHDFLKYLAKNSA.LF.ASDY.VA..EYHRKA.
RetrocopyLHDFLKYLAKNSAALFTASDYKVASAEYHRKAL

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_62 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 28 parental genes, and 72 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000123441 retrocopy
retro_amel_124,
Bos taurus ENSBTAG000000109881 retrocopy
retro_btau_137,
Canis familiaris ENSCAFG000000141131 retrocopy
retro_cfam_20,
Callithrix jacchus ENSCJAG000000022145 retrocopies
retro_cjac_2113, retro_cjac_2280, retro_cjac_2574, retro_cjac_3026, retro_cjac_3179,
Cavia porcellus ENSCPOG000000037783 retrocopies
retro_cpor_114, retro_cpor_1409, retro_cpor_915,
Equus caballus ENSECAG000000080911 retrocopy
retro_ecab_62,
Felis catus ENSFCAG000000121971 retrocopy
retro_fcat_75,
Homo sapiens ENSG000001857873 retrocopies
retro_hsap_309, retro_hsap_3125, retro_hsap_850,
Gorilla gorilla ENSGGOG000000168263 retrocopies
retro_ggor_125, retro_ggor_2141, retro_ggor_694,
Loxodonta africana ENSLAFG00000009851 1 retrocopy
retro_lafr_62 ,
Myotis lucifugus ENSMLUG000000017561 retrocopy
retro_mluc_324,
Macaca mulatta ENSMMUG000000229261 retrocopy
retro_mmul_1064,
Monodelphis domestica ENSMODG000000115172 retrocopies
retro_mdom_150, retro_mdom_158,
Mustela putorius furoENSMPUG000000154291 retrocopy
retro_mputfur_180,
Mus musculus ENSMUSG000000622709 retrocopies
retro_mmus_1454, retro_mmus_1697, retro_mmus_176, retro_mmus_1771, retro_mmus_1825, retro_mmus_1833, retro_mmus_2500, retro_mmus_2612, retro_mmus_289,
Nomascus leucogenys ENSNLEG000000086783 retrocopies
retro_nleu_417, retro_nleu_445, retro_nleu_51,
Oryctolagus cuniculus ENSOCUG000000151172 retrocopies
retro_ocun_108, retro_ocun_21,
Otolemur garnettii ENSOGAG000000060474 retrocopies
retro_ogar_1594, retro_ogar_2616, retro_ogar_2896, retro_ogar_50,
Pongo abelii ENSPPYG000000067034 retrocopies
retro_pabe_1046, retro_pabe_201, retro_pabe_2581, retro_pabe_695,
Pan troglodytes ENSPTRG000000073513 retrocopies
retro_ptro_2114, retro_ptro_47, retro_ptro_591,
Rattus norvegicus ENSRNOG000000144106 retrocopies
retro_rnor_1076, retro_rnor_2270, retro_rnor_2357, retro_rnor_374, retro_rnor_793, retro_rnor_980,
Sorex araneus ENSSARG000000045191 retrocopy
retro_sara_15,
Sarcophilus harrisii ENSSHAG000000184021 retrocopy
retro_shar_393,
Sus scrofa ENSSSCG000000017691 retrocopy
retro_sscr_93,
Ictidomys tridecemlineatus ENSSTOG000000132943 retrocopies
retro_itri_111, retro_itri_1545, retro_itri_1608,
Tupaia belangeri ENSTBEG000000018978 retrocopies
retro_tbel_1694, retro_tbel_1704, retro_tbel_4638, retro_tbel_518, retro_tbel_550, retro_tbel_69, retro_tbel_753, retro_tbel_76,
Tursiops truncatus ENSTTRG000000166061 retrocopy
retro_ttru_472,
Vicugna pacos ENSVPAG000000088471 retrocopy
retro_vpac_229,


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