RetrogeneDB ID:

retro_lafr_157

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_0:39626701..39627565(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL6
Ensembl ID:ENSLAFG00000002201
Aliases:None
Description:60S ribosomal protein L6 [Source:UniProtKB/TrEMBL;Acc:G3SQ07]


Retrocopy-Parental alignment summary:






>retro_lafr_157
ATGGCAGGTGAAAAGCCTGAGAAGCTGGACACTAAGGAGAATAAGCCTGAAGTCAAGAAAGCAGATGCCAGTGGCAAGGC
TAAGAATGGTAACCTCAAGGGCAAAAAGTCCAAGAAGGGGAAGCCCCACTACAGCCGAAATTCCATCCTAGTCAGAGGAA
CTGGCAGATATTCCTGGTCAGCCATGTATTCCAGAAAGGCCATGTACAAGAGGAAGTATTCAGCAGCTAAATCCAGGGTT
GAAAAGAAGAAGAAGGAGAAGGTTCTTGCTTCTGTCATGAAACCAGTTGGTGGTGACAAGAATGGTAGTACCTGAGTGGT
TAAACTTCGCAAAATGCCTAGGTATTACCCTACTGAAGATGTGCCTCGGAAGCTCTTGAGCCACGGCAAAAAACCCTTCA
GTCAGTATGTGAGAAAGCTGCAATCTAGCATCACTCCTGGGACCGTTCTGATCATCCTCACTTGGTGCCGCAGAGGCAAG
AGAGTGATTTTCCAGAAGCAGTTGGACAGTGGCTTGCTACTTGTGATGGGACCTCTGTCCCTCAATCAAGTTCCTCTGCG
TAGAACACACCAGAAATTTGTCATTGCCACCTCCACCGAAATTGGTATCAGTGGTGTGAAAATTCCAAAACATCTCATGG
ACACTTACTTTAAGAAGAAGAAGCTGCGTAAGCCCAGGCACCAAGAAGGCAAGATCTTCGACACAGAGAAAGAGAAATAC
GAGATTACAGAGCAGCGTAAGGTTGATCAGAAAGCTGTAGACTCACAAATTATGCCAAAAATCAAAGCCATTCCCCAGCT
CCAAGGCTACCTGTGTTCTTTGTTTGCTCTCACAAATGGAATGTATCCTCACAAGTTGGTGTTC

ORF - retro_lafr_157 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.62 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMASEKAEKPDTKENKPEVKKADASGKAKDGNLKGKKPKKGKPHCSRNPVLVRGIGRYSRSAMYSRKAMYK
MA.EK.EK.DTKENKPEVKKADASGKAK.GNLKGKK.KKGKPH.SRN..LVRG.GRYS.SAMYSRKAMYK
RetrocopyMAGEKPEKLDTKENKPEVKKADASGKAKNGNLKGKKSKKGKPHYSRNSILVRGTGRYSWSAMYSRKAMYK
ParentalRKYSAAKSRVEKKKKEKVLATVTKPVGGDKNGGTRVVKLRKMPRYYPTEDVPRKLLSHGKKPFSQHVRKL
RKYSAAKSRVEKKKKEKVLA.V.KPVGGDKNG.T.VVKLRKMPRYYPTEDVPRKLLSHGKKPFSQ.VRKL
RetrocopyRKYSAAKSRVEKKKKEKVLASVMKPVGGDKNGST*VVKLRKMPRYYPTEDVPRKLLSHGKKPFSQYVRKL
ParentalRSSITPGTVLIILTGRHRGKRVIFLKQLDSGLLLVTGPLSLNRVPLRRTHQKFVIATSTKIDISGVKIPK
.SSITPGTVLIILT...RGKRVIF.KQLDSGLLLV.GPLSLN.VPLRRTHQKFVIATST.I.ISGVKIPK
RetrocopyQSSITPGTVLIILTWCRRGKRVIFQKQLDSGLLLVMGPLSLNQVPLRRTHQKFVIATSTEIGISGVKIPK
ParentalHLTDTYFKKKKLRKPRHQEGEIFDTEKEKYEITEQRKVDQKAVDSQIMPKIKAIPQLQGYLRSLFALTNG
HL.DTYFKKKKLRKPRHQEG.IFDTEKEKYEITEQRKVDQKAVDSQIMPKIKAIPQLQGYL.SLFALTNG
RetrocopyHLMDTYFKKKKLRKPRHQEGKIFDTEKEKYEITEQRKVDQKAVDSQIMPKIKAIPQLQGYLCSLFALTNG
ParentalMYPHKLVF
MYPHKLVF
RetrocopyMYPHKLVF

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_157 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 21 parental genes, and 123 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000030601 retrocopy
retro_acar_171,
Bos taurus ENSBTAG000000317236 retrocopies
retro_btau_1038, retro_btau_1117, retro_btau_1305, retro_btau_16, retro_btau_424, retro_btau_809,
Canis familiaris ENSCAFG000000088731 retrocopy
retro_cfam_36,
Choloepus hoffmanni ENSCHOG0000000291713 retrocopies
retro_chof_1152, retro_chof_1285, retro_chof_1334, retro_chof_1688, retro_chof_2127, retro_chof_2151, retro_chof_2164, retro_chof_321, retro_chof_421, retro_chof_532, retro_chof_587, retro_chof_930, retro_chof_976,
Callithrix jacchus ENSCJAG000000124507 retrocopies
retro_cjac_1362, retro_cjac_1620, retro_cjac_1949, retro_cjac_2723, retro_cjac_328, retro_cjac_349, retro_cjac_497,
Cavia porcellus ENSCPOG000000135268 retrocopies
retro_cpor_1105, retro_cpor_1149, retro_cpor_1486, retro_cpor_382, retro_cpor_412, retro_cpor_651, retro_cpor_731, retro_cpor_982,
Dasypus novemcinctus ENSDNOG000000170323 retrocopies
retro_dnov_1370, retro_dnov_1910, retro_dnov_2098,
Equus caballus ENSECAG000000175141 retrocopy
retro_ecab_811,
Felis catus ENSFCAG0000000685812 retrocopies
retro_fcat_1264, retro_fcat_1370, retro_fcat_1844, retro_fcat_232, retro_fcat_398, retro_fcat_500, retro_fcat_625, retro_fcat_637, retro_fcat_643, retro_fcat_690, retro_fcat_926, retro_fcat_935,
Gorilla gorilla ENSGGOG0000000337216 retrocopies
retro_ggor_1602, retro_ggor_1893, retro_ggor_1898, retro_ggor_2047, retro_ggor_2138, retro_ggor_236, retro_ggor_2569, retro_ggor_2597, retro_ggor_2709, retro_ggor_2745, retro_ggor_290, retro_ggor_2938, retro_ggor_356, retro_ggor_426, retro_ggor_566, retro_ggor_816,
Loxodonta africana ENSLAFG00000002201 2 retrocopies
retro_lafr_157 , retro_lafr_683,
Macaca mulatta ENSMMUG000000074331 retrocopy
retro_mmul_171,
Monodelphis domestica ENSMODG000000030964 retrocopies
retro_mdom_1556, retro_mdom_1624, retro_mdom_1784, retro_mdom_615,
Mustela putorius furoENSMPUG000000025269 retrocopies
retro_mputfur_1116, retro_mputfur_1279, retro_mputfur_1320, retro_mputfur_1367, retro_mputfur_1407, retro_mputfur_1445, retro_mputfur_1489, retro_mputfur_401, retro_mputfur_571,
Mus musculus ENSMUSG0000002961413 retrocopies
retro_mmus_1264, retro_mmus_1336, retro_mmus_1898, retro_mmus_2684, retro_mmus_276, retro_mmus_3065, retro_mmus_3579, retro_mmus_3611, retro_mmus_3622, retro_mmus_3719, retro_mmus_445, retro_mmus_465, retro_mmus_730,
Nomascus leucogenys ENSNLEG000000270932 retrocopies
retro_nleu_1813, retro_nleu_43,
Oryctolagus cuniculus ENSOCUG000000038025 retrocopies
retro_ocun_129, retro_ocun_17, retro_ocun_189, retro_ocun_229, retro_ocun_245,
Pongo abelii ENSPPYG0000002585513 retrocopies
retro_pabe_1764, retro_pabe_1891, retro_pabe_2451, retro_pabe_2493, retro_pabe_2573, retro_pabe_2897, retro_pabe_3314, retro_pabe_358, retro_pabe_3677, retro_pabe_3725, retro_pabe_43, retro_pabe_472, retro_pabe_868,
Rattus norvegicus ENSRNOG000000259361 retrocopy
retro_rnor_129,
Sarcophilus harrisii ENSSHAG000000070962 retrocopies
retro_shar_506, retro_shar_536,
Ictidomys tridecemlineatus ENSSTOG000000094093 retrocopies
retro_itri_1024, retro_itri_1125, retro_itri_684,


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