RetrogeneDB ID:

retro_cfam_1840

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:7:20044203..20044916(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCAFG00000013797
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:YWHAZ
Ensembl ID:ENSCAFG00000000580
Aliases:None
Description:tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide [Source:HGNC Symbol;Acc:12855]


Retrocopy-Parental alignment summary:






>retro_cfam_1840
GATCGGGAGGATCTGGTGTACCAGGCGAAGCTGGCCGAGCAGGCTGAGCGATACGACGAAATGGTGGAATCAATGAAGAA
AGTAGCAGGGATGGATGTGGAGTTGACAGTTGAAGAAAGAAACCTCCTATCTGTTGCATATAAAAATGTGATTGGAGCCA
GAAGAGCTTCCTGGAGAATAATCAGCAGCGTTGAACAGAAAGAAGAAAACAAGGGAGAAGACAAACTAAAAATGATTCGG
GAATATCGGCAAATGGTTGAGACTGAGCTAAAGTTAATCTGTTGTGACATTCTGGATGTACTGGACAAACACCTCATTCC
AGCAGCTAACACTGGCGAGTCCAAGGTTTTCTATTATAAGATGAAAGGGGACTATCACAGGTATCTGGCTGAATTTGCCA
CAGGAAATGACAGGAAGGAGGCAGCAGAGAACAGCCTGGTGGCTTATAAAGCTGCTAGTGATATTGCAATGACAGAACTT
CCACCAACGCATCCAATTCGCTTAGGTCTTGCTCTCAACTTTTCTGTATTCTACTATGAAATTCTTAATTCCCCCAACCG
TGCCTGCAGGTTGCAAAAGCAGCTTTTGATGATGCAATTGCAGAACTGGATACGCTGAGTGAAGAAAGCTATAAGGACTC
TACACTTATCATGCAGTTGTTACATGATAATCTGACACTATGGACTTCAGACGTGCAGGGTGATGGTGAAGAG

ORF - retro_cfam_1840 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 67.78 %
Parental protein coverage: 96.73 %
Number of stop codons detected: 0
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalDKNELVQKAKLAEQAERYDDMAACMKSVTEQGAELSNEERNLLSVAYKNVVGARRSSWRVVSSIEQKTEG
D...LV..AKLAEQAERYD.M...MK.V.....EL..EERNLLSVAYKNV.GARR.SWR..SS.EQK.E.
RetrocopyDREDLVYQAKLAEQAERYDEMVESMKKVAGMDVELTVEERNLLSVAYKNVIGARRASWRIISSVEQKEEN
Parental-AEKKQQMAREYREKIETELRDICNDVLSLLEKFLIPNASQAESKVFYLKMKGDYYRYLAEVAAGDDKKG
..E.K..M.REYR...ETEL..IC.D.L..L.K.LIP.A...ESKVFY.KMKGDY.RYLAE.A.G.D.K.
RetrocopyKGEDKLKMIREYRQMVETELKLICCDILDVLDKHLIPAANTGESKVFYYKMKGDYHRYLAEFATGNDRKE
ParentalIVDQSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFYYEILNSPEKACSL-AKTAFDEAIAELDTLSEE
....S..AY..A..I...E..PTHPIRLGLALNFSVFYYEILNSP..AC.L.AK.AFD.AIAELDTLSEE
RetrocopyAAENSLVAYKAASDIAMTELPPTHPIRLGLALNFSVFYYEILNSPNRACRL<AKAAFDDAIAELDTLSEE
ParentalSYKDSTLIMQLLRDNLTLWTSDTQGDEAE
SYKDSTLIMQLL.DNLTLWTSD.QGD..E
RetrocopySYKDSTLIMQLLHDNLTLWTSDVQGDGEE

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 31 .92 RPM 101 .18 RPM
SRP017611_brain 16 .43 RPM 88 .44 RPM
SRP017611_kidney 16 .05 RPM 50 .85 RPM
SRP017611_liver 2 .97 RPM 4 .13 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_1840 retrocopy.

TSS - click to see more details

Canis familiaris was not studied using FANTOM5 data.

Lab - click to see more details

retro_cfam_1840 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_1840 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 34 parental genes, and 133 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000086942 retrocopies
retro_acar_25, retro_acar_44,
Ailuropoda melanoleuca ENSAMEG000000003281 retrocopy
retro_amel_562,
Bos taurus ENSBTAG000000002364 retrocopies
retro_btau_1482, retro_btau_635, retro_btau_68, retro_btau_910,
Canis familiaris ENSCAFG00000000580 6 retrocopies
retro_cfam_1302, retro_cfam_1521, retro_cfam_158, retro_cfam_1840 , retro_cfam_233, retro_cfam_465,
Choloepus hoffmanni ENSCHOG000000027989 retrocopies
retro_chof_1572, retro_chof_1703, retro_chof_1890, retro_chof_2321, retro_chof_2346, retro_chof_2669, retro_chof_292, retro_chof_315, retro_chof_933,
Callithrix jacchus ENSCJAG000000158445 retrocopies
retro_cjac_1769, retro_cjac_2164, retro_cjac_3000, retro_cjac_31, retro_cjac_881,
Cavia porcellus ENSCPOG000000202855 retrocopies
retro_cpor_220, retro_cpor_323, retro_cpor_434, retro_cpor_592, retro_cpor_644,
Dasypus novemcinctus ENSDNOG0000000167210 retrocopies
retro_dnov_1007, retro_dnov_117, retro_dnov_1354, retro_dnov_1579, retro_dnov_1769, retro_dnov_1907, retro_dnov_1993, retro_dnov_2588, retro_dnov_892, retro_dnov_99,
Equus caballus ENSECAG000000218823 retrocopies
retro_ecab_202, retro_ecab_31, retro_ecab_624,
Ficedula albicollis ENSFALG000000058601 retrocopy
retro_falb_13,
Felis catus ENSFCAG000000320174 retrocopies
retro_fcat_1563, retro_fcat_1631, retro_fcat_1697, retro_fcat_60,
Homo sapiens ENSG000001649241 retrocopy
retro_hsap_549,
Gallus gallus ENSGALG000000107251 retrocopy
retro_ggal_3,
Gorilla gorilla ENSGGOG000000221339 retrocopies
retro_ggor_1092, retro_ggor_1754, retro_ggor_211, retro_ggor_2379, retro_ggor_2997, retro_ggor_2998, retro_ggor_3020, retro_ggor_499, retro_ggor_544,
Loxodonta africana ENSLAFG000000049442 retrocopies
retro_lafr_1089, retro_lafr_112,
Myotis lucifugus ENSMLUG000000173233 retrocopies
retro_mluc_1617, retro_mluc_1686, retro_mluc_296,
Macaca mulatta ENSMMUG000000064897 retrocopies
retro_mmul_1859, retro_mmul_1883, retro_mmul_2136, retro_mmul_2247, retro_mmul_2422, retro_mmul_2503, retro_mmul_451,
Monodelphis domestica ENSMODG000000061588 retrocopies
retro_mdom_1589, retro_mdom_1664, retro_mdom_1763, retro_mdom_1815, retro_mdom_1875, retro_mdom_1958, retro_mdom_255, retro_mdom_446,
Mustela putorius furoENSMPUG000000151584 retrocopies
retro_mputfur_1000, retro_mputfur_239, retro_mputfur_7, retro_mputfur_864,
Mus musculus ENSMUSG000000222853 retrocopies
retro_mmus_163, retro_mmus_2187, retro_mmus_744,
Nomascus leucogenys ENSNLEG000000032207 retrocopies
retro_nleu_1368, retro_nleu_1426, retro_nleu_2186, retro_nleu_23, retro_nleu_449, retro_nleu_487, retro_nleu_722,
Oryctolagus cuniculus ENSOCUG000000007342 retrocopies
retro_ocun_1091, retro_ocun_248,
Ochotona princeps ENSOPRG000000002763 retrocopies
retro_opri_1218, retro_opri_218, retro_opri_967,
Procavia capensis ENSPCAG000000107441 retrocopy
retro_pcap_170,
Pongo abelii ENSPPYG000000187917 retrocopies
retro_pabe_103, retro_pabe_1242, retro_pabe_2047, retro_pabe_3417, retro_pabe_3740, retro_pabe_556, retro_pabe_89,
Pelodiscus sinensis ENSPSIG000000037031 retrocopy
retro_psin_13,
Pteropus vampyrus ENSPVAG000000166411 retrocopy
retro_pvam_1101,
Sarcophilus harrisii ENSSHAG000000126712 retrocopies
retro_shar_126, retro_shar_409,
Sus scrofa ENSSSCG000000060622 retrocopies
retro_sscr_222, retro_sscr_35,
Ictidomys tridecemlineatus ENSSTOG000000238643 retrocopies
retro_itri_162, retro_itri_483, retro_itri_887,
Taeniopygia guttata ENSTGUG000000120781 retrocopy
retro_tgut_4,
Tarsius syrichta ENSTSYG0000000615010 retrocopies
retro_tsyr_1047, retro_tsyr_1075, retro_tsyr_1419, retro_tsyr_1941, retro_tsyr_2022, retro_tsyr_2066, retro_tsyr_2085, retro_tsyr_720, retro_tsyr_900, retro_tsyr_985,
Tursiops truncatus ENSTTRG000000159064 retrocopies
retro_ttru_15, retro_ttru_1540, retro_ttru_207, retro_ttru_455,
Vicugna pacos ENSVPAG000000058651 retrocopy
retro_vpac_350,


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