RetrogeneDB ID:

retro_fcat_140

Retrocopy
location
Organism:Cat (Felis catus)
Coordinates:B2:87406581..87408243(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSFCAG00000000429
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSFCAG00000004264
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_fcat_140
ATGGCAGCCGCGAAGAAAGCAGTTTTGGGGCCATTGGTGGGGGCAGTGGACCAGGGCACCAGCTCAACGCGCTTTTTGGT
TTTCAATTCAAAAACAGCCGAACTACTTAGTCATCATCAAGTGGAAATAAAACAAGAGTTTCCAAGAGAAGGATGGGTGG
AACAAGACCCTAAGGAAATTCTGCAGTCTGTCTATGAGTGTATAGAGAAAACATGTGAGAAGCTTGGACAGCTTAATATT
GATATTTCCAACATAAAAGCTATTGGTGTCAGTAACCAAAGGGAAACCACTGTAGTCTGGGACAAGTTAACTGGAGAGCC
TCTCTACAATGCTGTGGTGTGGCTTGATTTAAGAACCCAGTCTACCGTTGAGAATCTTAGTAAAAAAATTCCAGGAAATA
ATAACTTTGTCAAGTCTAAGACAGGCCTTCCACTTAGCACCTACTTCAGTGCTGTGAAACTTCGCTGGCTCCTTGACAAT
GTAAGAACAGTGAAAGAGGCTGTTGAAGAAGACAGAGCTCTTTTTGGGACCATTGATGCGTGGCTTATTTGGAGTTTGAC
AGGAGGGACCAACAGAGGTGTCCATTGTACAGACGTAACCAATGCAAGTAGGACAATGCTTTTCAACATTCATTCTCTGG
AGTGGGATAAAGAGCTCTGTGAATTTTTTGAAATTCCAATGAAAATTCTTCCAAATGTCCGGAGTTCTTCTGAGATCTAC
GGCCTAATGAAAGCTGGGGTCTTGGAAGGTGTCCCAATATCTGGGTGTTTGGGAGACCAGTCTGCTGCATTGGTGGGACA
AATGTGCTTCCAGGATGGACAAGCCAAAAATACCTATGGAACAGGCTGCTTCTTACTGTGTAATACAGGCCATAAGTGTG
TGTTTTCTGAACATGGCCTTCTGACCACAGTGGCTTACAAGCTTGGCAGAGACAAACCAGTGTATTATGCATTGGAAGGT
TCTGTAGCTATAGCTGGTGCTGTTATTCGCTGGCTAAGAGACAATCTTGGAATTATAAAGAGCTCAGAGGAAATAGAAAA
ACTTGCTAAAGAAGTAGGTACATCGTATGGCTGCTATTTCGTCCCTGCGTTTTCAGGGTTATATGCACCTTACTGGGAGC
CCAGTGCAAGAGGGATCATCTGTGGGCTCACTCAGTTCACCAATAAATGCCATATTGCTTTTGCTGCATTAGAAGCTGTT
TGTTTCCAAACCCGGGAGATTTTGGATGCCATGAACCGCGACTGTGGGATTCCACTCAGCCATTTACAGGTAGATGGAGG
AATGACCAACAACAAAATTCTTATGCAGCTACAAGCAGATATTCTGTATATTCCAGTAGTGAAATCCTCAATGCCTGAAA
CAACTGCCCTGGGAGCTGCCATGGCAGCAGGGGCTGCAGAAGGAGTTGATGTTTGGAGTCTCCAACCCGAGGATTTGTCA
GCGGTTATGATGGAGCGGTTTGAACCCCAGATCAACGCTGAGGAAAGTGAAATTCGTTACTCTACATGGAAGAAAGCTGT
GATAAAGTCAATGGGTTGGGTTACAACTCAGTCTTCGGAAAGTGGTGACCCTAGTATCTTCTGTAGTCTACCCTTGGGCT
TTTTTATAGTGAGTAGCATGGTAATGTTAATTGGAGCAAGGTACATCTCAGGTATCCCATAA

ORF - retro_fcat_140 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 97.1 %
Parental protein coverage: 99.64 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMAAAKKAVLGPLVGAVDQGTSSTRFLVFNSKTAELLSHHQVEIKQEFPREGWVEQDPKEILQSVYECIEK
MAAAKKAVLGPLVGAVDQGTSSTRFLVFNSKTAELLSHHQVEIKQEFPREGWVEQDPKEILQSVYECIEK
RetrocopyMAAAKKAVLGPLVGAVDQGTSSTRFLVFNSKTAELLSHHQVEIKQEFPREGWVEQDPKEILQSVYECIEK
ParentalTCEKLGQLNIDISNIKAIGVSNQRETTVVWDKLTGEPLYNAVVWLDLRTQSTVENLSKRIPGNNNFVKSK
TCEKLGQLNIDISNIKAIGVSNQRETTVVWDKLTGEPLYNAVVWLDLRTQSTVENLSK.IPGNNNFVKSK
RetrocopyTCEKLGQLNIDISNIKAIGVSNQRETTVVWDKLTGEPLYNAVVWLDLRTQSTVENLSKKIPGNNNFVKSK
ParentalTGLPLSTYFSAVKLRWLLDNVRKVQKAVEEDRALFGTIDSWLIWSLTGGANGGVHCTDVTNASRTMLFNI
TGLPLSTYFSAVKLRWLLDNVR.V..AVEEDRALFGTID.WLIWSLTGG.N.GVHCTDVTNASRTMLFNI
RetrocopyTGLPLSTYFSAVKLRWLLDNVRTVKEAVEEDRALFGTIDAWLIWSLTGGTNRGVHCTDVTNASRTMLFNI
ParentalHSLEWDKELCEFFEIPMKVLPNVRSSSEIYGLMKAGALEGVPISGCLGDQSAALVGQMCFQDGQAKNTYG
HSLEWDKELCEFFEIPMK.LPNVRSSSEIYGLMKAG.LEGVPISGCLGDQSAALVGQMCFQDGQAKNTYG
RetrocopyHSLEWDKELCEFFEIPMKILPNVRSSSEIYGLMKAGVLEGVPISGCLGDQSAALVGQMCFQDGQAKNTYG
ParentalTGCFLLCNTGRKCVFSEHGLLTTVAYKLGRDKPVYYALEGSVAIAGAVIRWLRDNLGIIKSSEEIEKLAK
TGCFLLCNTG.KCVFSEHGLLTTVAYKLGRDKPVYYALEGSVAIAGAVIRWLRDNLGIIKSSEEIEKLAK
RetrocopyTGCFLLCNTGHKCVFSEHGLLTTVAYKLGRDKPVYYALEGSVAIAGAVIRWLRDNLGIIKSSEEIEKLAK
ParentalEVGTSYGCYFVPAFSGLYAPYWEPSARGIICGLTQFTNKCHIAFAALEAVCFQTREILDAMNRDCGIPLS
EVGTSYGCYFVPAFSGLYAPYWEPSARGIICGLTQFTNKCHIAFAALEAVCFQTREILDAMNRDCGIPLS
RetrocopyEVGTSYGCYFVPAFSGLYAPYWEPSARGIICGLTQFTNKCHIAFAALEAVCFQTREILDAMNRDCGIPLS
ParentalHLQVDGGMTNNKILMQLQADILYIPVVKPSMPETTALGAAMAAGAAEGVGVWSLEPEDLSAVTMERFEPQ
HLQVDGGMTNNKILMQLQADILYIPVVK.SMPETTALGAAMAAGAAEGV.VWSL.PEDLSAV.MERFEPQ
RetrocopyHLQVDGGMTNNKILMQLQADILYIPVVKSSMPETTALGAAMAAGAAEGVDVWSLQPEDLSAVMMERFEPQ
ParentalINAEESEIRYSTWKKAVMKSVGWVTTQSSESGDPSIFCSLPLGFFIVSSMVMLIGARYISG
INAEESEIRYSTWKKAV.KS.GWVTTQSSESGDPSIFCSLPLGFFIVSSMVMLIGARYISG
RetrocopyINAEESEIRYSTWKKAVIKSMGWVTTQSSESGDPSIFCSLPLGFFIVSSMVMLIGARYISG

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 6 .31 RPM
SRP017611_kidney 0 .00 RPM 137 .69 RPM
SRP017611_liver 0 .00 RPM 76 .73 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_140 retrocopy.

TSS - click to see more details

Felis catus was not studied using FANTOM5 data.

Lab - click to see more details

retro_fcat_140 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 21 parental genes, and 34 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000091611 retrocopy
retro_amel_45,
Canis familiaris ENSCAFG000000137131 retrocopy
retro_cfam_19,
Callithrix jacchus ENSCJAG000000076333 retrocopies
retro_cjac_125, retro_cjac_3161, retro_cjac_4035,
Cavia porcellus ENSCPOG000000032612 retrocopies
retro_cpor_11, retro_cpor_20,
Equus caballus ENSECAG000000035991 retrocopy
retro_ecab_9,
Echinops telfairi ENSETEG000000082792 retrocopies
retro_etel_2000, retro_etel_247,
Felis catus ENSFCAG00000004264 1 retrocopy
retro_fcat_140 ,
Homo sapiens ENSG000001988144 retrocopies
retro_hsap_3087, retro_hsap_3120, retro_hsap_4885, retro_hsap_70,
Loxodonta africana ENSLAFG000000076321 retrocopy
retro_lafr_30,
Myotis lucifugus ENSMLUG000000010462 retrocopies
retro_mluc_151, retro_mluc_853,
Monodelphis domestica ENSMODG000000024171 retrocopy
retro_mdom_234,
Mus musculus ENSMUSG000000250592 retrocopies
retro_mmus_119, retro_mmus_97,
Nomascus leucogenys ENSNLEG000000101022 retrocopies
retro_nleu_1650, retro_nleu_771,
Oryctolagus cuniculus ENSOCUG000000130232 retrocopies
retro_ocun_2, retro_ocun_81,
Otolemur garnettii ENSOGAG000000169521 retrocopy
retro_ogar_261,
Pteropus vampyrus ENSPVAG000000124601 retrocopy
retro_pvam_1417,
Rattus norvegicus ENSRNOG000000341162 retrocopies
retro_rnor_114, retro_rnor_34,
Sarcophilus harrisii ENSSHAG000000064701 retrocopy
retro_shar_35,
Sus scrofa ENSSSCG000000122022 retrocopies
retro_sscr_479, retro_sscr_59,
Ictidomys tridecemlineatus ENSSTOG000000087321 retrocopy
retro_itri_1436,
Tarsius syrichta ENSTSYG000000082491 retrocopy
retro_tsyr_29,


Copyright © RetrogeneDB 2014-2017