RetrogeneDB ID:

retro_lafr_602

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_24:20362791..20363561(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:ATP5F1
Ensembl ID:ENSLAFG00000004809
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lafr_602
ATGTTGTCATGGATGGTACTTTCTGCCGTCACCACAGCATTCCCCTCTCTGAAGAACGCAGCCCTTCTAGGTCCAGGGGT
ATTACAGGCAACAAAGATCTTTCACACAGGGCAGCCAAGTCTTGCACCTGTACCACCTCTTCCTGAACGTGGAGGAAAAG
TTCACTTTGGGCTGATCCCTGAGGAATTCTTCCAGTTACTTTATCCTAAAACTGGTGTCACAGGACCCTACATGCTTGGA
ACTGGGCTTATCTTATATTTCCTGTCCAAAAAAACTTATGTGATTACCCCCAGAAACCATCTCTCCCATATCAACAATAG
GGCTGCTCATCTACGGAATTAAAAAATATGGTGCTTCTGTTGGACAATTCGCTGATAAAATCAATGTGGAAAAAATTACC
AAACTAGAAGAGGTGAAGAAGACTTCCATCAAAAACATCCAAGATGCAACTGATTTTGAGAAGGCACAGCAGGCACTGGC
TCAGAAACTCCATTACCTTTTTAATGTTCAGAGGAATAATATTGCTATGGCTTTGGAGGTTACTTACCAGGAACGTCTGC
ACAGAATATACAAGGAGGTAAAAAATTTGGCTGCACTATCAGATCTCTGTGCAGAACCTGATGCATCAAAAGGAACAAGA
GCACATGATAAACAGGGTAGAGAACAGCGTGGTACAGAGTATCTCTACACAGCAGTAGACAGAGACAATTGCCAAGTGCA
TTGAAGATCTACAGCTGCTTGCAAAGAAGGCTCAGATACAGCCAGTTATG

ORF - retro_lafr_602 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 72.48 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMLSRVVLSAAATAASSLKNAAFIGPGVIQATRIFHTGQPSLAPVPPLPEYGGKVRFGLIPEEFFQLLYPK
MLS..VLSA..TA..SLKNAA..GPGV.QAT.IFHTGQPSLAPVPPLPE.GGKV.FGLIPEEFFQLLYPK
RetrocopyMLSWMVLSAVTTAFPSLKNAALLGPGVLQATKIFHTGQPSLAPVPPLPERGGKVHFGLIPEEFFQLLYPK
ParentalTGVTGPYVLGTGLILYFLSKEIYVIT-SETVSGAALAVLVIYAVKKYGAFIGQFADKLSEEKIARLEEFK
TGVTGPY.LGTGLILYFLSK..YVIT..ET.S......L.IY..KKYGA..GQFADK...EKI..LEE.K
RetrocopyTGVTGPYMLGTGLILYFLSKKTYVIT>PETISPISTIGLLIYGIKKYGASVGQFADKINVEKITKLEEVK
ParentalQSCIKYAEDGIDFEKEKQAVVQKRHYLFDVQRNNIAMAFEVAYRERLHTVYREVKNR-LDYHISVQNMMR
...IK...D..DFEK..QA..QK.HYLF.VQRNNIAMA.EV.Y.ERLH..Y.EVKN..L.Y.ISVQN.M.
RetrocopyKTSIKNIQDATDFEKAQQALAQKLHYLFNVQRNNIAMALEVTYQERLHRIYKEVKNL>LHYQISVQNLMH
ParentalRKEQEHMINWLEKKVVQSISAQQEKETIAKCIEDLKLLAKKAQAQPVM
.KEQEHMIN..E..VVQSIS.QQ..ETIAKCIEDL.LLAKKAQ.QPVM
RetrocopyQKEQEHMINRVENSVVQSISTQQ*TETIAKCIEDLQLLAKKAQIQPVM

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_602 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 26 parental genes, and 77 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000054331 retrocopy
retro_amel_1118,
Bos taurus ENSBTAG000000064411 retrocopy
retro_btau_745,
Callithrix jacchus ENSCJAG000000133539 retrocopies
retro_cjac_1943, retro_cjac_2270, retro_cjac_2482, retro_cjac_2747, retro_cjac_2815, retro_cjac_2854, retro_cjac_3067, retro_cjac_528, retro_cjac_833,
Cavia porcellus ENSCPOG000000140703 retrocopies
retro_cpor_1120, retro_cpor_448, retro_cpor_563,
Equus caballus ENSECAG000000185991 retrocopy
retro_ecab_494,
Echinops telfairi ENSETEG000000107133 retrocopies
retro_etel_105, retro_etel_1784, retro_etel_408,
Felis catus ENSFCAG000000283211 retrocopy
retro_fcat_1012,
Homo sapiens ENSG000001164596 retrocopies
retro_hsap_1705, retro_hsap_1951, retro_hsap_3673, retro_hsap_3762, retro_hsap_3812, retro_hsap_828,
Gorilla gorilla ENSGGOG000000052156 retrocopies
retro_ggor_1279, retro_ggor_1721, retro_ggor_2482, retro_ggor_2530, retro_ggor_2564, retro_ggor_678,
Loxodonta africana ENSLAFG00000004809 1 retrocopy
retro_lafr_602 ,
Microcebus murinus ENSMICG000000119921 retrocopy
retro_mmur_846,
Myotis lucifugus ENSMLUG000000124171 retrocopy
retro_mluc_2184,
Macaca mulatta ENSMMUG000000033133 retrocopies
retro_mmul_1086, retro_mmul_1659, retro_mmul_1791,
Mus musculus ENSMUSG000000005632 retrocopies
retro_mmus_2215, retro_mmus_791,
Nomascus leucogenys ENSNLEG000000039718 retrocopies
retro_nleu_172, retro_nleu_2090, retro_nleu_2153, retro_nleu_2154, retro_nleu_2546, retro_nleu_260, retro_nleu_524, retro_nleu_975,
Oryctolagus cuniculus ENSOCUG000000078091 retrocopy
retro_ocun_25,
Otolemur garnettii ENSOGAG000000114863 retrocopies
retro_ogar_2102, retro_ogar_2295, retro_ogar_2887,
Pongo abelii ENSPPYG000000010323 retrocopies
retro_pabe_2056, retro_pabe_3012, retro_pabe_3111,
Pan troglodytes ENSPTRG000000010995 retrocopies
retro_ptro_1154, retro_ptro_1305, retro_ptro_2553, retro_ptro_2586, retro_ptro_578,
Pteropus vampyrus ENSPVAG000000106043 retrocopies
retro_pvam_1061, retro_pvam_1110, retro_pvam_283,
Sorex araneus ENSSARG000000021073 retrocopies
retro_sara_424, retro_sara_428, retro_sara_610,
Sarcophilus harrisii ENSSHAG000000131851 retrocopy
retro_shar_700,
Ictidomys tridecemlineatus ENSSTOG000000076303 retrocopies
retro_itri_1146, retro_itri_1219, retro_itri_503,
Tarsius syrichta ENSTSYG000000004205 retrocopies
retro_tsyr_1226, retro_tsyr_1553, retro_tsyr_1852, retro_tsyr_502, retro_tsyr_511,
Tursiops truncatus ENSTTRG000000015461 retrocopy
retro_ttru_1654,
Vicugna pacos ENSVPAG000000002062 retrocopies
retro_vpac_154, retro_vpac_319,


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