RetrogeneDB ID:

retro_lcha_4

Retrocopy
location
Organism:Coelacanth (Latimeria chalumnae)
Coordinates:JH126591.1:1079149..1080232(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSLACG00000014695
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:SLC25A3
Ensembl ID:ENSLACG00000007024
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lcha_4
ATGTATCCCTCATTAGTTCAGCTCTTAAAGTGCAACCCATTTAACACACCGCGCTTCCAGCTTCACTGGCATGGCCAGGA
GCTGCAGGAGCAACCAAGGAATGCATCCGGCACGGTAGGGGGACCCAGGAATATGGCCACTGCTGCTTCCACGGAGTACA
GCTGTGAGTTTGGATCCAACAAGTACTTTGCTCTCTGCAGTTTAGGAGGCTTGGTGTGCTGCGGAGTGACCCACACCGCT
GTGGTGCCACTAGATCTAGTCAAGTGCCGCATTCAGGTGGACCCCACAAAGTACCAAAGCATCTTCTATGCTTTCAAGCT
CACCATCAAGGAAGAAGGGGCGATGGGACTGACCAAGGGCTGGGCACCCACTTTAATTGGCTATTCCATGCAAGGGTTTT
TCAAGTTCGGCCTTTATGAGTTCTTCAAGGTGAAGTACAGCAATCTACTGGGGGAGGAGAATGCCTACTTGTGGAGGACC
AGCTGCTACCTGGCTGCTTCAGCCAGTGCTGAATTCTTTGCTGACATAGCTCTGTCCCCCATGGAAGCGATGAAGGTCCG
CATCCAGACCCAGGAAGGTTTTGCCAACACCATGAGGGAGGCAGCCCCAAAGATGTATGCTGAGGAGGGGCTGCAGGCCT
TCTACAAGGGAGTGGTCCCACTCTGGATGCGTCAGATCCCCTACACGATGATGAAGTTCACCTCTTTTGAGCGTACGGTG
GAACTGCTGTACCATTATGTCGTACCAAGGCCTCGAAATGAGTGTTCGAAGCCTGAGCAGTTGGCCGTCACCTTTTTGGC
TGGCTATATTGCCGGCATTTTCTGCGCTGTGGTCTCCCACCCTGCCGACTCGGTGGTCTCCCTCCTTAACAAGGAGAAGG
GCAGTACTGCTCAGCAAGTGTTGGCTCGGTTGGGCCCGATGGGGGTCTGGAAGGGGCTTTTGCCCCGTACTTTCATGATT
GGCACCCTCACTGCCCTGCAGTGGTTCATCTATGATTTCATCAAAGTCACCTTAGGCATACCTCGTCCCCCGCCCCCCGA
GATGCCTGCGTCGCTGAAGCGGAAGCTGGAAGCTCACAAGTGA

ORF - retro_lcha_4 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 76.21 %
Parental protein coverage: 86.15 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalAVQETEDYSCEYGSTKFYALCGFGGILSCGTTHTAVVPLDLVKCRIQVDPAKYKSIFNGFSITIREDGFR
A......YSCE.GS.K..ALC..GG...CG.THTAVVPLDLVKCRIQVDP.KY.SIF..F..TI.E.G..
RetrocopyATAASTEYSCEFGSNKYFALCSLGGLVCCGVTHTAVVPLDLVKCRIQVDPTKYQSIFYAFKLTIKEEGAM
ParentalGLAKGWAPTFIGYSMQGLCKFGFYEVFKVLYGNMLGEENAYLWRTSLYLAASASAEFFADIALAPMEAAK
GL.KGWAPT.IGYSMQG..KFG.YE.FKV.Y.N.LGEENAYLWRTS.YLAASASAEFFADIAL.PMEA.K
RetrocopyGLTKGWAPTLIGYSMQGFFKFGLYEFFKVKYSNLLGEENAYLWRTSCYLAASASAEFFADIALSPMEAMK
ParentalVRIQTQPGYANTLREAVPKMYAEEGIWAFYKGVAPLWMRQIPYTMMKFACFERTVEALYRYVVPKPRSEC
VRIQTQ.G.ANT.REA.PKMYAEEG..AFYKGV.PLWMRQIPYTMMKF..FERTVE.LY.YVVP.PR.EC
RetrocopyVRIQTQEGFANTMREAAPKMYAEEGLQAFYKGVVPLWMRQIPYTMMKFTSFERTVELLYHYVVPRPRNEC
ParentalSKGEQLVVTFVAGYIAGVFCAIVSHPADSVVSVLNKEKGSSALQVLKRLGFKGVWKGLVARIIMIGTLTA
SK.EQL.VTF.AGYIAG.FCA.VSHPADSVVS.LNKEKGS.A.QVL.RLG..GVWKGL..R..MIGTLTA
RetrocopySKPEQLAVTFLAGYIAGIFCAVVSHPADSVVSLLNKEKGSTAQQVLARLGPMGVWKGLLPRTFMIGTLTA
ParentalLQWFIYDSVKVYFRLPRPPPPEMPESLKKKL
LQWFIYD..KV....PRPPPPEMP.SLK.KL
RetrocopyLQWFIYDFIKVTLGIPRPPPPEMPASLKRKL

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
DRP000627_gill 0 .00 RPM 105 .71 RPM
DRP000627_kidney 0 .00 RPM 146 .84 RPM
DRP000627_pectoral_fin 0 .00 RPM 99 .67 RPM
DRP000627_pelvic_fin 0 .00 RPM 105 .62 RPM
DRP000627_pharynx 0 .00 RPM 145 .88 RPM
DRP000627_tail_muscle 0 .00 RPM 122 .69 RPM

ChIP-Seq - click to see more details

Latimeria chalumnae was not studied using ChIP-Seq data.

EST - click to see more details

Latimeria chalumnae was not studied using EST data.

TSS - click to see more details

Latimeria chalumnae was not studied using FANTOM5 data.

Lab - click to see more details

retro_lcha_4 was not experimentally validated.

Retrocopy orthology:
Latimeria chalumnae 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 27 parental genes, and 32 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000132321 retrocopy
retro_acar_35,
Bos taurus ENSBTAG000000128901 retrocopy
retro_btau_172,
Canis familiaris ENSCAFG000000065451 retrocopy
retro_cfam_880,
Callithrix jacchus ENSCJAG000000023922 retrocopies
retro_cjac_3315, retro_cjac_812,
Dipodomys ordii ENSDORG000000114311 retrocopy
retro_dord_321,
Equus caballus ENSECAG000000151351 retrocopy
retro_ecab_481,
Echinops telfairi ENSETEG000000126781 retrocopy
retro_etel_1748,
Homo sapiens ENSG000000754151 retrocopy
retro_hsap_392,
Gorilla gorilla ENSGGOG000000158861 retrocopy
retro_ggor_394,
Latimeria chalumnae ENSLACG00000007024 1 retrocopy
retro_lcha_4 ,
Macropus eugenii ENSMEUG000000165932 retrocopies
retro_meug_405, retro_meug_658,
Microcebus murinus ENSMICG000000035201 retrocopy
retro_mmur_298,
Myotis lucifugus ENSMLUG000000083301 retrocopy
retro_mluc_1184,
Macaca mulatta ENSMMUG000000230361 retrocopy
retro_mmul_496,
Monodelphis domestica ENSMODG000000077172 retrocopies
retro_mdom_2026, retro_mdom_293,
Mus musculus ENSMUSG000000619041 retrocopy
retro_mmus_1959,
Nomascus leucogenys ENSNLEG000000059731 retrocopy
retro_nleu_2402,
Oryctolagus cuniculus ENSOCUG000000118471 retrocopy
retro_ocun_390,
Otolemur garnettii ENSOGAG000000122222 retrocopies
retro_ogar_1816, retro_ogar_2052,
Pongo abelii ENSPPYG000000048581 retrocopy
retro_pabe_1768,
Pan troglodytes ENSPTRG000000053331 retrocopy
retro_ptro_302,
Pteropus vampyrus ENSPVAG000000058901 retrocopy
retro_pvam_212,
Sorex araneus ENSSARG000000011491 retrocopy
retro_sara_262,
Ictidomys tridecemlineatus ENSSTOG000000276332 retrocopies
retro_itri_485, retro_itri_90,
Tupaia belangeri ENSTBEG000000145481 retrocopy
retro_tbel_1792,
Tursiops truncatus ENSTTRG000000047391 retrocopy
retro_ttru_692,
Vicugna pacos ENSVPAG000000047041 retrocopy
retro_vpac_455,


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