RetrogeneDB ID:

retro_fcat_248

Retrocopy
location
Organism:Cat (Felis catus)
Coordinates:A1:110626393..110626902(-)
Located in intron of:ENSFCAG00000012426
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RNPS1
Ensembl ID:ENSFCAG00000007690
Aliases:None
Description:RNA binding protein S1, serine-rich domain [Source:HGNC Symbol;Acc:10080]


Retrocopy-Parental alignment summary:






>retro_fcat_248
GCTCCTTCTCCTACCAAAAGCAAAGACCACTCTGCCGAGAAGTCCCAGGATCATTCTAAAGATAAAGGGGCCACCAAGTA
GTCTAGCGAGAATGATCACCGCAGGAATAAAGCTTGGAAGAGATGCAGTGCTTCCATGCTTCCTCTGGTGGCAGCAACAC
CAGGTCGTGGTCCAGCTCTACCACCAGCACAGGTGTGAGCAGAGGCCCTTGCTCCTCTTTAGCATCTAGCTGCTGGGGAA
GTTCCAGCGTGCCCTGCAGCTCCAGCTCCAGCTCCAGCAGTTCCTCTGGCTCACAGAGTCCTAGGCATCGACACGACAAC
AGACAGTGCTCCCATTTGAAATCCAAACCACCCAAAAGAGGTGCAAAGCAAAGGAAAAAGCAGAGTCCTTCCCCTAAACC
AACCCAAGTGCACATCAGAAGGCTCACTAGGAACGTGAGCACGGACCACATCATGGAGACATTGTCCACCTCTGGGAAAA
CTTAAATGATTAACGTGCTTGTTTCTAAA

ORF - retro_fcat_248 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 58.05 %
Parental protein coverage: 56.21 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalAPSPTKRKDRSDEKSKDRSKDKGATKESSEKDRGREKTRKRRSAS-SGSSSTRSRSSSTSSSGSSTSTGS
APSPTK.KD.S.EKS.D.SKDKGATK.SSE.D..R.K..KR.SAS...SS......S..SS....TSTG.
RetrocopyAPSPTKSKDHSAEKSQDHSKDKGATK*SSENDHRRNKAWKRCSAS<HASSGGSNTRSWSSS---TTSTGV
ParentalSSGSSSSSASSRSGSSSTSRSSSSSSSSGSPSPS-RRRHDNRRRSRSKSKPPKRDEKERKRRSPSPKPTK
S.G..SS.ASS..GSSS..........S.S.S.S.R.RHDNR..S..KSKPPKR..K.RK..SPSPKPT.
RetrocopySRGPCSSLASSCWGSSSVPXXXXXXXXSSSGSQSPRHRHDNRQCSHLKSKPPKRGAKQRKKQSPSPKPTQ
ParentalVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVER
VHI.RLTRNV..DHIME..ST.GK..MI...V..
RetrocopyVHIRRLTRNVSTDHIMETLSTSGKT*MINVLVSK

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 31 .79 RPM
SRP017611_kidney 0 .10 RPM 24 .94 RPM
SRP017611_liver 0 .10 RPM 9 .10 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_248 retrocopy.

TSS - click to see more details

Felis catus was not studied using FANTOM5 data.

Lab - click to see more details

retro_fcat_248 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 43 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000178611 retrocopy
retro_amel_194,
Bos taurus ENSBTAG000000099697 retrocopies
retro_btau_1187, retro_btau_1239, retro_btau_1283, retro_btau_1515, retro_btau_764, retro_btau_776, retro_btau_85,
Canis familiaris ENSCAFG000000193971 retrocopy
retro_cfam_449,
Equus caballus ENSECAG000000232881 retrocopy
retro_ecab_524,
Felis catus ENSFCAG00000007690 1 retrocopy
retro_fcat_248 ,
Homo sapiens ENSG000002059371 retrocopy
retro_hsap_2911,
Gorilla gorilla ENSGGOG000000142751 retrocopy
retro_ggor_2016,
Macropus eugenii ENSMEUG000000088821 retrocopy
retro_meug_1996,
Myotis lucifugus ENSMLUG000000168083 retrocopies
retro_mluc_2237, retro_mluc_2618, retro_mluc_643,
Macaca mulatta ENSMMUG000000192381 retrocopy
retro_mmul_794,
Monodelphis domestica ENSMODG000000158911 retrocopy
retro_mdom_1171,
Mus musculus ENSMUSG000000346811 retrocopy
retro_mmus_173,
Otolemur garnettii ENSOGAG000000315821 retrocopy
retro_ogar_3241,
Rattus norvegicus ENSRNOG000000087034 retrocopies
retro_rnor_1537, retro_rnor_2135, retro_rnor_2988, retro_rnor_649,
Sarcophilus harrisii ENSSHAG000000169511 retrocopy
retro_shar_390,
Ictidomys tridecemlineatus ENSSTOG000000132001 retrocopy
retro_itri_1160,
Tupaia belangeri ENSTBEG000000090988 retrocopies
retro_tbel_1262, retro_tbel_1851, retro_tbel_2132, retro_tbel_2154, retro_tbel_2216, retro_tbel_3193, retro_tbel_3286, retro_tbel_4688,
Tarsius syrichta ENSTSYG000000016291 retrocopy
retro_tsyr_957,
Tursiops truncatus ENSTTRG000000082207 retrocopies
retro_ttru_1010, retro_ttru_1033, retro_ttru_1558, retro_ttru_1808, retro_ttru_1809, retro_ttru_203, retro_ttru_986,


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