RetrogeneDB ID:

retro_fcat_1608

Retrocopy
location
Organism:Cat (Felis catus)
Coordinates:D4:7028412..7029048(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:HPRT1
Ensembl ID:ENSFCAG00000004575
Aliases:None
Description:Hypoxanthine phosphoribosyltransferase 1 [Source:UniProtKB/TrEMBL;Acc:Q001C4]


Retrocopy-Parental alignment summary:






>retro_fcat_1608
CCCCAGCGTCTGGTTAGTGATGATGAACCAGGTTATGGCCTAGATTTATTTTGTATACCTCATCATTACGCTGAGGATTT
GGAAAAGGCATTTATTCCTCATGGACTAATTATGGACAGGACCTAGCGTCTTGCCTGAGACGTGTTGAAGATGGGTGGCC
ATCACATGGTAGCCCTCTGTGTGCTCAAGGGGGGCTATAAATTCTTCGCGGACCTCCTGGATTACATCAAAGCACTGAAC
AGAAATAGTGATGGATCCATTCCCATGACTGTAGATTTCATCAGACTGAAGAGCTACTGTAATGACCAGTCAACAGGGAA
CATAAAAGAAACTGGTGGAGATGATCTCTCCACTTTAACTGGAAAGAATGTCTTGATTGTTGAGGATATAATTGACACTG
GCAAAACAATGCAAACCTTGCTCTCCATGGTCAAGCAGCATAATCCAAAGATGGTCAAGGTTGCAAGGCTGCTGGTGAAG
AGGACCCCTCGAAGTGTTGGCTATAAACCAGACTTGGTCAGATTTGAAATCCCAGACAAGTTTGTCGTAGGATATGCCCT
TGCCTACAATGAATACTTCAGTGACTTGAATCATGTTTGCGTCATTAGTGAAACCGGAAAAGTAAAATACAAAGCC

ORF - retro_fcat_1608 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.08 %
Parental protein coverage: 99.53 %
Number of stop codons detected: 2
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalPTLRISDDEPGYDLDLFCIPHHYAEDLEKVFIPHGLIMDRTERLARDVLKEMGGHHIVALCVLKGGYKFF
P....SDDEPGY.LDLFCIPHHYAEDLEK.FIPHGLIMDRT.RLA.DVLK.MGGHH.VALCVLKGGYKFF
RetrocopyPQRLVSDDEPGYGLDLFCIPHHYAEDLEKAFIPHGLIMDRT*RLA*DVLK-MGGHHMVALCVLKGGYKFF
ParentalADLLDYIKALNRNSDGSIPMTVDFIRLKSYCNDQSTGDIKVIGGDDLSTLTGKNVLIVEDIIDTGKTMQT
ADLLDYIKALNRNSDGSIPMTVDFIRLKSYCNDQSTG.IK..GGDDLSTLTGKNVLIVEDIIDTGKTMQT
RetrocopyADLLDYIKALNRNSDGSIPMTVDFIRLKSYCNDQSTGNIKETGGDDLSTLTGKNVLIVEDIIDTGKTMQT
ParentalLLSMVKQHNPKMVKVASLLVKRTPRSVGYKPDFVGFEIPDKFVVGYALDYNEYFRDLNHVCVISETGKAK
LLSMVKQHNPKMVKVA.LLVKRTPRSVGYKPD.V.FEIPDKFVVGYAL.YNEYF.DLNHVCVISETGK.K
RetrocopyLLSMVKQHNPKMVKVARLLVKRTPRSVGYKPDLVRFEIPDKFVVGYALAYNEYFSDLNHVCVISETGKVK
ParentalYKA
YKA
RetrocopyYKA

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 1 .03 RPM 57 .85 RPM
SRP017611_kidney 0 .52 RPM 22 .88 RPM
SRP017611_liver 0 .30 RPM 12 .33 RPM

ChIP-Seq - click to see more details

Felis catus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_fcat_1608 retrocopy.

TSS - click to see more details

Felis catus was not studied using FANTOM5 data.

Lab - click to see more details

retro_fcat_1608 was not experimentally validated.

Retrocopy orthology:
Felis catus 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 25 parental genes, and 54 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000013391 retrocopy
retro_amel_129,
Bos taurus ENSBTAG000000146853 retrocopies
retro_btau_162, retro_btau_179, retro_btau_721,
Canis familiaris ENSCAFG000000188701 retrocopy
retro_cfam_2014,
Cavia porcellus ENSCPOG000000025121 retrocopy
retro_cpor_1299,
Dasypus novemcinctus ENSDNOG000000084955 retrocopies
retro_dnov_1480, retro_dnov_1908, retro_dnov_2057, retro_dnov_255, retro_dnov_763,
Equus caballus ENSECAG000000175341 retrocopy
retro_ecab_734,
Felis catus ENSFCAG00000004575 2 retrocopies
retro_fcat_104, retro_fcat_1608 ,
Homo sapiens ENSG000001657041 retrocopy
retro_hsap_917,
Gorilla gorilla ENSGGOG000000080501 retrocopy
retro_ggor_740,
Loxodonta africana ENSLAFG000000098922 retrocopies
retro_lafr_1042, retro_lafr_475,
Microcebus murinus ENSMICG000000065471 retrocopy
retro_mmur_1186,
Myotis lucifugus ENSMLUG000000035911 retrocopy
retro_mluc_2107,
Macaca mulatta ENSMMUG000000083031 retrocopy
retro_mmul_1118,
Mustela putorius furoENSMPUG000000126993 retrocopies
retro_mputfur_1317, retro_mputfur_1638, retro_mputfur_836,
Oryctolagus cuniculus ENSOCUG000000031861 retrocopy
retro_ocun_1082,
Otolemur garnettii ENSOGAG000000038813 retrocopies
retro_ogar_1886, retro_ogar_3298, retro_ogar_3463,
Pongo abelii ENSPPYG000000207332 retrocopies
retro_pabe_3601, retro_pabe_791,
Pan troglodytes ENSPTRG000000222872 retrocopies
retro_ptro_2042, retro_ptro_636,
Rattus norvegicus ENSRNOG000000313672 retrocopies
retro_rnor_1208, retro_rnor_2491,
Sorex araneus ENSSARG000000080451 retrocopy
retro_sara_288,
Sarcophilus harrisii ENSSHAG000000079653 retrocopies
retro_shar_470, retro_shar_513, retro_shar_661,
Tupaia belangeri ENSTBEG000000008595 retrocopies
retro_tbel_1607, retro_tbel_2234, retro_tbel_3627, retro_tbel_4320, retro_tbel_729,
Tarsius syrichta ENSTSYG000000095791 retrocopy
retro_tsyr_2050,
Tursiops truncatus ENSTTRG000000099549 retrocopies
retro_ttru_1007, retro_ttru_1272, retro_ttru_1523, retro_ttru_1598, retro_ttru_1620, retro_ttru_276, retro_ttru_641, retro_ttru_732, retro_ttru_829,
Vicugna pacos ENSVPAG000000091331 retrocopy
retro_vpac_122,


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