RetrogeneDB ID:

retro_lafr_790

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_39:1368989..1370663(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:HSPA8
Ensembl ID:ENSLAFG00000030312
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lafr_790
ATGCCTAAGAGACCTGCAGTTGGCATTGATCTTGGCACCATCTACTCCCATGTGGGTGTCTTCCAGCTAGGGAAAGTGGA
GATAATTGCAAATGATCAGGGCAACCGAACCACCCCAAGCTATACCTCTTTTATTGATATTGAGTGATTGATCGGTGATG
CCAGAAAGAACCAAGTTGCGATGAATCCCACTAACACTGTTTTTGATGCCAAATGTCTGACTGGATAAAGATTTGATGAT
GCTGTTGTCCAGTCTGATATGAAGTATTGGCCCTTCATGGAGTAGAGTGATGCAGGCAGACCCAAGGTCCAAATAGAATA
TAAGGATAAGGGAGAGACCAAAAGTTTCTATCCAGAGGAGGTGTCATCTATGGTTCTGACGAAGATGAAGGAAATTGCAG
AAGCCTACCTTGGGAAGACTGTTGCCAATGCCATTGTCACTGTACCAGCCTACTGTAATGACTCTTTGTGTCAGGCTACC
AAAGATGCTGGAACCATTGCTGGCCTCAATGTACTCAGAATCATCAACAAGCCAACTGCTGCTTATGTCTCAGATAAAAA
AGTTGGTGTGAAAGACATGTGTTAATCTTTGACTTAGGAGGTGGCACTTTTGATGTGTAAATCCTCACCACGGAAGATGG
AATCTTTGAGGTCAAATCTATAGATGGAGGCACTCACTTAGGTGGAGAAGACTTTGGCAATCAAATTTTTATTGCCGAGT
TCAAGCACAAGCATAAGAAGGACATCAGCGAGAACAAGAGGGCTGTTCGTCGCCTCCACACTGCTTTTGAACGTGCAAAG
CACACTCTATCTTCCAGCACCCAGGCCAGTACTGAGATTGATTCTCTCTACGAAGGATCTACTTCTATTCATCCATCACC
CGTGCCCGTTTGAAGAATTGAATGGTGACCTGTTCCATGGCACCCTGAACCCTGTGGAGAAAGCCCTTAGGGATTCCAAG
CTAGATGAGTCATAAATCCATGACATTCTCCTGGTGGGTGGTTCTATCAGTATTCCCAAGATTCGAAACTTCTTCATGAT
TTCTTCAGTGGAAAAGAATTGAACAAGACCATCAGTGCTGATTGCTTATGGTGCAGCTATACAGGCAGCTATCTTATCTG
GAGACAAATCAAAATGTTCAGGATTTACTGCTCTTGACACTCCTCTTTCCCTTGGTATTGAAACTGCTGGTGGAGTCATG
ACTGTCCTCATCAAGTACAATACTACCATTCCTACCAAGGAGACACAGACCTTCACAACCTACTCTGAGAACAACCCTGG
AGTACTCATTCACGTTTGTGAAGGTGAGAGTGCCATGACCAAGGATAACAACCTACTTGGCAAGTTTGAACTCACTGGCA
TACCTCCTGCACTCTGTGGTGCGCCTCAGATTGAAGTCATTTTTGCTATTTATGCCAACGGCATCCTCAGTGTCTCAGCT
GAGGATAAGAGTACTGGAAAAGAGAACAAGATTGCCATCACTAATGACAAGGGCCGCTTGAGTAATGAAGACATTGAGCA
TATGGTCTAGGACACTGAGAAGTACGAAGCTGAAGATGAGAAACAGAGGGACAAGATGTCCTCTAAGAATTCACTTGAAT
CCTATGCATTTAACATGAAAGGAACAGTTGAAGATGAAAAACTTCAAGGCAAGACCAATGATGAGGACAAACAA

ORF - retro_lafr_790 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78.75 %
Parental protein coverage: 87.38 %
Number of stop codons detected: 7
Number of frameshifts detected: 3


Retrocopy - Parental Gene Alignment:

ParentalMSKGPAVGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQVAMNPTNTVFDA
M.K.PAVGIDLGT.YS.VGVFQ.GKVEIIANDQGNRTTPSY..F.D.E.LIGDA.KNQVAMNPTNTVFDA
RetrocopyMPKRPAVGIDLGTIYSHVGVFQLGKVEIIANDQGNRTTPSYTSFIDIE*LIGDARKNQVAMNPTNTVFDA
ParentalKRLIGRRFDDAVVQSDMKHWPFVVVNDAGRPKVQVEYK--GETKSFYPEEVSSMVLTKMKEIAEAYLGKT
K.L.G.RFDDAVVQSDMK.WPF....DAGRPKVQ.EYK..GETKSFYPEEVSSMVLTKMKEIAEAYLGKT
RetrocopyKCLTG*RFDDAVVQSDMKYWPFME*SDAGRPKVQIEYKDKGETKSFYPEEVSSMVLTKMKEIAEAYLGKT
ParentalVTNAVVTVPAYFNDSQRQATKDAGTIAGLNVLRIINEPTAAAIAYGLDKKVGA-ERNVLIFDLGGGTFDV
V.NA.VTVPAY.NDS..QATKDAGTIAGLNVLRIIN.PTA...AY..DKKVG..ER.VLIFDLGGGTFDV
RetrocopyVANAIVTVPAYCNDSLCQATKDAGTIAGLNVLRIINKPTA---AYVSDKKVGV<ERHVLIFDLGGGTFDV
ParentalSILTIEDGIFEVKSTAGDTHLGGEDFDNRMVNHFIAEFKRKHKKDISENKRAVRRLRTACERAKRTLSSS
.ILT.EDGIFEVKS..G.THLGGEDF.N.....FIAEFK.KHKKDISENKRAVRRL.TA.ERAK.TLSSS
Retrocopy*ILTTEDGIFEVKSIDGGTHLGGEDFGNQI---FIAEFKHKHKKDISENKRAVRRLHTAFERAKHTLSSS
ParentalTQASIEIDSLYEG-IDFYTSITRAR-FEELNADLFRGTLDPVEKALRDAKLDKSQIHDIVLVGGSTRIPK
TQAS.EIDSLYEG.I.FY.SITRAR.FEELN.DLF.GTL.PVEKALRD.KLD.S.IHDI.LVGGS..IPK
RetrocopyTQASTEIDSLYEG<IYFYSSITRAR<FEELNGDLFHGTLNPVEKALRDSKLDES*IHDILLVGGSISIPK
ParentalIQKLLQDFFNGKELNKS-INPDEAVAYGAAVQAAILSGDKSENVQDLLLLDVTPLSLGIETAGGVMTVLI
.......FF......K....P....AYGAA.QAAILSGDKS........LD.TPLSLGIETAGGVMTVLI
Retrocopy----IRNFFMISSVEKN*TRPSVLIAYGAAIQAAILSGDKSK-CSGFTALD-TPLSLGIETAGGVMTVLI
ParentalKRNTTIPTKQTQTFTTYSDNQPGVLIQVYEGERAMTKDNNLLGKFELTGIPPAPRGVPQIEVTFDIDANG
K.NTTIPTK.TQTFTTYS.N.PGVLI.V.EGE.AMTKDNNLLGKFELTGIPPA..G.PQIEV.F.I.ANG
RetrocopyKYNTTIPTKETQTFTTYSENNPGVLIHVCEGESAMTKDNNLLGKFELTGIPPALCGAPQIEVIFAIYANG
ParentalILNVSAVDKSTGKENKITITNDKGRLSKEDIERMVQEAEKYKAEDEKQRDKVSSKNSLESYAFNMKATVE
IL.VSA.DKSTGKENKI.ITNDKGRLS.EDIE.MV...EKY.AEDEKQRDK.SSKNSLESYAFNMK.TVE
RetrocopyILSVSAEDKSTGKENKIAITNDKGRLSNEDIEHMV*DTEKYEAEDEKQRDKMSSKNSLESYAFNMKGTVE
ParentalDEKLQGKISDEDKQ
DEKLQGK..DEDKQ
RetrocopyDEKLQGKTNDEDKQ

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_790 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 35 parental genes, and 119 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000048842 retrocopies
retro_acar_21, retro_acar_6,
Ailuropoda melanoleuca ENSAMEG000000084251 retrocopy
retro_amel_126,
Anas platyrhynchos ENSAPLG000000106671 retrocopy
retro_apla_6,
Bos taurus ENSBTAG000000131621 retrocopy
retro_btau_354,
Canis familiaris ENSCAFG000000116663 retrocopies
retro_cfam_140, retro_cfam_191, retro_cfam_509,
Ciona intestinalis ENSCING000000096651 retrocopy
retro_cint_12,
Callithrix jacchus ENSCJAG000000076485 retrocopies
retro_cjac_2388, retro_cjac_3306, retro_cjac_3898, retro_cjac_4057, retro_cjac_721,
Cavia porcellus ENSCPOG000000041693 retrocopies
retro_cpor_1072, retro_cpor_619, retro_cpor_938,
Ciona savignyi ENSCSAVG000000085881 retrocopy
retro_csav_3,
Dipodomys ordii ENSDORG000000154671 retrocopy
retro_dord_16,
Equus caballus ENSECAG000000135102 retrocopies
retro_ecab_291, retro_ecab_628,
Echinops telfairi ENSETEG000000109961 retrocopy
retro_etel_43,
Ficedula albicollis ENSFALG000000058121 retrocopy
retro_falb_18,
Felis catus ENSFCAG000000011326 retrocopies
retro_fcat_132, retro_fcat_1331, retro_fcat_1571, retro_fcat_1775, retro_fcat_556, retro_fcat_79,
Homo sapiens ENSG000001099718 retrocopies
retro_hsap_2384, retro_hsap_2710, retro_hsap_2758, retro_hsap_340, retro_hsap_3698, retro_hsap_4892, retro_hsap_4896, retro_hsap_68,
Gallus gallus ENSGALG000000065121 retrocopy
retro_ggal_8,
Gorilla gorilla ENSGGOG000000083818 retrocopies
retro_ggor_1053, retro_ggor_1810, retro_ggor_1888, retro_ggor_1918, retro_ggor_2501, retro_ggor_3054, retro_ggor_3057, retro_ggor_360,
Loxodonta africana ENSLAFG00000030312 4 retrocopies
retro_lafr_1218, retro_lafr_391, retro_lafr_790 , retro_lafr_797,
Meleagris gallopavo ENSMGAG000000019291 retrocopy
retro_mgal_9,
Myotis lucifugus ENSMLUG000000048343 retrocopies
retro_mluc_1800, retro_mluc_2300, retro_mluc_777,
Macaca mulatta ENSMMUG000000046967 retrocopies
retro_mmul_1536, retro_mmul_2188, retro_mmul_2628, retro_mmul_2632, retro_mmul_580, retro_mmul_778, retro_mmul_963,
Monodelphis domestica ENSMODG000000129582 retrocopies
retro_mdom_127, retro_mdom_99,
Mustela putorius furoENSMPUG000000058109 retrocopies
retro_mputfur_1048, retro_mputfur_1056, retro_mputfur_1144, retro_mputfur_131, retro_mputfur_188, retro_mputfur_309, retro_mputfur_627, retro_mputfur_694, retro_mputfur_958,
Mus musculus ENSMUSG000000156568 retrocopies
retro_mmus_2244, retro_mmus_2584, retro_mmus_26, retro_mmus_2621, retro_mmus_2840, retro_mmus_316, retro_mmus_351, retro_mmus_620,
Nomascus leucogenys ENSNLEG000000074198 retrocopies
retro_nleu_119, retro_nleu_1258, retro_nleu_1261, retro_nleu_1582, retro_nleu_175, retro_nleu_1781, retro_nleu_370, retro_nleu_64,
Oryctolagus cuniculus ENSOCUG000000155334 retrocopies
retro_ocun_1308, retro_ocun_53, retro_ocun_584, retro_ocun_753,
Oreochromis niloticus ENSONIG000000047591 retrocopy
retro_onil_2,
Pongo abelii ENSPPYG000000039879 retrocopies
retro_pabe_183, retro_pabe_2193, retro_pabe_2254, retro_pabe_2260, retro_pabe_2261, retro_pabe_3153, retro_pabe_355, retro_pabe_3804, retro_pabe_3808,
Pelodiscus sinensis ENSPSIG000000124502 retrocopies
retro_psin_17, retro_psin_5,
Pan troglodytes ENSPTRG000000044045 retrocopies
retro_ptro_1743, retro_ptro_2507, retro_ptro_272, retro_ptro_3259, retro_ptro_3264,
Ictidomys tridecemlineatus ENSSTOG000000037561 retrocopy
retro_itri_51,
Taeniopygia guttata ENSTGUG000000004911 retrocopy
retro_tgut_7,
Takifugu rubripes ENSTRUG000000052651 retrocopy
retro_trub_30,
Tursiops truncatus ENSTTRG000000111396 retrocopies
retro_ttru_1507, retro_ttru_1650, retro_ttru_1696, retro_ttru_35, retro_ttru_741, retro_ttru_808,
Xiphophorus maculatus ENSXMAG000000016021 retrocopy
retro_xmac_20,


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