RetrogeneDB ID:

retro_cfam_269

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:1:75517487..75518113(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PSAT1
Ensembl ID:ENSCAFG00000001570
Aliases:None
Description:phosphoserine aminotransferase 1 [Source:HGNC Symbol;Acc:19129]


Retrocopy-Parental alignment summary:






>retro_cfam_269
TTTACTAAAATTATTAACACAGAGAATCTTGTGCAGAAATTGTCAGCTGTTCCAGACAACCACAAGGTGATTTTTGTGCA
GAGAGGTATGTCAAGGCCAATTCCCTGCTGGTCCTCTTAAACCTGATTGGCCTGAAAGCAAGAAGGTATGCTACATACAA
GATGACAGGAGCTTAGTTAGCTGAGGCAGCAGAAGCCTAGAACTTTGGGAAGTGAATATTGTCTACCCTAAACTTGGGAG
TTATGCAAGAATTCCAATCCAAGCCCTTGGAACCTCAGCCCAGATACCTCCTCTGTGCATTCTGCACTGACAAGACCATG
CATAAAGTGGAGTTTGCCTTTATCTCTGACGTAAGAGACCAGTGGTGGTTTGCTGCCTGCCCTCAAGCTTCCTATCCAAG
CCAATGGATGTTTCCTAGTTTGGTGTGATTTTTGCTGGTGCTCAGAAGAATGCTGGCTCTGCAGGGACCACATTGGTGAT
CACTGGGGATGACCTCCTGGGGTTTGCCTTCAGAGTATTCCTTGGTCCTGGAATACAAAGTACAGGCCCCAAACCACTCC
TCATATGACACACCTCTGAGTTTCAGCATCTGTGACATGGGCTTGGTCCTGAAGTAGATTAAGAAC

ORF - retro_cfam_269 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 63.18 %
Parental protein coverage: 51.58 %
Number of stop codons detected: 4
Number of frameshifts detected 8


Retrocopy - Parental Gene Alignment:

ParentalFAKIINNAENLVRELLAVPDNYKVIFVQGGGS-GQFSAVPL-NLISRKAGRCADYVVTGSWSAKAAEEAK
F.KIIN..ENLV..L.AVPDN.KVIFVQ.G.S.GQF.A.PL.NLI..KA.R.A.Y..TG...A.AAE.A.
RetrocopyFTKIINT-ENLVQKLSAVPDNHKVIFVQRGMS>GQFPAGPL>NLIGLKARRYATYKMTGA*LAEAAE-A*
ParentalKFGT-VNVVHPKLGSYTKIP-DPSTWNLSPDASYVY-YCANETVHGVEFDFIPDV-KGAVLVCDMSSNFL
.FG..VN.V.PKLGSY..IP..PS.WNLSPD.S.V...C...T.H.VEF.FI.DV.K..V.VC...S.FL
RetrocopyNFGK<VNIVYPKLGSYARIP<NPSPWNLSPDTSSVH<FCTDKTMHKVEFAFISDV<KRPVVVCCLPSSFL
ParentalSKPVDVSKFGVIFAGAQKNVGSAGVTIVIIRDDLL-GFALRECP-SVLEYKVQAGNSSLYNTPPCFSIYV
SKP.DVS.FGVIFAGAQKN.GSAG.T.VI..DDLL.G..L...P..VLEYKVQA.N.S.Y.TP..FSI..
RetrocopySKPMDVS*FGVIFAGAQKNAGSAGTTLVITGDDLL<GVCLQSIP<LVLEYKVQAPNHSSYDTPLSFSICD
ParentalMGLVLEWIKN
MGLVL..IKN
RetrocopyMGLVLK*IKN

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
SRP012049_cerebellum 0 .00 RPM 89 .25 RPM
SRP017611_brain 0 .00 RPM 42 .87 RPM
SRP017611_kidney 0 .00 RPM 49 .00 RPM
SRP017611_liver 0 .00 RPM 2 .83 RPM

ChIP-Seq - click to see more details

Canis familiaris was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_cfam_269 retrocopy.

TSS - click to see more details

Canis familiaris was not studied using FANTOM5 data.

Lab - click to see more details

retro_cfam_269 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_269 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 18 parental genes, and 28 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000068981 retrocopy
retro_amel_375,
Bos taurus ENSBTAG000000139601 retrocopy
retro_btau_1658,
Canis familiaris ENSCAFG00000001570 1 retrocopy
retro_cfam_269 ,
Choloepus hoffmanni ENSCHOG000000038171 retrocopy
retro_chof_2702,
Callithrix jacchus ENSCJAG000000033191 retrocopy
retro_cjac_1203,
Echinops telfairi ENSETEG000000041581 retrocopy
retro_etel_99,
Homo sapiens ENSG000001350693 retrocopies
retro_hsap_2267, retro_hsap_4054, retro_hsap_412,
Gorilla gorilla ENSGGOG000000154801 retrocopy
retro_ggor_407,
Loxodonta africana ENSLAFG000000179172 retrocopies
retro_lafr_1249, retro_lafr_660,
Macaca mulatta ENSMMUG000000118682 retrocopies
retro_mmul_1029, retro_mmul_2341,
Mustela putorius furoENSMPUG000000125661 retrocopy
retro_mputfur_808,
Nomascus leucogenys ENSNLEG000000029893 retrocopies
retro_nleu_1010, retro_nleu_1288, retro_nleu_2805,
Oryctolagus cuniculus ENSOCUG000000077651 retrocopy
retro_ocun_1092,
Pongo abelii ENSPPYG000000193133 retrocopies
retro_pabe_1950, retro_pabe_308, retro_pabe_3328,
Pan troglodytes ENSPTRG000000210452 retrocopies
retro_ptro_1606, retro_ptro_316,
Rattus norvegicus ENSRNOG000000139711 retrocopy
retro_rnor_1663,
Tupaia belangeri ENSTBEG000000129461 retrocopy
retro_tbel_1577,
Tarsius syrichta ENSTSYG000000000932 retrocopies
retro_tsyr_1073, retro_tsyr_1212,


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