RetrogeneDB ID:

retro_lafr_843

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_4:57544706..57545553(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSLAFG00000031759
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:ESD
Ensembl ID:ENSLAFG00000006901
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lafr_843
ATGGCATTGAAACAGATTTCCAGCAACAAATGCTTTGGGGGCTTGCAGAAAGTGTTTGAACATGACAGTGTTGAACTGAA
CTGCAAAATGAAATTTGCTATCTATTTACCCCCGAAGGCAGAAACTGGCAAATGCCCTGCACTCTATTGGTTGTCTGGCT
TAACTTGCACAGAACAAAATTTTATAGCAAAATCCGGTTACCATCAAGCAGCTTCAGAACATGGCCTTGTCGTCATTGCT
CCAGATACCAGCCCTCGTGGCTGCAACATTAAAGGGGAAGATGATAGCTGGGACTTTGGCACTGGCGCTGGGTTTTATGT
GGATACCACTGAAGATCCTTGGAAGACTAACTACAGAATGTACTCTTATGTAACTCAAGAGCTTCCCCAACTCATAAATG
GCAATTTTCCAGTGGACCCTCAAAGAATGTCTGTTTTTGGCCATTCCATGGGAGGTCATGGAGCGCTGATTTGTACTTTG
AAGAATCCTGGAAAATACAAATCAGTTTCAGCATTTGCTCCAATTTGCAACCCAGTGCTTTGTCCTTGGGGCAAAAAAAG
CCTTTAGTGGATATTTGGGATTGGATCCAGGTAAATGGAAGGCTTATGATGCCACCCATCTTGTGCAGTCCTATCCAGAC
TCTCAGCTGGACATACTGATTGATCAAGGGAAAGACAACCAGTTCCTTTCAGATGGACAGTTACTTCCTGATAACTTCAT
AGCTGCCTGTACAGAAAAGAAAATCCCCGTTGTTTTTAGATTGCAAGAAGGTTATGGTCATAGCTACTACTTCATTGCAA
CCTTTATTACTGACCACATCAGACATCATGCAAAATGCCTGAATGCA

ORF - retro_lafr_843 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 96.82 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMALKQISSNKCFGGLQKVFEHDSVELNCKMKFAIYLPPKAETGKCPALYWLSGLTCTEQNFISKSGYHQA
MALKQISSNKCFGGLQKVFEHDSVELNCKMKFAIYLPPKAETGKCPALYWLSGLTCTEQNFI.KSGYHQA
RetrocopyMALKQISSNKCFGGLQKVFEHDSVELNCKMKFAIYLPPKAETGKCPALYWLSGLTCTEQNFIAKSGYHQA
ParentalASEHGLVVIAPDTSPRGCNIKGEDDSWDFGTGAGFYVDATEDPWKTNYRMYSYVTQELPQLINANFPVDP
ASEHGLVVIAPDTSPRGCNIKGEDDSWDFGTGAGFYVD.TEDPWKTNYRMYSYVTQELPQLIN.NFPVDP
RetrocopyASEHGLVVIAPDTSPRGCNIKGEDDSWDFGTGAGFYVDTTEDPWKTNYRMYSYVTQELPQLINGNFPVDP
ParentalQRMSVFGHSMGGHGALICALKNPGKYKSVSAFAPICNPVLCPWG-KKAFSGYLGLDQGKWKAYDATHLVQ
QRMSVFGHSMGGHGALIC.LKNPGKYKSVSAFAPICNPVLCPWG.KKAFSGYLGLD.GKWKAYDATHLVQ
RetrocopyQRMSVFGHSMGGHGALICTLKNPGKYKSVSAFAPICNPVLCPWG>KKAFSGYLGLDPGKWKAYDATHLVQ
ParentalSYPDSQLDILIDQGKDDQFLSDGQLLPDNFIAACTEKKIPVVFRLQEGYDHSYYFIATFITDHIRHHAKY
SYPDSQLDILIDQGKD.QFLSDGQLLPDNFIAACTEKKIPVVFRLQEGY.HSYYFIATFITDHIRHHAK.
RetrocopySYPDSQLDILIDQGKDNQFLSDGQLLPDNFIAACTEKKIPVVFRLQEGYGHSYYFIATFITDHIRHHAKC
ParentalLNA
LNA
RetrocopyLNA

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_843 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 22 parental genes, and 52 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000133772 retrocopies
retro_amel_1085, retro_amel_1803,
Bos taurus ENSBTAG000000034151 retrocopy
retro_btau_908,
Canis familiaris ENSCAFG000000044732 retrocopies
retro_cfam_1381, retro_cfam_1762,
Callithrix jacchus ENSCJAG000000093802 retrocopies
retro_cjac_24, retro_cjac_257,
Cavia porcellus ENSCPOG000000110893 retrocopies
retro_cpor_1253, retro_cpor_1396, retro_cpor_568,
Dasypus novemcinctus ENSDNOG000000175532 retrocopies
retro_dnov_2502, retro_dnov_96,
Equus caballus ENSECAG000000243501 retrocopy
retro_ecab_808,
Felis catus ENSFCAG000000268262 retrocopies
retro_fcat_1641, retro_fcat_812,
Loxodonta africana ENSLAFG00000006901 1 retrocopy
retro_lafr_843 ,
Macaca mulatta ENSMMUG000000042091 retrocopy
retro_mmul_1013,
Monodelphis domestica ENSMODG000000112902 retrocopies
retro_mdom_1607, retro_mdom_1608,
Mustela putorius furoENSMPUG000000014942 retrocopies
retro_mputfur_1339, retro_mputfur_543,
Mus musculus ENSMUSG000000219969 retrocopies
retro_mmus_1159, retro_mmus_1160, retro_mmus_1161, retro_mmus_1162, retro_mmus_1163, retro_mmus_1166, retro_mmus_1168, retro_mmus_1236, retro_mmus_1237,
Oryctolagus cuniculus ENSOCUG000000099681 retrocopy
retro_ocun_709,
Otolemur garnettii ENSOGAG000000100481 retrocopy
retro_ogar_162,
Ochotona princeps ENSOPRG000000114612 retrocopies
retro_opri_230, retro_opri_845,
Procavia capensis ENSPCAG000000044021 retrocopy
retro_pcap_354,
Pteropus vampyrus ENSPVAG000000099103 retrocopies
retro_pvam_1309, retro_pvam_299, retro_pvam_87,
Rattus norvegicus ENSRNOG000000095122 retrocopies
retro_rnor_1053, retro_rnor_1593,
Sarcophilus harrisii ENSSHAG000000095813 retrocopies
retro_shar_307, retro_shar_337, retro_shar_570,
Ictidomys tridecemlineatus ENSSTOG000000028542 retrocopies
retro_itri_182, retro_itri_639,
Tupaia belangeri ENSTBEG000000051207 retrocopies
retro_tbel_1621, retro_tbel_1776, retro_tbel_2, retro_tbel_296, retro_tbel_3059, retro_tbel_3072, retro_tbel_3698,


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