RetrogeneDB ID:

retro_fcat_713

Retrocopy
location
Organism:Cat (Felis catus)
Coordinates:B2:77487039..77487904(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSFCAG00000028827
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PSMC1
Ensembl ID:ENSFCAG00000011310
Aliases:None
Description:proteasome (prosome, macropain) 26S subunit, ATPase, 1 [Source:HGNC Symbol;Acc:9547]


Retrocopy-Parental alignment summary:






>retro_fcat_713
GGTCAAAGTCAGAGTAGTGGTCATGGCCCTGGAGGTGTCAAGAAGGATGACAAGGACAAGAGAAAGAAGTACAAACCTCC
TGTACCAAACAGAGTACCAACCAAAGGGACTGATGCTGCCAGCAAGCTGCCACTGGTGACACCTCACACTCGGTGCCACT
TAAAATTACTCAAGTTAGAATTAAAGACTATCTTCTCATGGAGGAAGAATTCATTAGAAATCAGGAACAAATGAAGCCTT
TAGAAGAAAAGCAAGAGGAGGAAAGATCAAAGGTGGATGATCTGAGGGGGACCCCAATGTTGGTAGGAACGTTGGAAGAG
ATCATTGATGACAATCATACCATCGTGTCCACATCTGTGGGCTCAGAACACTACATCAGCATTCTTTCCTTTGTAGACAA
GGACCTGCTGGAGCCAGGCTGTTCAGTTCTGCTCAACCGCAAGGTACATGCCATAATAGGGGTGCTCATGGATGACACGG
ATCCCTTGGTCATGATGATGAAAGTAGAAAAGGCCCCCAGGAAACCCAAGCTGATATTGGGGGGTTGGACAACCAAATCC
AGGAAATTAAGGAATCTGTGGAGCTTCCTCTCACTCATCCTGAATATTATGAAGAGATGGGTATAAAGCCCCCAACAGGG
GTCATTCTCTATGGACCAACTGGCACAGGTAAAACCTTATTAGCCAAAGCGGTAGCAAACCAAACCTCAGCCACTTTCCC
AAGAGTGGTTGGCTCTGAACTTATTCAGAAGTACCTAGGTGATAGGCCCAAACTCGTTTGGGAGTTGTTTCGAGTTGCAG
AAGAACATGGGCCATTCATCGTGTTTATTGGTGAAATTGATGCCATTGGAACAAAAAGATATGAT

ORF - retro_fcat_713 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.51 %
Parental protein coverage: 67.05 %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalGQSQSGGHGPGGGKKDDKDKKKKYEPPVPTRVGKKKKKTKGPDAASKLPLVTPHTQCRL-KLLKLERIKD
GQSQS.GHGPGG.KKD..DK.K......P.........TKG.DAASKLPLVTPHT.C.L.K.....RIKD
RetrocopyGQSQSSGHGPGGVKKD--DKDKRKKYKPPV---PNRVPTKGTDAASKLPLVTPHTRCHL<KITQV-RIKD
ParentalYLLMEEEFIRNQEQMKPLEEKQEEERSKVDDLRGTPMSVGTLEEIIDDNHAIVSTSVGSEHYVSILSFVD
YLLMEEEFIRNQEQMKPLEEKQEEERSKVDDLRGTPM.VGTLEEIIDDNH.IVSTSVGSEHY.SILSFVD
RetrocopyYLLMEEEFIRNQEQMKPLEEKQEEERSKVDDLRGTPMLVGTLEEIIDDNHTIVSTSVGSEHYISILSFVD
ParentalKDLLEPGCSVLLNHKVHAVIGVLMDDTDPLVTVMKVEKA-PQETYADIGGLDNQIQEIKESVELPLTHPE
KDLLEPGCSVLLN.KVHA.IGVLMDDTDPLV..MKVEKA.PQET.ADIGGLDNQIQEIKESVELPLTHPE
RetrocopyKDLLEPGCSVLLNRKVHAIIGVLMDDTDPLVMMMKVEKA<PQETQADIGGLDNQIQEIKESVELPLTHPE
ParentalYYEEMGIKPPKGVILYGPPGTGKTLLAKAVANQTSATFLRVVGSELIQKYLGDGPKLVRELFRVAEEHAP
YYEEMGIKPP.GVILYGP.GTGKTLLAKAVANQTSATF.RVVGSELIQKYLGD.PKLV.ELFRVAEEH.P
RetrocopyYYEEMGIKPPTGVILYGPTGTGKTLLAKAVANQTSATFPRVVGSELIQKYLGDRPKLVWELFRVAEEHGP
ParentalSIVFIDEIDAIGTKRYD
.IVFI.EIDAIGTKRYD
RetrocopyFIVFIGEIDAIGTKRYD

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 .00 RPM 34 .55 RPM
SRP017611_kidney 0 .21 RPM 43 .08 RPM
SRP017611_liver 0 .00 RPM 27 .90 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_713 retrocopy.

TSS - click to see more details

Felis catus was not studied using FANTOM5 data.

Lab - click to see more details

retro_fcat_713 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 19 parental genes, and 50 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000018394 retrocopies
retro_amel_1536, retro_amel_1886, retro_amel_405, retro_amel_962,
Canis familiaris ENSCAFG000000175102 retrocopies
retro_cfam_1238, retro_cfam_1562,
Choloepus hoffmanni ENSCHOG000000135951 retrocopy
retro_chof_1954,
Cavia porcellus ENSCPOG000000024241 retrocopy
retro_cpor_144,
Dasypus novemcinctus ENSDNOG000000064581 retrocopy
retro_dnov_2162,
Equus caballus ENSECAG000000036011 retrocopy
retro_ecab_355,
Echinops telfairi ENSETEG000000026611 retrocopy
retro_etel_580,
Felis catus ENSFCAG00000011310 8 retrocopies
retro_fcat_1444, retro_fcat_1559, retro_fcat_2015, retro_fcat_344, retro_fcat_614, retro_fcat_691, retro_fcat_713 , retro_fcat_924,
Macropus eugenii ENSMEUG000000015261 retrocopy
retro_meug_623,
Myotis lucifugus ENSMLUG000000074712 retrocopies
retro_mluc_2490, retro_mluc_508,
Macaca mulatta ENSMMUG000000229901 retrocopy
retro_mmul_255,
Mustela putorius furoENSMPUG000000081504 retrocopies
retro_mputfur_1602, retro_mputfur_409, retro_mputfur_654, retro_mputfur_815,
Mus musculus ENSMUSG000000211783 retrocopies
retro_mmus_1517, retro_mmus_1826, retro_mmus_812,
Oryctolagus cuniculus ENSOCUG000000062314 retrocopies
retro_ocun_1135, retro_ocun_1212, retro_ocun_1654, retro_ocun_411,
Otolemur garnettii ENSOGAG000000323432 retrocopies
retro_ogar_3014, retro_ogar_367,
Pongo abelii ENSPPYG000000259489 retrocopies
retro_pabe_1059, retro_pabe_153, retro_pabe_2379, retro_pabe_2408, retro_pabe_2737, retro_pabe_2832, retro_pabe_3099, retro_pabe_825, retro_pabe_907,
Pteropus vampyrus ENSPVAG000000100203 retrocopies
retro_pvam_1190, retro_pvam_350, retro_pvam_500,
Ictidomys tridecemlineatus ENSSTOG000000016551 retrocopy
retro_itri_780,
Tursiops truncatus ENSTTRG000000135821 retrocopy
retro_ttru_239,


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