RetrogeneDB ID:

retro_fcat_136

Retrocopy
location
Organism:Cat (Felis catus)
Coordinates:B1:106868580..106869693(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSFCAG00000030065
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:TRAM1
Ensembl ID:ENSFCAG00000028775
Aliases:None
Description:translocation associated membrane protein 1 [Source:HGNC Symbol;Acc:20568]


Retrocopy-Parental alignment summary:






>retro_fcat_136
ATGGCGTTTCGTAAGAAGAGCACCAAGAACCCCCCAGTCCTGAGCCACGAATTCATCCTGCAGAATCATGCGGACCTCGT
CGCCTGTGTGGGGATGTTCTTCGTGCTGGGGCTTATGTTCGAGGGAACAGCAGAAGCGTCTATCGTTTTTATTACTCTTC
AGCACAGCGTTACCTTCCCTGCAGCAGAAGACCGAGCCACAGAATCAAAGTTCCTTTACTATTATGGCATCAAAGACCTG
GCCACGGTTTTCTTTTACATGCTAGTGGCAATCATCATTCACGCCACAATTCAGGAGTATGTGTTGGATAAAATTAACAG
GCGAATGCAGTTCCCCAAACCGAAACAAAGCAAATTTAATGAATCTGGTCAGTTCAGTGTATTCTACCTTGTCTCTTGTA
TTTGGGGCACATTCATTCTAATTTCTGAAAACTGTCTGGCAGACCCAACTCTCTTATGGAGGGCTCATCCCCATAATATG
ATGACATTTCAGATGAAGTTTTTCTACATATCACAGTTGGCTTACTGGTTTCATGCCTTCCCCGAACTCTATTTCCAGAG
AACCAAAAAGCAAGATATCCCTCGTCAACTTGTCTACATTGGCCTTCACCTCTTTCACATCGCTGGAGCTTACCTCTTGT
ACTTGAACCATCTAGGACTCGTTCTCTTGATGATGCATTATTTTGTGGAATTACTTTCCCACATTTGTGACCTGTTTTAT
TTTAGCGATGAAAAGTATCAGAAAGAGGTTTCTCTATGGGCAATTGTGTTTATTTTGGGTCGACTTGTGACTTTAATTGT
TTCTGTACTGACTGTTGGCTTTCACCTGGCGGGAGGGCAGAATCGGAATCCGGATGGCATTACTGGGAACGTAAATGTGT
TGGCAGCTAAAATTGCTGTTCTGTCCTCCAGTTGCACTATCCAGGCATACATAACATGGAATTTATTTAATGTTCAACTT
CAGAGGTGGATGGAGGAAGATGCTACTCTTCAGGCCCCAAGTGTGAAGAAGAAACGGACCAAAGGGAGGTCTTCTAGAAA
AGGGACAGAAAATGGTGTGGCAGCTTCACACAGAGTAGACTCTCCCCATAAAAAGAAAGAGAAATCTTCATAA

ORF - retro_fcat_136 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 72.3 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalFFLIGTLFMITAKASIIFVTLQYNVTLPATEEQAAESASLYYYGIKDLATVFFYMLVAIIIHAIIQEYVL
FF..G..F..TA.ASI.F.TLQ..VT.PA.E..A.ES..LYYYGIKDLATVFFYMLVAIIIHA.IQEYVL
RetrocopyFFVLGLMFEGTAEASIVFITLQHSVTFPAAEDRATESKFLYYYGIKDLATVFFYMLVAIIIHATIQEYVL
ParentalDKINRRMHFSKTKHSKFNESGQLSAFYLFSCIWGTFILISENYISDPTILWRAYPHNLMTFQMKFFYIAQ
DKINRRM.F.K.K.SKFNESGQ.S.FYL.SCIWGTFILISEN...DPT.LWRA.PHN.MTFQMKFFYI.Q
RetrocopyDKINRRMQFPKPKQSKFNESGQFSVFYLVSCIWGTFILISENCLADPTLLWRAHPHNMMTFQMKFFYISQ
ParentalLAYWFHAFPELYFQKTKKEDIPRQLVYIGLYLFHIAGAYLLNLNHLGLVLLVLHYFVEFLFHISRLFYFS
LAYWFHAFPELYFQ.TKK.DIPRQLVYIGL.LFHIAGAYLL.LNHLGLVLL..HYFVE.L.HI..LFYFS
RetrocopyLAYWFHAFPELYFQRTKKQDIPRQLVYIGLHLFHIAGAYLLYLNHLGLVLLMMHYFVELLSHICDLFYFS
ParentalDEKYQKGFSLWAVLFVLGRLLTLILSVLTVGFGLARAENQKLDFSAGNFNVLAVRIAVLASICITQAFMM
DEKYQK..SLWA..F.LGRL.TLI.SVLTVGF.LA...N...D...GN.NVLA..IAVL.S.C..QA...
RetrocopyDEKYQKEVSLWAIVFILGRLVTLIVSVLTVGFHLAGGQNRNPDGITGNVNVLAAKIAVLSSSCTIQAYIT
ParentalWKFINFQLRRW-REHSTFQAPTVKKKPTVTKGRSSRKGTENGVNGTVTSNGADSPRNRKEKSS
W...N.QL.RW..E..T.QAP.VKKK...TKGRSSRKGTENGV.....S...DSP...KEKSS
RetrocopyWNLFNVQLQRWMEEDATLQAPSVKKKR--TKGRSSRKGTENGV---AASHRVDSPHKKKEKSS

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 4 .36 RPM 23 .18 RPM
SRP017611_kidney 0 .62 RPM 102 .23 RPM
SRP017611_liver 0 .00 RPM 111 .00 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_136 retrocopy.

TSS - click to see more details

Felis catus was not studied using FANTOM5 data.

Lab - click to see more details

retro_fcat_136 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 26 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000063251 retrocopy
retro_amel_78,
Bos taurus ENSBTAG000000075621 retrocopy
retro_btau_24,
Canis familiaris ENSCAFG000000078661 retrocopy
retro_cfam_15,
Callithrix jacchus ENSCJAG000000078931 retrocopy
retro_cjac_168,
Dasypus novemcinctus ENSDNOG000000092962 retrocopies
retro_dnov_27, retro_dnov_906,
Dipodomys ordii ENSDORG000000019011 retrocopy
retro_dord_27,
Equus caballus ENSECAG000000183781 retrocopy
retro_ecab_506,
Echinops telfairi ENSETEG000000184471 retrocopy
retro_etel_674,
Felis catus ENSFCAG00000028775 1 retrocopy
retro_fcat_136 ,
Homo sapiens ENSG000000671671 retrocopy
retro_hsap_51,
Loxodonta africana ENSLAFG000000116251 retrocopy
retro_lafr_9,
Macaca mulatta ENSMMUG000000015161 retrocopy
retro_mmul_235,
Monodelphis domestica ENSMODG000000073161 retrocopy
retro_mdom_308,
Mustela putorius furoENSMPUG000000106161 retrocopy
retro_mputfur_558,
Mus musculus ENSMUSG000000259351 retrocopy
retro_mmus_117,
Nomascus leucogenys ENSNLEG000000113761 retrocopy
retro_nleu_73,
Oryctolagus cuniculus ENSOCUG000000087341 retrocopy
retro_ocun_52,
Otolemur garnettii ENSOGAG000000063791 retrocopy
retro_ogar_2932,
Pongo abelii ENSPPYG000000186601 retrocopy
retro_pabe_169,
Pan troglodytes ENSPTRG000000203341 retrocopy
retro_ptro_2081,
Rattus norvegicus ENSRNOG000000078921 retrocopy
retro_rnor_287,
Sus scrofa ENSSSCG000000061931 retrocopy
retro_sscr_980,
Ictidomys tridecemlineatus ENSSTOG000000055371 retrocopy
retro_itri_38,
Tarsius syrichta ENSTSYG000000138871 retrocopy
retro_tsyr_24,
Tursiops truncatus ENSTTRG000000003281 retrocopy
retro_ttru_24,


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