RetrogeneDB ID:

retro_itri_90

Retrocopy
location
Organism:Squirrel (Ictidomys tridecemlineatus)
Coordinates:JH393332.1:7625643..7626624(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSSTOG00000020556
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:SLC25A3
Ensembl ID:ENSSTOG00000027633
Aliases:None
Description:solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 3 [Source:HGNC Symbol;Acc:10989]


Retrocopy-Parental alignment summary:






>retro_itri_90
GGTTCCCGAGCCCCGCAGGCGAGTAGTGCGGGCCAGGGTTGGGGCAGGCCATGGGCGGCGGCGTCGCCCGAGGAGTACAG
CTTCGAATACGGCTCCCCGCGGTACCTGCTGCTGTGCGGTCTGGGCGGGATGCTGAGCTGCGGGCTGACGCACATGGCCA
TCGTGCCCCTGGACCTGGTCAAGTGCCGCATGCAGGTGGACCCCGACAAGTACAAGGGCATCTTCAGCGGCTTCGGCGTG
ACAGTGCGCGAGGAGGGGCTGCGCGGCCTGGCTCGTGGCTGGGCCCCGACCTTCATAGGCTACTCCCTGCAGGGCTTCTT
CAAGTTCGGCCTCTACGAGGTCTTCAAGATTCACTACAAGAAGCTCCTGGGCGAGGAGAAGGCCTATACGTGGAGGACCA
CCTTGTATCTGGCCGCCTCGGCCAGCGCCGAGTTCTTCGCCGACGTGGCCCTGGCGCCCATGGAGGCGGTCAAGGTCCGC
GTGCAGACGCAGCCAGACTACGCCCGCACCCTGCGTGAAGCCGTCCCCAAGATGTATGCCGAGGAGGGCCTGTGGGCCTT
CTACAAGGGCCTGGCGCCGCTGTGGATGCGGCAGATCCCCTACACCATGATGAAGTTCGCCTGCTTCGAGCGCACGGTGG
AGGCGCTCTACAAGTACGTGGTGCCCAAGCCGCAGTGCGAGTGCACCAAGGCCGAGCAGCTTGGTGTCACTTTTGTGGCG
GGCTACATCGCCGGCGTCTTCTGCGCGATCGTGTCCCACCCCGCCGATTCCGTGGTGTCGGTGCTGAACAAGGAGAAGGG
CAGCACGGCCCTGGAGGTGCTCCGCAGACTGGGGCCCCTGGGCGTGTGGAAGGGCCTATTCGCTCGCATCATCATGATCG
GCACCCTGACGGCCCTGCAGTGGTTCATCTACGACTCGGTCAAAGTGTATCTCAATCTGCCGCGCCCTCCCATTGCCGAA
GAGCCTGCATCCCTGAAGAAG

ORF - retro_itri_90 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.58 %
Parental protein coverage: 85.36 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalAAAVEEQYSCDYGSGRFFILCGLGGIISCGTTHTALVPLDLVKCRMQVDPQKYKGIFNGFSVTLKEDGVR
AAA..E.YS..YGS.R...LCGLGG..SCG.TH.A.VPLDLVKCRMQVDP.KYKGIF.GF.VT..E.G.R
RetrocopyAAASPEEYSFEYGSPRYLLLCGLGGMLSCGLTHMAIVPLDLVKCRMQVDPDKYKGIFSGFGVTVREEGLR
ParentalGLAKGWAPTFIGYSMQGLCKFGFYEVFKVLYSNMLGEENAYLWRTSLYLAASASAEFFADIALAPMEATK
GLA.GWAPTFIGYS.QG..KFG.YEVFK..Y...LGEE.AY.WRT.LYLAASASAEFFAD.ALAPMEA.K
RetrocopyGLARGWAPTFIGYSLQGFFKFGLYEVFKIHYKKLLGEEKAYTWRTTLYLAASASAEFFADVALAPMEAVK
ParentalVRIQTQPGYANTLRDAAPKMYKEEGLKAFYKGVAPLWMRQIPYTMMKFACFERTVEALYKFVVPKPRSEC
VR.QTQP.YA.TLR.A.PKMY.EEGL.AFYKG.APLWMRQIPYTMMKFACFERTVEALYK.VVPKP..EC
RetrocopyVRVQTQPDYARTLREAVPKMYAEEGLWAFYKGLAPLWMRQIPYTMMKFACFERTVEALYKYVVPKPQCEC
ParentalTKAEQLVVTFVAGYIAGVFCAIVSHPADSVVSVLNKEKGSSASQVLQRLGFKGVWKGLFARIIMIGTLTA
TKAEQL.VTFVAGYIAGVFCAIVSHPADSVVSVLNKEKGS.A..VL.RLG..GVWKGLFARIIMIGTLTA
RetrocopyTKAEQLGVTFVAGYIAGVFCAIVSHPADSVVSVLNKEKGSTALEVLRRLGPLGVWKGLFARIIMIGTLTA
ParentalLQWFIYDSVKVYFRLPRPPPPEMPESLKK
LQWFIYDSVKVY..LPRPP..E.P.SLKK
RetrocopyLQWFIYDSVKVYLNLPRPPIAEEPASLKK

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






RNA-Seq - click to see more details

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_itri_90 retrocopy.

TSS - click to see more details

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_itri_90 was not experimentally validated.

Retrocopy orthology:
Ictidomys tridecemlineatus 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 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 ENSPTRG000000053331 retrocopy
retro_ptro_302,
Pteropus vampyrus ENSPVAG000000058901 retrocopy
retro_pvam_212,
Sorex araneus ENSSARG000000011491 retrocopy
retro_sara_262,
Ictidomys tridecemlineatus ENSSTOG00000027633 2 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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