RetrogeneDB ID:

retro_fcat_257

Retrocopy
location
Organism:Cat (Felis catus)
Coordinates:A1:126198984..126200106(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSFCAG00000003001
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:BETA-ACTIN
Ensembl ID:ENSFCAG00000026434
Aliases:None
Description:Beta-actin [Source:UniProtKB/TrEMBL;Acc:Q9GLY0]


Retrocopy-Parental alignment summary:






>retro_fcat_257
GATGATGAGCTGTCTGCCTTGGTGGTAGATAATGGTTCAGGGATGTGCAAGGCAGGTTTTGGTGGTGACGATGCCCCCCG
GGCTGTCTTCCCCTCCATGGTAGGTCGCCCCCGGCACCAGGGGGTCATGGTAGGCATGGGTCAGAAGGACTGCTATGTGG
GGGATGAGGCTCAGAGCAAGAGAGGCATCCTGACCCTGAAGTATCCCATTGAGCATGGAGTAGTCACCAACTGGGACGAT
ATGGAGAAGATCTGGCACCACACTTTCTACAACGAGCTCCGTGTGGCACCGGATGAGCATCCCATCCTCCTCACCGAGGC
ACCCCTCAACCCCAAGATCAACCGGGAAAAGATGACTCAGATCATGTTTGAGGCCTTCAATACACCAGCCATGTATGTAG
CTATCCAGGCTGTGCTGTCTCTCTATGCCTCGGGGAGAACCACAGGCATCGTGATGGATTCTGGTGATGGAGTTACTCAC
ACCGTGCCCATCTATGAAGGTTATGCCCTACCTCATGCCATTCTACGTCTAGATCTGGCTGGCAGAGACCTGACTGACTA
CCTCATGAAGATTCTGACAGAACGAGGCTACAACTTCACCACCACAGCCGAGCGGGAGATTGTCCGTGATGTCAAAGAGA
AACTGTGCTATGTGGCCCTGGACTTTGAGCAAGAGATGGTCAGTGCTTCTGCATCCTCCTCACTGGAAAGAAGCTATGAG
CTTCCTGATGGGCAAGTGATCACCATTGGGAACGAACGTTTTCGATGCCCTGAATCCATTTTCCAGCCTTCCTTTTTGGG
CATTGAGTCCAGTGGGATCCACGAGACAACCTTCAATTCTATCATGAAGTGTGATGTGGATATTCGCAAGGATCTATATG
CCAACACTGTCTTGTCTGGAGGCAGCACAATGTACCCTGGCATTGCTGACCGAATGCAGAAGGAAATCGTAACCCTGGCA
CCTAGCACAATGAAAATCAAGATCATAGCTCCCCCAGAGAGGAAGTATTCCGTTTGGATTGGGGGTTCCATTCTGGCCAG
CCTGTCAACATTCCAGCAAATGTGGATCAGTAAGCAGGAATATGATGAGGCTGGTCCTCCCATAGTTCATAGAAAATGTT
TC

ORF - retro_fcat_257 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.25 %
Parental protein coverage: 99.73 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalEEEIAALVIDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPI
..E..ALV.DNGSGMCKAGF.GDDAPRAVFPS.VGRPRHQGVMVGMGQKD.YVGDEAQSKRGILTLKYPI
RetrocopyDDELSALVVDNGSGMCKAGFGGDDAPRAVFPSMVGRPRHQGVMVGMGQKDCYVGDEAQSKRGILTLKYPI
ParentalEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVLS
EHG.VTNWDDMEKIWHHTFYNELRVAP.EHP.LLTEAPLNPK.NREKMTQIMFE.FNTPAMYVAIQAVLS
RetrocopyEHGVVTNWDDMEKIWHHTFYNELRVAPDEHPILLTEAPLNPKINREKMTQIMFEAFNTPAMYVAIQAVLS
ParentalLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVRD
LYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGY.FTTTAEREIVRD
RetrocopyLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYNFTTTAEREIVRD
ParentalIKEKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFNS
.KEKLCYVALDFEQEM..A..SSSLE.SYELPDGQVITIGNERFRCPE..FQPSFLG.ES.GIHETTFNS
RetrocopyVKEKLCYVALDFEQEMVSASASSSLERSYELPDGQVITIGNERFRCPESIFQPSFLGIESSGIHETTFNS
ParentalIMKCDVDIRKDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLST
IMKCDVDIRKDLYANTVLSGG.TMYPGIADRMQKEI..LAPSTMKIKIIAPPERKYSVWIGGSILASLST
RetrocopyIMKCDVDIRKDLYANTVLSGGSTMYPGIADRMQKEIVTLAPSTMKIKIIAPPERKYSVWIGGSILASLST
ParentalFQQMWISKQEYDESGPSIVHRKCF
FQQMWISKQEYDE.GP.IVHRKCF
RetrocopyFQQMWISKQEYDEAGPPIVHRKCF

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 616 .10 RPM
SRP017611_kidney 0 .00 RPM 715 .43 RPM
SRP017611_liver 0 .00 RPM 775 .36 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_257 retrocopy.

TSS - click to see more details

Felis catus was not studied using FANTOM5 data.

Lab - click to see more details

retro_fcat_257 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 66 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000152383 retrocopies
retro_acar_176, retro_acar_199, retro_acar_7,
Ailuropoda melanoleuca ENSAMEG000000160151 retrocopy
retro_amel_929,
Callithrix jacchus ENSCJAG000000028853 retrocopies
retro_cjac_139, retro_cjac_336, retro_cjac_377,
Cavia porcellus ENSCPOG000000121011 retrocopy
retro_cpor_361,
Equus caballus ENSECAG000000186001 retrocopy
retro_ecab_98,
Felis catus ENSFCAG000000067881 retrocopy
retro_fcat_1613,
Felis catus ENSFCAG00000026434 2 retrocopies
retro_fcat_257 , retro_fcat_377,
Homo sapiens ENSG0000018400910 retrocopies
retro_hsap_1548, retro_hsap_1607, retro_hsap_2405, retro_hsap_2591, retro_hsap_2605, retro_hsap_3466, retro_hsap_3631, retro_hsap_409, retro_hsap_4818, retro_hsap_4935,
Gallus gallus ENSGALG000000287491 retrocopy
retro_ggal_6,
Gorilla gorilla ENSGGOG000000140436 retrocopies
retro_ggor_1495, retro_ggor_2338, retro_ggor_2449, retro_ggor_273, retro_ggor_413, retro_ggor_520,
Loxodonta africana ENSLAFG000000091671 retrocopy
retro_lafr_116,
Monodelphis domestica ENSMODG000000026473 retrocopies
retro_mdom_187, retro_mdom_59, retro_mdom_89,
Mustela putorius furoENSMPUG000000116101 retrocopy
retro_mputfur_279,
Mus musculus ENSMUSG000000628257 retrocopies
retro_mmus_1043, retro_mmus_1524, retro_mmus_2383, retro_mmus_3128, retro_mmus_3265, retro_mmus_3607, retro_mmus_3705,
Nomascus leucogenys ENSNLEG000000155063 retrocopies
retro_nleu_1525, retro_nleu_1536, retro_nleu_1930,
Oryctolagus cuniculus ENSOCUG000000058671 retrocopy
retro_ocun_720,
Petromyzon marinus ENSPMAG000000041611 retrocopy
retro_pmar_4,
Pongo abelii ENSPPYG0000000873511 retrocopies
retro_pabe_1091, retro_pabe_1391, retro_pabe_1727, retro_pabe_2187, retro_pabe_2308, retro_pabe_2621, retro_pabe_2945, retro_pabe_3381, retro_pabe_3475, retro_pabe_3760, retro_pabe_600,
Pelodiscus sinensis ENSPSIG000000021022 retrocopies
retro_psin_25, retro_psin_4,
Rattus norvegicus ENSRNOG000000367011 retrocopy
retro_rnor_715,
Sorex araneus ENSSARG000000121971 retrocopy
retro_sara_267,
Sus scrofa ENSSSCG000000283551 retrocopy
retro_sscr_389,
Ictidomys tridecemlineatus ENSSTOG000000068682 retrocopies
retro_itri_1675, retro_itri_531,
Tupaia belangeri ENSTBEG000000107811 retrocopy
retro_tbel_422,
Xenopus tropicalis ENSXETG000000251161 retrocopy
retro_xtro_6,


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