RetrogeneDB ID:

retro_fcat_576

Retrocopy
location
Organism:Cat (Felis catus)
Coordinates:B1:142882811..142883199(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:KRTCAP2
Ensembl ID:ENSFCAG00000025085
Aliases:None
Description:keratinocyte associated protein 2 [Source:HGNC Symbol;Acc:28942]


Retrocopy-Parental alignment summary:






>retro_fcat_576
GCCTCTCTGGCACTCTCCTCCCTCATGTACCTGCTACTCTTCACCAGGATGCAGATGGTAGCCACCAGCTTGTCTGCAGC
GAGTAGCTCGCCATTCACGGGGACTGCTGGGCTTTGGCCTTTTTGTCTTCTCTCTGACCGCTTTCAATAATCTGGAGAAT
CTTGTCTTTGGCAAAGGATTCCAAGCAAAGATCTTCCATGAGATTCTTCTCTGCCTCCCGTTGGCTCTTTTTGCATCCGG
CCTCACCCACCGAGTCTGCCTCACCACCTGATTCACATTCTCCATGGTTGGCCTATGCTACATCAACAAGGCCTCCTCCA
CTCTGTATCAGGCAGCAGTCCCAGGCCTCCCACCCGCCAAAGTCACAGGGAAGGGCAAAAAGAGAAAC

ORF - retro_fcat_576 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78.03 %
Parental protein coverage: 95.59 %
Number of stop codons detected: 2
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalASMMLSSLLSLLLFAGMQMY-SRQLASTEWLTIQG-GLLGSGLFVFSLTAFNNLENLVFGKGFQAKIFPE
AS..LSSL..LLLF..MQM..S.QL...E.L.I.G.GLLG.GLFVFSLTAFNNLENLVFGKGFQAKIF.E
RetrocopyASLALSSLMYLLLFTRMQMV<SHQLVCSE*LAIHG<GLLGFGLFVFSLTAFNNLENLVFGKGFQAKIFHE
ParentalILLCLLLALFASGLIHRVCVTTCFIFSMVGLYYINKISSTLYQATAPVLAPAKVTGKGKKRN
ILLCL.LALFASGL.HRVC.TT.F.FSMVGL.YINK.SSTLYQA..P.L.PAKVTGKGKKRN
RetrocopyILLCLPLALFASGLTHRVCLTT*FTFSMVGLCYINKASSTLYQAAVPGLPPAKVTGKGKKRN

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 14 .12 RPM
SRP017611_kidney 0 .00 RPM 30 .09 RPM
SRP017611_liver 0 .00 RPM 17 .69 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_576 retrocopy.

TSS - click to see more details

Felis catus was not studied using FANTOM5 data.

Lab - click to see more details

retro_fcat_576 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 16 parental genes, and 20 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000113361 retrocopy
retro_amel_1789,
Canis familiaris ENSCAFG000000170551 retrocopy
retro_cfam_1487,
Callithrix jacchus ENSCJAG000000090171 retrocopy
retro_cjac_1289,
Felis catus ENSFCAG00000025085 3 retrocopies
retro_fcat_1496, retro_fcat_477, retro_fcat_576 ,
Homo sapiens ENSG000001634631 retrocopy
retro_hsap_2100,
Gorilla gorilla ENSGGOG000000093031 retrocopy
retro_ggor_1635,
Macaca mulatta ENSMMUG000000121802 retrocopies
retro_mmul_745, retro_mmul_987,
Mustela putorius furoENSMPUG000000056471 retrocopy
retro_mputfur_1653,
Nomascus leucogenys ENSNLEG000000118641 retrocopy
retro_nleu_1306,
Oryctolagus cuniculus ENSOCUG000000003471 retrocopy
retro_ocun_157,
Otolemur garnettii ENSOGAG000000302711 retrocopy
retro_ogar_1306,
Pongo abelii ENSPPYG000000007561 retrocopy
retro_pabe_1999,
Pan troglodytes ENSPTRG000000014101 retrocopy
retro_ptro_1541,
Rattus norvegicus ENSRNOG000000205421 retrocopy
retro_rnor_2128,
Ictidomys tridecemlineatus ENSSTOG000000088291 retrocopy
retro_itri_1127,
Tarsius syrichta ENSTSYG000000132282 retrocopies
retro_tsyr_1096, retro_tsyr_531,


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