RetrogeneDB ID:

retro_mdom_293

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:2:1755698..1756745(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMODG00000025430
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:SLC25A3
Ensembl ID:ENSMODG00000007717
Aliases:None
Description:solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 3 [Source:HGNC Symbol;Acc:10989]


Retrocopy-Parental alignment summary:






>retro_mdom_293
ACGGTCTCTGGACATCCCGCAGCCATGTCACCGTCATCGACCCCCCGAGGTCCGTGGACTGCGGTGTCGTCATCGCCATT
CCTGACATGGCAGAGGAGCCGGCGGCCAAGGGGGGATCGGGATAGTCCCGAGTACGGCTCGGCCAAGTACCTGGCACTGT
GCGGCTTGAGCGGTGGGATGAGCACCGGTCTCTCACATACTATGGTCCTGCCGCTGGACCTGATCAAATGCCGCCTGCAG
GTGGCGCCGACCAAATACCCGGGGCTGGTATCTGGCTTCAGCCTGGTGTCTCTCCAGGAAGGCATGCGTGGGATGACGCG
TGGCTGGGCACCCACACTGCTGGGCTTCTCCATGCAGGGTTTTGTCAAATTCAGCCTGTATGAAATGTTTAAACACCGCT
TGTCCCGCCGTCTAAGCGAGGAGGGATTCTATGTGTGGCGCACCGCTGTGTACATGCTAGCCGCGACTGGCGCTGGATTT
TTCGCCAGCTTAGTGCTCCTGCCCATGGATATCGTGAAGATGCGCATGCAGACGCAGCCGAACTTCCCCGGCATGCTGCG
CCAGGCGATGCCCAAGGTGTGGTCTCAGGAGGGTCCGATGGCCTTCTACCGGGGCCTGGGCCCGCTCTGGATGCGCCAGA
TGCCCTACACCGTAGTCAAGTTCGCGTGCTACGAGCGCACCTTGGAGATGCTCTACAAGTATGCCGTGGCCAAGCCCCAG
TGCCAGTGCAGCCTGCCCCAGCAGCTGGCCGTCACCTTTGTGGCAGGCTACGTTTCTGGCATCCTAGGTGCCATTGTCTC
ACACCCAGCTGACACTGCCATGACCATACTCAGCAAGGAGAACTACAAGAAAAATATGTTCGACATTCTGCAGCAGCTCG
GGCCCACCAGCGTGTGGAATGGGCTCTCAACGCGCATCCTCATGATCGGCACGCTTTCAGCGTTCCAGTGGTTCTTCTAC
AACGTATTCAAGGTCATGTATCGGCTGCCACGGCCCCCGCCCCCACAGATGCCGGAGTCCCTGCGCTGGAGGCTGGAGCA
GCAGCGG

ORF - retro_mdom_293 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 55.26 %
Parental protein coverage: 83.93 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalSCEYGSGRFFVLCGLGGIISCGTTHTAVVPLDLVKCRMQVDPQKYKGIFNGFSITLREDGVRGLARGWAP
S.EYGS.....LCGL.G..S.G..HT.V.PLDL.KCR.QV.P.KY.G...GFS......G.RG..RGWAP
RetrocopySPEYGSAKYLALCGLSGGMSTGLSHTMVLPLDLIKCRLQVAPTKYPGLVSGFSLVSLQEGMRGMTRGWAP
ParentalTFIGYSMQGLCKFGFYEAFKVLYSNILGEENSYLWRTSLYLAASASAEFFADIALAPMEAAKVRIQTQPG
T..G.SMQG..KF..YE.FK...S..L.EE..Y.WRT..Y..A...A.FFA...L.PM...K.R.QTQP.
RetrocopyTLLGFSMQGFVKFSLYEMFKHRLSRRLSEEGFYVWRTAVYMLAATGAGFFASLVLLPMDIVKMRMQTQPN
ParentalYANTLREAAPKMFKEEGLFAFYKGVAPLWMRQIPYTMMKFACFERTVEALYKYVVPKPRSECSKGEQLVV
....LR.A.PK....EG..AFY.G..PLWMRQ.PYT..KFAC.ERT.E.LYKY.V.KP...CS...QL.V
RetrocopyFPGMLRQAMPKVWSQEGPMAFYRGLGPLWMRQMPYTVVKFACYERTLEMLYKYAVAKPQCQCSLPQQLAV
ParentalTFVAGYIAGVFCAIVSHPADSVVSVLNKEK-GSSASQVLQRLGFRGVWKGLFARIIMIGTLTALQWFIYD
TFVAGY..G...AIVSHPAD.....L.KE.........LQ.LG...VW.GL..RI.MIGTL.A.QWF.Y.
RetrocopyTFVAGYVSGILGAIVSHPADTAMTILSKENYKKNMFDILQQLGPTSVWNGLSTRILMIGTLSAFQWFFYN
ParentalSVKVYFRLPRPPPPEMPESLKKKL
..KV..RLPRPPPP.MPESL...L
RetrocopyVFKVMYRLPRPPPPQMPESLRWRL

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 0 .00 RPM 0 .00 RPM
SRP007412_cerebellum 0 .00 RPM 0 .00 RPM
SRP007412_heart 0 .00 RPM 0 .00 RPM
SRP007412_kidney 0 .00 RPM 0 .00 RPM
SRP007412_liver 0 .00 RPM 0 .00 RPM
SRP007412_testis 0 .00 RPM 0 .00 RPM

ChIP-Seq - click to see more details

Monodelphis domestica was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_mdom_293 retrocopy.

TSS - click to see more details

Monodelphis domestica was not studied using FANTOM5 data.

Lab - click to see more details

retro_mdom_293 was not experimentally validated.

Retrocopy orthology:
Monodelphis domestica 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 ENSMODG00000007717 2 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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