RetrogeneDB ID:

retro_lafr_164

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_0:77115388..77115866(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSLAFG00000031595
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL29
Ensembl ID:ENSLAFG00000005757
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lafr_164
ATCACCAAGTCTAAGAACTGCACCACACACAGCCAGTCCTGAAAATGGCACAGAAATGACATCAAGAAACCCCAATCACA
ACAATATGAATCTCTTAAGGGGATGGACCCCAAGTTTCTTGTGGAACAAGCACTTTGCCAAGAAGCACGATAAAAATGGC
CTGAAGAAGATGCAGGCCAACAATGCCAAGGTCATAGATACACATGCTGAGGCTGTCAAAGCTCTCATAAAGCCCAAGGA
GGTCAAACCCAAGATCCCAAGGAGCATCAACCACAAGGTCAGTCGACTCACCTATACAGCCCATCCCAAGCTTGAGAAGA
GTGCTTGTGCCTGCGTTGCCAAGGGTCTCAAGCTCTACTGGCCAAAGTCCAAAGCCAAGCCTCAAAGGAAGGCCAAAGCT
CAAGCCAAGACTTGGACTGAGGTTCTGGCTCTGGATCAGCCTCCCAAAGGTGCCCAGGCCCCCACAAAGGCTCCAGAG

ORF - retro_lafr_164 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 66.25 %
Parental protein coverage: 96.95 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMAKSKNHTTHNQSRKWHRNGIKKPRSQRYESLKGVDPKFLR-NMRFAKKHNKKGLKKMQANNAKAMDART
..KSKN.TTH.QS.KWHRN.IKKP.SQ.YESLKG.DPKFL..N..FAKKH.K.GLKKMQANNAK..D...
RetrocopyITKSKNCTTHSQS*KWHRNDIKKPQSQQYESLKGMDPKFLV>NKHFAKKHDKNGLKKMQANNAKVIDTHA
ParentalEAIKTLLKPKQVKPKIPRGVNRKLSRLAYIAHPKLGKRARARIAKGLRLCRPKSKAKAQSKAEAPAQASI
EA.K.L.KPK.VKPKIPR..N.K.SRL.Y.AHPKL.K.A.A..AKGL.L..PKSKAK.Q.KA.A.A....
RetrocopyEAVKALIKPKEVKPKIPRSINHKVSRLTYTAHPKLEKSACACVAKGLKLYWPKSKAKPQRKAKAQAKTWT
ParentalQDPAPAQAPKGAQAPTKASD
...A..Q.PKGAQAPTKA..
RetrocopyEVLALDQPPKGAQAPTKAPE

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_164 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 162 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000091636 retrocopies
retro_amel_1373, retro_amel_1740, retro_amel_345, retro_amel_379, retro_amel_686, retro_amel_913,
Callithrix jacchus ENSCJAG000000059519 retrocopies
retro_cjac_135, retro_cjac_160, retro_cjac_241, retro_cjac_29, retro_cjac_331, retro_cjac_348, retro_cjac_358, retro_cjac_73, retro_cjac_96,
Felis catus ENSFCAG000000017629 retrocopies
retro_fcat_1032, retro_fcat_1132, retro_fcat_1753, retro_fcat_1774, retro_fcat_1897, retro_fcat_249, retro_fcat_485, retro_fcat_687, retro_fcat_952,
Gorilla gorilla ENSGGOG0000002469116 retrocopies
retro_ggor_1007, retro_ggor_1090, retro_ggor_1205, retro_ggor_1315, retro_ggor_1330, retro_ggor_142, retro_ggor_1480, retro_ggor_1929, retro_ggor_224, retro_ggor_2247, retro_ggor_254, retro_ggor_2684, retro_ggor_312, retro_ggor_715, retro_ggor_863, retro_ggor_892,
Loxodonta africana ENSLAFG00000005757 5 retrocopies
retro_lafr_164 , retro_lafr_184, retro_lafr_257, retro_lafr_461, retro_lafr_831,
Microcebus murinus ENSMICG000000027059 retrocopies
retro_mmur_192, retro_mmur_198, retro_mmur_303, retro_mmur_446, retro_mmur_508, retro_mmur_519, retro_mmur_657, retro_mmur_816, retro_mmur_938,
Myotis lucifugus ENSMLUG0000001508814 retrocopies
retro_mluc_1086, retro_mluc_1160, retro_mluc_134, retro_mluc_1377, retro_mluc_1699, retro_mluc_1955, retro_mluc_2228, retro_mluc_2522, retro_mluc_2523, retro_mluc_2575, retro_mluc_297, retro_mluc_421, retro_mluc_889, retro_mluc_915,
Macaca mulatta ENSMMUG000000192482 retrocopies
retro_mmul_1352, retro_mmul_218,
Monodelphis domestica ENSMODG0000002875017 retrocopies
retro_mdom_1013, retro_mdom_1187, retro_mdom_1201, retro_mdom_1328, retro_mdom_1445, retro_mdom_1452, retro_mdom_1505, retro_mdom_1532, retro_mdom_1604, retro_mdom_1665, retro_mdom_1904, retro_mdom_35, retro_mdom_504, retro_mdom_589, retro_mdom_612, retro_mdom_639, retro_mdom_995,
Mustela putorius furoENSMPUG000000117346 retrocopies
retro_mputfur_137, retro_mputfur_187, retro_mputfur_370, retro_mputfur_467, retro_mputfur_816, retro_mputfur_970,
Mus musculus ENSMUSG000000487583 retrocopies
retro_mmus_203, retro_mmus_231, retro_mmus_86,
Otolemur garnettii ENSOGAG000000137662 retrocopies
retro_ogar_290, retro_ogar_31,
Procavia capensis ENSPCAG000000097124 retrocopies
retro_pcap_100, retro_pcap_101, retro_pcap_44, retro_pcap_97,
Pongo abelii ENSPPYG0000001381821 retrocopies
retro_pabe_1062, retro_pabe_1162, retro_pabe_1306, retro_pabe_1503, retro_pabe_1714, retro_pabe_1882, retro_pabe_2125, retro_pabe_2131, retro_pabe_2398, retro_pabe_2718, retro_pabe_2952, retro_pabe_3254, retro_pabe_3284, retro_pabe_3504, retro_pabe_3525, retro_pabe_404, retro_pabe_459, retro_pabe_491, retro_pabe_673, retro_pabe_687, retro_pabe_911,
Rattus norvegicus ENSRNOG0000001113815 retrocopies
retro_rnor_1045, retro_rnor_1158, retro_rnor_1161, retro_rnor_1422, retro_rnor_1702, retro_rnor_184, retro_rnor_1951, retro_rnor_2207, retro_rnor_2222, retro_rnor_2356, retro_rnor_2561, retro_rnor_338, retro_rnor_397, retro_rnor_63, retro_rnor_928,
Sorex araneus ENSSARG000000135728 retrocopies
retro_sara_108, retro_sara_309, retro_sara_329, retro_sara_347, retro_sara_400, retro_sara_53, retro_sara_637, retro_sara_669,
Sarcophilus harrisii ENSSHAG000000068542 retrocopies
retro_shar_355, retro_shar_444,
Ictidomys tridecemlineatus ENSSTOG0000002048814 retrocopies
retro_itri_1345, retro_itri_1433, retro_itri_1482, retro_itri_1586, retro_itri_1664, retro_itri_1667, retro_itri_194, retro_itri_482, retro_itri_520, retro_itri_592, retro_itri_622, retro_itri_874, retro_itri_934, retro_itri_942,


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