RetrogeneDB ID:

retro_ptro_302

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:1:53887864..53888526(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:SLC25A3
Ensembl ID:ENSPTRG00000005333
Aliases:None
Description:phosphate carrier protein, mitochondrial [Source:RefSeq peptide;Acc:NP_001233352]


Retrocopy-Parental alignment summary:






>retro_ptro_302
GCGGCGGCTGTGGAGGAGGCCAGCGTGGAGTACGGCTCGGCCCGGTACCTGCTGCTGTGCGGCCTGGGCGGGATGCTGAG
CTGCGGCTGACACACACGGCCATCGTGTCCCTGCACCTGGTCAAGTGCCGCATGCAGGTGGACCCCGGCTGGTACAAGGG
CGTCCTCAGCGGCTTCGGCGTGACGATGCGCAGCGACGGGCTGTGCGGCCTGGCTCGCGGCTGCGCCCAGACCTTCTTCG
GCTACTCCCTGCAGGGCTTCTTCAAGTTCGGCCTTTACGAGGTCTTCAAGATCCGCTCCGCGGAGCTCCTGGGCCCAGAG
AAAGCCTACGGGTGGAGAGCCGGCCTGTACCTTTTCGCCTGGGCCAGCGCCGAGTTCTTCCCCGATGTCTCGCTGGCGCC
CATGGAGGCGGTCAAGGTCCGCGTGCAGACGCGACCGGGCTACGCCAGCACCCTGCGAGCCGCGGCGTCCAGGATGTAGG
GCGAGGAGGGCCTGTGGGCCTTCTACAAGGGCGTGGCGCCGCTGTGGCTGAGGTAGATCCGCTACACCATGATGAAGTTC
GCCTGCTTCGAGCGCACGGTAGAGGAGCTCTACAGGTATGCCGTGCCCAAGGCCCAGAGCCAGTGCACCAAGGCCAAGCA
GCTGGGCATCACCTTCGTGGCG

ORF - retro_ptro_302 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 65.92 %
Parental protein coverage: 61.33 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalAAAVEEQYSCDYGSGRFFILCGLGGIISCG-TTHTALVPLDLVKCRMQVDPQKYKGIFNGFSVTLKEDGV
AAAVEE..S..YGS.R...LCGLGG..SCG..THTA.V.L.LVKCRMQVDP..YKG...GF.VT...DG.
RetrocopyAAAVEEA-SVEYGSARYLLLCGLGGMLSCG<LTHTAIVSLHLVKCRMQVDPGWYKGVLSGFGVTMRSDGL
ParentalRGLAKGWAPTFLGYSMQGLCKFGFYEVFKVLYSNMLGEENTYLWRTSLYLAASASAEFFADIALAPMEAA
.GLA.G.A.TF.GYS.QG..KFG.YEVFK......LG.E..Y.WR..LYL.A.ASAEFF.D..LAPMEA.
RetrocopyCGLARGCAQTFFGYSLQGFFKFGLYEVFKIRSAELLGPEKAYGWRAGLYLFAWASAEFFPDVSLAPMEAV
ParentalKVRIQTQPGYANTLRDAAPKMYKEEGLKAFYKGVAPLWMRQIPYTMMKFACFERTVEALYKFVVPKPRSE
KVR.QT.PGYA.TLR.AA..M..EEGL.AFYKGVAPLW.R.I.YTMMKFACFERTVE.LY...VPK..S.
RetrocopyKVRVQTRPGYASTLRAAASRM*GEEGLWAFYKGVAPLWLR*IRYTMMKFACFERTVEELYRYAVPKAQSQ
ParentalCSKPEQLVVTFVA
C.K..QL..TFVA
RetrocopyCTKAKQLGITFVA

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
SRP007412_brain_prefrontal_cortex 0 .00 RPM 159 .67 RPM
SRP007412_cerebellum 0 .04 RPM 145 .22 RPM
SRP007412_heart 0 .00 RPM 651 .39 RPM
SRP007412_kidney 0 .00 RPM 301 .90 RPM
SRP007412_liver 0 .00 RPM 132 .61 RPM
SRP007412_testis 1 .48 RPM 45 .21 RPM

ChIP-Seq - click to see more details

Pan troglodytes was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ptro_302 retrocopy.

TSS - click to see more details

Pan troglodytes was not studied using FANTOM5 data.

Lab - click to see more details

retro_ptro_302 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_302 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_392
Gorilla gorilla retro_ggor_394
Equus caballus retro_ecab_481
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 ENSLACG000000070241 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 ENSPTRG00000005333 1 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,


Copyright © RetrogeneDB 2014-2017