RetrogeneDB ID:

retro_ocun_390

Retrocopy
location
Organism:Rabbit (Oryctolagus cuniculus)
Coordinates:1:134352297..134352763(-)
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:ENSOCUG00000011847
Aliases:None
Description:solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 3 [Source:HGNC Symbol;Acc:10989]


Retrocopy-Parental alignment summary:






>retro_ocun_390
AAGATTCAAATTCAAATCCAACCAGGTTATGCCAATACTTTAAGGGATGCAACTCCCAAAATGTATAAGGAAGAATGCCT
AAAAGCATTTTACAAGAGCATTGCTCCTCTCTGGATGAGAAAGGTACCATACGCCATGATGAAGGTTGTCTGCTTTGGAG
CTGTTGAAGCATTGTACAAGTTTGTGGTTCTTTAGTCCCGAAGGGAATGCACAAAGACAGAAAAGCTGGTTGTAATATTT
GCTACAGGTTACATAGCTGGAATCTTCTGTGCAATTGTTTCTCACCCTGCTGATTCTGTGGTGTCTGTGTTGAATAAAGA
GAAAAGTGGCAGTACTTCTGAGGTTCTCCAGAGACTTGGATTTAAGGAGTATGAGAGGGACTCTTTGCCTGTATCATCAT
GACTGGTACTCTGACTGTCCTACAGTTGTCGTTTATCACTCAGTAAAGGTCTACTACAGGCTCCCT

ORF - retro_ocun_390 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.58 %
Parental protein coverage: 50.16 %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalKVRIQTQPGYANTLRDAAPKMYKEEGLKAFYKGVAPLWMRQIPYTMMKFACFERTVEALYKFVVPKPRSE
K..IQ.QPGYANTLRDA.PKMYKEE.LKAFYK..APLWMR..PY.MMK..CF...VEALYKFVV...R.E
RetrocopyKIQIQIQPGYANTLRDATPKMYKEECLKAFYKSIAPLWMRKVPYAMMKVVCFG-AVEALYKFVVL*SRRE
ParentalCSKPEQLVVTFVAGYIAGVFCAIVSHPADSVVSVLNKEKGSSASQVLQRLGFK-GVWKGLFARIIMIGTL
C.K.E.LVV.F..GYIAG.FCAIVSHPADSVVSVLNKEK..S.S.VLQRLGFK.GV..GLFA.IIM.GTL
RetrocopyCTKTEKLVVIFATGYIAGIFCAIVSHPADSVVSVLNKEKSGSTSEVLQRLGFK<GV*EGLFACIIMTGTL
ParentalTALQW-FIYDSVKVYFRLP
T.LQ....Y.SVKVY.RLP
RetrocopyTVLQL<VVYHSVKVYYRLP

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
SRP017611_brain 0 .00 RPM 444 .38 RPM
SRP017611_kidney 0 .00 RPM 608 .14 RPM
SRP017611_liver 0 .00 RPM 139 .04 RPM

ChIP-Seq - click to see more details

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ocun_390 retrocopy.

TSS - click to see more details

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ocun_390 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ocun_390 has 0 orthologous retrocopies within eutheria group .

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 ENSOCUG00000011847 1 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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