RetrogeneDB ID:

retro_lafr_1103

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_7:83905976..83906855(+)
Located in intron of:ENSLAFG00000017608
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSLAFG00000004696
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lafr_1103
ATGGCAGATGACGCCGGTGCAGCGGGAGGGCCTGGAGGCCCCAGGGGCCTGGGGATGGAAACCCGTGGCGGTTTCCACGG
AGGCATTGGCAGTGGCCTGCGGGACCGGGGTCGTGGCCGGGGCTGGGGCTGAGGCCGGGGTCACGGAGCTCGCGGAGGCA
AAGCCGAAGATAAGGAATGGCTTCCAGTTACCAAGCTGGGCCACCTGGTCAAGGATATGAAGATCAAGTCCCTGGAGGAG
ATCTGTCGCTTCTCCCTGCCTATCAAGGAGTCTGAGATCATTGACTTCTTCTTGGGGGTGGCCCTAAAGGACGAGGTTTT
GAAAATTATGCCTGTGCAGAAGCAGACGCGTGCTGGCCAGCGGACCAGATTCAGGGCATTTGTTGCCATTGGGGACTACA
ACGGCCATGTTGGCCTAGGTGTGAAGTGTTCTAAGGAAGTGGCCACCGCCATCCGTGGGGCCATCATTCTGGCCAAGCTC
TCCATTGTCCCTGTGTGGCAAGGCTACTGGGGAAACAAGATCAGCAAGCCCCATACTGTTCCCTGCAAGGTGACTGGCTG
CTGTGGTTCTGTGCTGGTGCACCTCATCCCTGCACCCAGGGGCACTGGCATAGTCTCAGCCCCTGTGCCCAAGAAACTGT
TGATGATGGCTGGTATCAATGACTGCTACACCTCAGCCAGGGGCTGCACTGCCACCCTGGGCAACTTTGCTAAGGCCACT
TTTGATGCTATCTCCAAGACCTACAGCTATTTCACCCCTGATCTCTAGAAGGAGACTGTGTTCACCAAGTCTCCCTACCA
GGAATTTACTGACCACCTGGTAAAGACTCACACCAGAGTCTCCGTGCAGAGAACCTAAGCTCCAGCTGTGGCCACCTCA

ORF - retro_lafr_1103 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.05 %
Parental protein coverage: 100. %
Number of stop codons detected: 2
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMADDAGAAGGPAGPGGPGMGTRGGFRGGFGSGLRGRGRGRGRGRGRGRGARGGKAEDKEWLPVTKLGRLV
MADDAGAAGGP.GP.G.GM.TRGGF.GG.GSGL...............GARGGKAEDKEWLPVTKLG.LV
RetrocopyMADDAGAAGGPGGPRGLGMETRGGFHGGIGSGLXXXXXXXXXXXXXXHGARGGKAEDKEWLPVTKLGHLV
ParentalKDMKIKSLEEIYLFSLPIKESEIIDFFLGMALKDEVLKIMPVQKQTRAGQRTRFKAFVAIGDYNGHVGLG
KDMKIKSLEEI..FSLPIKESEIIDFFLG.ALKDEVLKIMPVQKQTRAGQRTRF.AFVAIGDYNGHVGLG
RetrocopyKDMKIKSLEEICRFSLPIKESEIIDFFLGVALKDEVLKIMPVQKQTRAGQRTRFRAFVAIGDYNGHVGLG
ParentalVKCSKEVATAIRGAIILAKLSIVPVRRGYWGNKIGKPHTVPCKVTGRCGSVLVRLIPAPRGTGIVSAPVP
VKCSKEVATAIRGAIILAKLSIVPV..GYWGNKI.KPHTVPCKVTG.CGSVLV.LIPAPRGTGIVSAPVP
RetrocopyVKCSKEVATAIRGAIILAKLSIVPVWQGYWGNKISKPHTVPCKVTGCCGSVLVHLIPAPRGTGIVSAPVP
ParentalKKLLMMAGIDDCYTSARGCTATLGNFAKATFDAISKTYSYLTPDLWKETVFTKSPYQEFTDHLVKTHTRV
KKLLMMAGI.DCYTSARGCTATLGNFAKATFDAISKTYSY.TPDL.KETVFTKSPYQEFTDHLVKTHTRV
RetrocopyKKLLMMAGINDCYTSARGCTATLGNFAKATFDAISKTYSYFTPDL*KETVFTKSPYQEFTDHLVKTHTRV
ParentalSVQRTQAPAVATS
SVQRT.APAVATS
RetrocopySVQRT*APAVATS

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_1103 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 15 parental genes, and 102 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000025491 retrocopy
retro_acar_57,
Bos taurus ENSBTAG000000095357 retrocopies
retro_btau_1236, retro_btau_1420, retro_btau_1656, retro_btau_317, retro_btau_590, retro_btau_661, retro_btau_956,
Canis familiaris ENSCAFG0000001947219 retrocopies
retro_cfam_1028, retro_cfam_1252, retro_cfam_1321, retro_cfam_1460, retro_cfam_1560, retro_cfam_1592, retro_cfam_1842, retro_cfam_1848, retro_cfam_1932, retro_cfam_1983, retro_cfam_2007, retro_cfam_2012, retro_cfam_2046, retro_cfam_2053, retro_cfam_2110, retro_cfam_271, retro_cfam_323, retro_cfam_490, retro_cfam_629,
Cavia porcellus ENSCPOG0000001165111 retrocopies
retro_cpor_1030, retro_cpor_1238, retro_cpor_1376, retro_cpor_1469, retro_cpor_1527, retro_cpor_177, retro_cpor_19, retro_cpor_437, retro_cpor_718, retro_cpor_769, retro_cpor_808,
Loxodonta africana ENSLAFG00000004696 11 retrocopies
retro_lafr_1072, retro_lafr_1092, retro_lafr_1103 , retro_lafr_174, retro_lafr_284, retro_lafr_327, retro_lafr_376, retro_lafr_75, retro_lafr_801, retro_lafr_812, retro_lafr_917,
Macropus eugenii ENSMEUG000000045082 retrocopies
retro_meug_156, retro_meug_2103,
Myotis lucifugus ENSMLUG000000116601 retrocopy
retro_mluc_76,
Monodelphis domestica ENSMODG000000160771 retrocopy
retro_mdom_536,
Mustela putorius furoENSMPUG0000001554711 retrocopies
retro_mputfur_1100, retro_mputfur_1209, retro_mputfur_1212, retro_mputfur_1214, retro_mputfur_1391, retro_mputfur_1497, retro_mputfur_1566, retro_mputfur_369, retro_mputfur_540, retro_mputfur_624, retro_mputfur_931,
Mus musculus ENSMUSG000000445331 retrocopy
retro_mmus_148,
Procavia capensis ENSPCAG000000020902 retrocopies
retro_pcap_251, retro_pcap_433,
Rattus norvegicus ENSRNOG0000001417912 retrocopies
retro_rnor_1882, retro_rnor_2191, retro_rnor_2257, retro_rnor_2274, retro_rnor_2903, retro_rnor_438, retro_rnor_631, retro_rnor_681, retro_rnor_690, retro_rnor_809, retro_rnor_810, retro_rnor_878,
Sarcophilus harrisii ENSSHAG000000152135 retrocopies
retro_shar_186, retro_shar_288, retro_shar_456, retro_shar_525, retro_shar_783,
Tursiops truncatus ENSTTRG0000001139312 retrocopies
retro_ttru_1341, retro_ttru_1346, retro_ttru_1414, retro_ttru_149, retro_ttru_1762, retro_ttru_1816, retro_ttru_37, retro_ttru_375, retro_ttru_419, retro_ttru_650, retro_ttru_719, retro_ttru_872,
Vicugna pacos ENSVPAG000000068676 retrocopies
retro_vpac_114, retro_vpac_164, retro_vpac_220, retro_vpac_354, retro_vpac_379, retro_vpac_518,


Copyright © RetrogeneDB 2014-2017