RetrogeneDB ID:

retro_cfam_1322

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:3:1626646..1627342(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCAFG00000012109
Aliases:PRDX3, AOP1
Description:None


Retrocopy-Parental alignment summary:






>retro_cfam_1322
GCTTCTGCAGCCCTAGCCCTGCTGCTTTCCAAAGAACATGGCTGACAAATGTATTATGGTCTGGTTCCGGTCAAACAAAA
TTCACTTTTCGCACCAATTGCTCATACCATGCTCTTGCATCACCCAGCTCACACCCTATTGTAAGGGCATTGCCATTGTC
AACAGAGAGTTCAAAGACCTAAGCCTTGATGATTTTAAAATCACCAAATATTTGGTGCTTTTCTTCTGTCATTTGGACTT
CATCTTTGTGTGTCCTAACAAAAAATTGTTGTTTTACTGACAAAGCCCAATGAATTTCATGACATGAACTGTGAAGTTGT
TGCAATTTCAGTGCATCCCCTCTCCATCCATCTTGCCTAGATCAACACACCAAGGAAGAATGGTGGTTTGGGCCGCATGA
ACATTGTATTCTTGTCAGATTTGACTAAACAGATTTCCTGAGACTACAGTGGGCTGTTAGAAGGCCCAGGTAGTTGCTCT
CAGAGGACTTTTCATCATTGACCCCAGTGGAGGCATCAAGCACTTGAGTGTCAATGATCTCTCTCTCCTGGGCCACGGTG
TGGAAGAAACCCTCTGCTTGGTGAAGGTGTTCCAGTTTGTGGAAATCCACGGAGAAGTCTGCCCAGCAACCTGGATTCTC
CTACAATCATGCCACATCCAACTGCTTCCACAGAATACTTTGAGGCGGTTAATCAG

ORF - retro_cfam_1322 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 71.25 %
Parental protein coverage: 90.27 %
Number of stop codons detected: 2
Number of frameshifts detected 6


Retrocopy - Parental Gene Alignment:

ParentalASAALR-PAASRRTCLTNVLWSGSGQAKFAFSTSSSYHAPA-VTQHAPYFKGTAVVNGEFKDLTLDDFK-
ASAAL..PAA..RT.LTNVLWSGSGQ.KF.F.T..SYHA.A..TQ..PY.KG.A.VN.EFKDL.LDDFK.
RetrocopyASAALA<PAAFQRTWLTNVLWSGSGQTKFTFRTNCSYHALA<ITQLTPYCKGIAIVNREFKDLSLDDFKI
ParentalGRYLVLFFYPLDFTFVCP-TEIVAFSDKAK-EFHDVNCDVVAVSVDSHFTHLAWINTPRKNGGLGHMNIA
..YLVLFF..LDF.FVCP.T....F.DKA..EFHD.NC.VVA.SV.....HLA.INTPRKNGGLG.MNI.
RetrocopyTKYLVLFFCHLDFIFVCP>TKNCCFTDKAQ>EFHDMNCEVVAISVHPLSIHLA*INTPRKNGGLGRMNIV
ParentalLLSDLTKQISRDYGVLLEGPG-IALRGLFIIDPNGVIKHLSVNDLPV-GRSVEETLRLVKAFQFVETHGE
.LSDLTKQIS.DY..LLEGPG..ALRGLFIIDP.G.IKHLSVNDL...G..VEETL.LVK.FQFVE.HGE
RetrocopyFLSDLTKQIS*DYSGLLEGPG>VALRGLFIIDPSGGIKHLSVNDLSLLGHGVEETLCLVKVFQFVEIHGE
ParentalVC-PANWTPDSPTIKPHPTASKEYFEKVNQ
VC.P.N...DSPTI.PHPTAS.EYFE.VNQ
RetrocopyVC<PSNL--DSPTIMPHPTASTEYFEAVNQ

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 .21 RPM 24 .70 RPM
SRP017611_brain 0 .00 RPM 29 .93 RPM
SRP017611_kidney 0 .00 RPM 320 .41 RPM
SRP017611_liver 0 .00 RPM 80 .34 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_1322 retrocopy.

TSS - click to see more details

Canis familiaris was not studied using FANTOM5 data.

Lab - click to see more details

retro_cfam_1322 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_1322 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 25 parental genes, and 53 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000087311 retrocopy
retro_btau_562,
Canis familiaris ENSCAFG000000045675 retrocopies
retro_cfam_1313, retro_cfam_270, retro_cfam_577, retro_cfam_834, retro_cfam_988,
Canis familiaris ENSCAFG00000012109 3 retrocopies
retro_cfam_1322 , retro_cfam_219, retro_cfam_9,
Canis familiaris ENSCAFG000000171633 retrocopies
retro_cfam_1603, retro_cfam_1624, retro_cfam_1739,
Callithrix jacchus ENSCJAG000000196363 retrocopies
retro_cjac_1333, retro_cjac_3082, retro_cjac_653,
Ciona savignyi ENSCSAVG000000012091 retrocopy
retro_csav_6,
Dasypus novemcinctus ENSDNOG000000013593 retrocopies
retro_dnov_1052, retro_dnov_2373, retro_dnov_745,
Equus caballus ENSECAG000000170261 retrocopy
retro_ecab_408,
Erinaceus europaeus ENSEEUG000000092991 retrocopy
retro_eeur_238,
Homo sapiens ENSG000001656723 retrocopies
retro_hsap_1253, retro_hsap_2587, retro_hsap_2653,
Gorilla gorilla ENSGGOG000000263641 retrocopy
retro_ggor_986,
Macropus eugenii ENSMEUG000000077323 retrocopies
retro_meug_1219, retro_meug_1735, retro_meug_62,
Microcebus murinus ENSMICG000000076271 retrocopy
retro_mmur_475,
Myotis lucifugus ENSMLUG000000128713 retrocopies
retro_mluc_1203, retro_mluc_1522, retro_mluc_2069,
Macaca mulatta ENSMMUG000000082942 retrocopies
retro_mmul_1307, retro_mmul_1517,
Monodelphis domestica ENSMODG000000092861 retrocopy
retro_mdom_1062,
Mustela putorius furoENSMPUG000000030741 retrocopy
retro_mputfur_1032,
Mus musculus ENSMUSG000000249971 retrocopy
retro_mmus_2443,
Nomascus leucogenys ENSNLEG000000166983 retrocopies
retro_nleu_1521, retro_nleu_2118, retro_nleu_2453,
Oryctolagus cuniculus ENSOCUG000000173342 retrocopies
retro_ocun_135, retro_ocun_1434,
Pongo abelii ENSPPYG000000027001 retrocopy
retro_pabe_1906,
Pan troglodytes ENSPTRG000000029921 retrocopy
retro_ptro_29,
Ictidomys tridecemlineatus ENSSTOG000000025372 retrocopies
retro_itri_1098, retro_itri_1753,
Tupaia belangeri ENSTBEG000000110645 retrocopies
retro_tbel_3138, retro_tbel_3994, retro_tbel_710, retro_tbel_770, retro_tbel_811,
Tursiops truncatus ENSTTRG000000108782 retrocopies
retro_ttru_1703, retro_ttru_881,


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