RetrogeneDB ID:

retro_fcat_1102

Retrocopy
location
Organism:Cat (Felis catus)
Coordinates:C1:87792144..87793130(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSFCAG00000027654
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_fcat_1102
ATGGTGGATGTGAAAATCCTGAATCCTGAGGCTGAGGTGGCCCAAGCTCAGGCAGTACTGACAGTCAACATCAGTGTGGT
CTAAGGGTCAGGATTTGCTGAGGACCAACTTGGAGACTAAGTGAGCCGTGGAGATGCTTATTTCTGGTACCAGAGACATT
ACATTTACTAAATATGGTAATGTGATGCTTCTTGAAATACAAATTCAACACCCAACAGCTGCCTTACAAGGCAAAGTAGC
AACAGCCCAGGATGACATAACTGGTGATGACACCACTTCCAATGACCTAATCATTGACAAGTTGCTGAAACAGGCCGTCT
GCATTTCTGAAGGTCTTTATCCCAGAATAACAGAAGGATTTGAAGCTGCAAAGGAAAGGCACTTCAGTTTTTAGAACAAG
CCAAAGTAAACAAAGAAATGGACAGGAAAACATTTATAGATGTGGCTAGAACATCTCCTCGTACTAAAGTGCATGTTGAC
CTTGCTAATGTCTTAACAGAGGCTGTAGTGGACTCCATTTTCACCATTAAAAAACAAGATGAACCAATTGATCTCTCTGT
TGTTGAGATCATGGAGATGAAACATAATTTTGAAACTGATACAAGCTTAATCAGAGGTCTTGTTTGAACCTTGGGGCATG
ACATCCTGATGTGAAAAAAAAAAAAAAAGATGCATATGTCCTTACATGCAATGTGTCATTAGAATATGAAAAAATGGAAG
TAAATTCTGGCTTTATTTTACAAGAGTGCACAAGAAAGAAAGAAACTTGTAAATACTGAAAGAAAACTCATTGAAGATAG
AGTTAAAAAATAATAGAACTGAAAAAGAAAGTCTGCAGTGATTCAGATAAAAGATTTGTTGTTAACCAAAAGGGAATTGA
CCTCATTTCCTTAGATGCTCTAACAAAAGAAGGCATAGTAGCTCTCTGTAGAGCTAAAAGAAGAAATATGGAAAGGCTGA
CCCTTGCTTGCAGTGGAATTCTTTTG

ORF - retro_fcat_1102 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 75.15 %
Parental protein coverage: 62.71 %
Number of stop codons detected: 2
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalMAAVKTLNPKAEVARAQAALAVNISA-ARGLQDVLRTNLGPKGTMKMLVSGAGDIKLTKDGNVLLHEMQI
M..VK.LNP.AEVA.AQA.L.VNIS....G.QD.LRTNL..K....ML.SG..DI..TK.GNV.L.E.QI
RetrocopyMVDVKILNPEAEVAQAQAVLTVNISV>SKG-QDLLRTNLETK*AVEMLISGTRDITFTKYGNVMLLEIQI
ParentalQHPTASLIAKVATAQDDITGDGTTSNVLIIGELLKQADLYISEGLHPRIITEGFEAAKE-KALQFLEQVK
QHPTA.L..KVATAQDDITGD.TTSN.LII..LLKQA...ISEGL.PRI.TEGFEAAKE.KALQFLEQ.K
RetrocopyQHPTAALQGKVATAQDDITGDDTTSNDLIIDKLLKQA-VCISEGLYPRI-TEGFEAAKE<KALQFLEQAK
ParentalVSKEMDRETLIDVARTSLRTKVHAELADVLTEAVVDSILAIKKQDEPIDLFMVEIMEMKHKSETDTSLIR
V.KEMDR.T.IDVARTS.RTKVH..LA.VLTEAVVDSI..IKKQDEPIDL..VEIMEMKH..ETDTSLIR
RetrocopyVNKEMDRKTFIDVARTSPRTKVHVDLANVLTEAVVDSIFTIKKQDEPIDLSVVEIMEMKHNFETDTSLIR
ParentalGLV-LDHGARHPDMKKRVEDAYILTCNVSLEYEKTEVNSGF-FYKSAEEREKLVKAERKFIEDRVK-KII
GLV.L..GA.HPD......DAY.LTCNVSLEYEK.EVNSGF.FYKSA.ER.KLV..ERK.IEDRVK.KII
RetrocopyGLV<LNLGA*HPDVXXXXXDAYVLTCNVSLEYEKMEVNSGF>FYKSAQERKKLVNTERKLIEDRVK<KII
ParentalELKKKVCGDSDKGFVVINQKGIDPFSLDALAKEGIVALRRAKRRNMERLTLACGGVAL
ELKKKVC.DSDK.FVV.NQKGID..SLDAL.KEGIVAL.RAKRRNMERLTLAC.G..L
RetrocopyELKKKVCSDSDKRFVV-NQKGIDLISLDALTKEGIVALCRAKRRNMERLTLACSGILL

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 .11 RPM 106 .97 RPM
SRP017611_kidney 0 .00 RPM 108 .21 RPM
SRP017611_liver 0 .00 RPM 71 .27 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_1102 retrocopy.

TSS - click to see more details

Felis catus was not studied using FANTOM5 data.

Lab - click to see more details

retro_fcat_1102 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 18 parental genes, and 24 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000160771 retrocopy
retro_amel_855,
Canis familiaris ENSCAFG000000101491 retrocopy
retro_cfam_431,
Choloepus hoffmanni ENSCHOG000000006543 retrocopies
retro_chof_1183, retro_chof_1193, retro_chof_150,
Callithrix jacchus ENSCJAG000000212792 retrocopies
retro_cjac_1320, retro_cjac_580,
Dipodomys ordii ENSDORG000000012491 retrocopy
retro_dord_617,
Felis catus ENSFCAG00000027654 2 retrocopies
retro_fcat_1102 , retro_fcat_320,
Homo sapiens ENSG000001467312 retrocopies
retro_hsap_2741, retro_hsap_3290,
Gorilla gorilla ENSGGOG000000114391 retrocopy
retro_ggor_133,
Loxodonta africana ENSLAFG000000127911 retrocopy
retro_lafr_808,
Macaca mulatta ENSMMUG000000152721 retrocopy
retro_mmul_2582,
Monodelphis domestica ENSMODG000000065651 retrocopy
retro_mdom_1330,
Nomascus leucogenys ENSNLEG000000156641 retrocopy
retro_nleu_1355,
Oryctolagus cuniculus ENSOCUG000000176741 retrocopy
retro_ocun_468,
Procavia capensis ENSPCAG000000155321 retrocopy
retro_pcap_263,
Pongo abelii ENSPPYG000000258201 retrocopy
retro_pabe_2719,
Pan troglodytes ENSPTRG000000192062 retrocopies
retro_ptro_1854, retro_ptro_2225,
Pteropus vampyrus ENSPVAG000000014211 retrocopy
retro_pvam_663,
Rattus norvegicus ENSRNOG000000009231 retrocopy
retro_rnor_2226,


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