RetrogeneDB ID:

retro_fcat_147

Retrocopy
location
Organism:Cat (Felis catus)
Coordinates:A1:23834186..23835594(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSFCAG00000026862
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:NONO
Ensembl ID:ENSFCAG00000014807
Aliases:None
Description:non-POU domain containing, octamer-binding [Source:HGNC Symbol;Acc:7871]


Retrocopy-Parental alignment summary:






>retro_fcat_147
AGGGGTGCAAAAATGCAGAGCAATAAAACCTTTAACTTGGAGAAGCAAAACCATACTCCAAGGAAGCATCATCAGCATCA
CCACCAGCAGCACCACCAACAGCAACAGCCACCACCGCCACCAATACCTGCAAATGGGCAACAAGCCAGCAGCCAAAATG
AAGGCTTGACTATTGACCTCAAGAATTTTAGGAAACCAGGAGAGAAGACCTTCACCCAACGTAGCCGGCTCTTTGTGGGC
AATCTTCCTCCTGACATCACTGAGGAGGAGATGAGGAAACTATTTGAGAAATACGGGAAGGCAGGCAAAGTCTTCATTCA
TAAGGATAAGGGCTTTGGCTTTATCCGCTTGGAAACGCGAACCTTAGCAGAGATTGCCAAAGTAGAGCTGGACAACAAGC
CACTTCGTGGAAAGCAGCTGCGGTGCGCTTTGCCTGCCATAGTGCATCGCTCACAGTCCGAAACCTTCCTCAGTATGTTT
CTAACGAACTGCTGGAGGAAGCTTTTTCTCTGTTTGGCCAAGTGGAAACAGCTGTAGTCATCATGGATGATAGAGAAAGG
CCCGCAGGAAAAGGCATTGTTGAATTCTCAGGGAAGCCAGCTGCTCGGAAAGCTCTGGACAGGTGCAGTGAAGACTCCTT
CCTGTTAACCACATTTCCTCGGCCTGTGACTGTGGAGCCCATGGACCAGTTGGATGATGAAGAGGGACTTCGAGAGAAGC
TGGTTATAAAGAACCAGCAATTTCATAAGGAGCGAGAACAGCCACCCAGATTTGCACAGCCTGGCTCCTTTGAGTATGAG
TATGCCATGCGCTGGAAGGCACTCATTGAGATGGAGAAGCAGCAGCAGGACCAAGTGGACTGCAACATCAAGGAAGCTTG
TGAGAAGCTGGAGATGGAGGCTGCTCGCCATGAGCACCAAGTCATGTTAATGAGACAGAATTTGATGAGGCATCAAGAAG
AACTCCGGAGGATGGAAGAGCTGCACAACCAAGAAGTGCAAAAACGAAAGCAACTGGAGCTCAGGCAGGAGGAAGAGAGT
GCAGGCGCCGTGAAGAAGAGATGTGGCAGCAACAGGAAGAAGTGATGCGGCGACAGCAGGAAGGATTCAAGGGAACATTC
CCTGATGCGAGAGAACAGGAAATACGGATGGGCCAGATGGCCATGGGAGGTGCTATGGGCATAAACAACAGAGGCGCCAT
GCCCCCTGCTCCAGTGCCAGCTGGTACCCCAGCTCCCCCAGGACCTGCCACTATGATGCCAGATGGAACCTTGGTATTGA
CCCCACCAACTGAACGCTTTGGCCAGGCTGCTACCATGGAAGGAATTGGGGCCATTGGTGGAACCCCTCCTGCGTTCAAC
CGTGCAGCTCCTGGAGCTGAATTTGCTCCAAACAAACGTCGCCGATAC

ORF - retro_fcat_147 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91. %
Parental protein coverage: 90.82 %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalKGAKMQSNKTFNLEKQNHTPRKHHQHHHQQHHQQQQQQPPPPPIPANGQQASSQNEGLTIDLKNFRKPGE
.GAKMQSNKTFNLEKQNHTPRKHHQHHHQQHHQQQQ..PPPPPIPANGQQASSQNEGLTIDLKNFRKPGE
RetrocopyRGAKMQSNKTFNLEKQNHTPRKHHQHHHQQHHQQQQ--PPPPPIPANGQQASSQNEGLTIDLKNFRKPGE
ParentalKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPLRGK
KTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAG.VFIHKDKGFGFIRLETRTLAEIAKVELDN.PLRGK
RetrocopyKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGKVFIHKDKGFGFIRLETRTLAEIAKVELDNKPLRGK
ParentalQLR-VRFACHSASLTVRNLPQYVSNELLEEAFSVFGQVERAVVIVDDRGRPSGKGIVEFSGKPAARKALD
QLR.VRFACHSASLTVRNLPQYVSNELLEEAFS.FGQVE.AVVI.DDR.RP.GKGIVEFSGKPAARKALD
RetrocopyQLR<VRFACHSASLTVRNLPQYVSNELLEEAFSLFGQVETAVVIMDDRERPAGKGIVEFSGKPAARKALD
ParentalRCSEGSFLLTTFPRPVTVEPMDQLDDEEGLPEKLVIKNQQFHKEREQPPRFAQPGSFEYEYAMRWKALIE
RCSE.SFLLTTFPRPVTVEPMDQLDDEEGL.EKLVIKNQQFHKEREQPPRFAQPGSFEYEYAMRWKALIE
RetrocopyRCSEDSFLLTTFPRPVTVEPMDQLDDEEGLREKLVIKNQQFHKEREQPPRFAQPGSFEYEYAMRWKALIE
ParentalMEKQQQDQVDRNIKEAREKLEMEMEAARHEHQVMLMRQDLMRRQEELRRMEELHNQEVQKRKQLELRQ-E
MEKQQQDQVD.NIKEA.EKLEME..AARHEHQVMLMRQ.LMR.QEELRRMEELHNQEVQKRKQLELRQ.E
RetrocopyMEKQQQDQVDCNIKEACEKLEME--AARHEHQVMLMRQNLMRHQEELRRMEELHNQEVQKRKQLELRQEE
ParentalE-ERRRREEEMRRQQEEMMRRQQEGFKGTFPDAREQEIRMGQMAMGGAMGINNRGAMPPAPVPAGTPAPP
E.E.RRR..................FKGTFPDAREQEIRMGQMAMGGAMGINNRGAMPPAPVPAGTPAPP
RetrocopyE<ECRRRXXXXXXXXXXXXXXXXXXFKGTFPDAREQEIRMGQMAMGGAMGINNRGAMPPAPVPAGTPAPP
ParentalGPATMMPDGTLGLKTPPTTERFGQAATMEGIGAIGGTPPAFNRAAPGAEFAPNKRRRY
GPATMMPDGTL.L.TPP.TERFGQAATMEGIGAIGGTPPAFNRAAPGAEFAPNKRRRY
RetrocopyGPATMMPDGTLVL-TPP-TERFGQAATMEGIGAIGGTPPAFNRAAPGAEFAPNKRRRY

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 .92 RPM 44 .65 RPM
SRP017611_kidney 1 .24 RPM 85 .13 RPM
SRP017611_liver 0 .71 RPM 57 .72 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_147 retrocopy.

TSS - click to see more details

Felis catus was not studied using FANTOM5 data.

Lab - click to see more details

retro_fcat_147 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 22 parental genes, and 32 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000160572 retrocopies
retro_amel_1438, retro_amel_795,
Bos taurus ENSBTAG000000121522 retrocopies
retro_btau_1027, retro_btau_313,
Canis familiaris ENSCAFG000000170711 retrocopy
retro_cfam_98,
Callithrix jacchus ENSCJAG000000367441 retrocopy
retro_cjac_3990,
Equus caballus ENSECAG000000085022 retrocopies
retro_ecab_357, retro_ecab_427,
Felis catus ENSFCAG00000014807 2 retrocopies
retro_fcat_1219, retro_fcat_147 ,
Felis catus ENSFCAG000000312871 retrocopy
retro_fcat_1989,
Homo sapiens ENSG000001471401 retrocopy
retro_hsap_1699,
Gorilla gorilla ENSGGOG000000061941 retrocopy
retro_ggor_1273,
Microcebus murinus ENSMICG000000002321 retrocopy
retro_mmur_569,
Myotis lucifugus ENSMLUG000000024891 retrocopy
retro_mluc_622,
Mustela putorius furoENSMPUG000000049371 retrocopy
retro_mputfur_937,
Mus musculus ENSMUSG000000313112 retrocopies
retro_mmus_3652, retro_mmus_632,
Nomascus leucogenys ENSNLEG000000012781 retrocopy
retro_nleu_1344,
Oryctolagus cuniculus ENSOCUG000000218482 retrocopies
retro_ocun_1317, retro_ocun_1804,
Otolemur garnettii ENSOGAG000000048343 retrocopies
retro_ogar_1525, retro_ogar_546, retro_ogar_593,
Pongo abelii ENSPPYG000000204511 retrocopy
retro_pabe_1398,
Pan troglodytes ENSPTRG000000220101 retrocopy
retro_ptro_1150,
Pteropus vampyrus ENSPVAG000000165031 retrocopy
retro_pvam_444,
Rattus norvegicus ENSRNOG000000036892 retrocopies
retro_rnor_1178, retro_rnor_1503,
Sorex araneus ENSSARG000000079592 retrocopies
retro_sara_661, retro_sara_663,
Drosophila melanogaster FBgn00042271 retrocopy
retro_dmel_11,


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