RetrogeneDB ID:

retro_fcat_1683

Retrocopy
location
Organism:Cat (Felis catus)
Coordinates:E2:11968014..11969374(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSFCAG00000031691
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:EEF1A1
Ensembl ID:ENSFCAG00000030977
Aliases:EEF1A1, EF1A
Description:Elongation factor 1-alpha 1 [Source:UniProtKB/Swiss-Prot;Acc:Q66RN5]


Retrocopy-Parental alignment summary:






>retro_fcat_1683
GTCATCGGACACGTAGATTTGGGCAAGCCTACCACTACTAGGCATCTGATCTACAGATGTGATGGGACTGACAAAAGAAC
TACTGAAAATTTTGAGAAGGAGGCTGCTGAGATGGGAAAGGTTCCTTGACGTATGCCTGGGTCTTGGATAAACTGAAAGC
TGAACACGAACGTGGTTATCACCATTGACAATTCCCTGTGGAAATTTGAGACCAGCAAGTATTATGTGATCATCACTGAT
GCCCCAGGACACAGAGACCTTATCAAAAACATAATTACAGGCACTTCTAGGGCTGGCTGTGCTGTCCTGATTGCTGCTGC
TGGTGGCGAATTTGCAGCAGGCATCTCCGAGAATGGGCAGACCCGTCCATGAGCATGCCCTTCTTCTGGCTTACACACTG
GGCGTGAAACAGCTAATTGTTGGTGTTGACAACATGGGTTCCGCTGAGCCAGCCCACAGCCAGAAGAGATACGAGGAAAT
TGTTGAGGAAGTCAGCACCTATATCAAGAAAATTGGCTACAACCCCAGCGCAGTTGCATGTTTGCCAATTTGGGGTTGGA
ATGGTGACAACAAGCTGGAGCCCAGTCGCTCACAGGCCTTGGTTCAAGAGATGGAAAGTCACCCGCAAAGATAGCAATGC
CAGGGGAACCACACTGCTTGAGGCTCTGGATTGCATTCTGCCACCTACTCGTCCAACTGACAAGCCCTGGCGTCTGCCCC
TCCAGGATGTCCACATAACTGATGGTATTGGTACTGTCCCTGTGGGCCGAGCGGAGACCGGTGCTCTTAAACCCAGCATG
GTGGTCACCTTTGCTCCAGTCAAGGTTACAACTGAAGTAAAGTCTGTTGAAATGCACCATGAAGCTTTGAGCGAGGCTCT
TCCCGAGGACAGCGTGGGCTTCAGGGTCAAGAACAAATCTGTTAAAGATGTTCGTCACGGCAGTGTGGCTGGTGACAGCA
GACGTGACCCACCGACGGCAGCAGCTGGCTTCACAGCTCAGGTGATTATCCTGAACCATCCGGGCCACATTAGTGCCGGA
TATGCACCTGTGCTGAACGGTCACACGGCCCACGTTGCTCACAAGTTTGCTGAGCTGAAAGAGAAGATTGATCGTCATTC
TGGAAAAAAGTTGGAAGATGGCCCCGAGTTCTTGAAATCTGGTGATGCTGCCTTCGTTGATACGGCTCCTGGCAAGACTG
TGTGTGTTGAGAGCGTCTCTGACTATCCTCCCGGGGGGCCGTTTTCGCTGTTAGTGACGTGAGACAGATGGTTGCTGTGG
AGGTCATCAAAGCAGTGGACAAGAAGGCAGCTGGGGCTGGCAAGGTCACCGAGCCTGGCCAGAAGGCTCAGAAGGCTAAA

ORF - retro_fcat_1683 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78. %
Parental protein coverage: 97.62 %
Number of stop codons detected: 0
Number of frameshifts detected 6


Retrocopy - Parental Gene Alignment:

ParentalVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAEMGK-GSFKYAWVLDKLKAERERG-ITIDISLWK
VIGHVD.GK.TTT.HLIY.C.G.DKRT.E.FEKEAAEMGK.GS..YAWVLDKLKAE.ERG.ITID.SLWK
RetrocopyVIGHVDLGKPTTTRHLIYRCDGTDKRTTENFEKEAAEMGK<GSLTYAWVLDKLKAEHERG>ITIDNSLWK
ParentalFETSKYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAG-VGEFEAGISKNGQ-TREHALL-AYTLGVK
FETSKYYV.I.DAPGHRD.IKN.ITGTS.A.CAV...AA..V..........G....EHALL.AYTLGVK
RetrocopyFETSKYYVIITDAPGHRDLIKNIITGTSRAGCAV-LIAAA>VANLQQASPRMGRPVHEHALLLAYTLGVK
ParentalQLIVGVNKMDSTEPPYSQKRYEEIVKEVSTYIKKIGYNPDTVAFVPISGWNGDNMLEPS-ANMPWFKGWK
QLIVGV..M.S.EP..SQKRYEEIV.EVSTYIKKIGYNP..VA..PI.GWNGDN.LEPS.A..PWFK.WK
RetrocopyQLIVGVDNMGSAEPAHSQKRYEEIVEEVSTYIKKIGYNPSAVACLPIWGWNGDNKLEPS>AHRPWFKRWK
ParentalVTRKDGNASGTTLLEALDCILPPTRPTDKPLRLPLQDVYKIGGIGTVPVGRVETGVLKPGMVVTFAPVNV
VTRKD.NA.GTTLLEALDCILPPTRPTDKP.RLPLQDV....GIGTVPVGR.ETG.LKP.MVVTFAPV.V
RetrocopyVTRKDSNARGTTLLEALDCILPPTRPTDKPWRLPLQDVHITDGIGTVPVGRAETGALKPSMVVTFAPVKV
ParentalTTEVKSVEMHHEALSEALPGDNVGFNVKNVSVKDVRRGNVAGDSKNDPPMEAAGFTAQVIILNHPGQISA
TTEVKSVEMHHEALSEALP.D.VGF.VKN.SVKDVR.G.VAGDS..DPP..AAGFTAQVIILNHPG.ISA
RetrocopyTTEVKSVEMHHEALSEALPEDSVGFRVKNKSVKDVRHGSVAGDSRRDPPTAAAGFTAQVIILNHPGHISA
ParentalGYAPVLDCHTAHIACKFAELKEKIDRRSGKKLEDGPKFLKSGDAAIVDMVPGKPMCVESFSDYP-PLGRF
GYAPVL..HTAH.A.KFAELKEKIDR.SGKKLEDGP.FLKSGDAA.VD..PGK..CVES.SDYP.P.GRF
RetrocopyGYAPVLNGHTAHVAHKFAELKEKIDRHSGKKLEDGPEFLKSGDAAFVDTAPGKTVCVESVSDYP>PGGRF
Parental-AVRDMRQTVAVGVIKAVDKKAAGAGKVTKSAQKAQKAK
.AV.D.RQ.VAV.VIKAVDKKAAGAGKVT...QKAQKAK
Retrocopy>AVSDVRQMVAVEVIKAVDKKAAGAGKVTEPGQKAQKAK

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 1486 .30 RPM
SRP017611_kidney 0 .00 RPM 9381 .03 RPM
SRP017611_liver 0 .00 RPM 6481 .18 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_1683 retrocopy.

TSS - click to see more details

Felis catus was not studied using FANTOM5 data.

Lab - click to see more details

retro_fcat_1683 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 20 parental genes, and 149 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000145343 retrocopies
retro_btau_114, retro_btau_115, retro_btau_192,
Canis familiaris ENSCAFG000000132491 retrocopy
retro_cfam_1007,
Dipodomys ordii ENSDORG000000096291 retrocopy
retro_dord_509,
Equus caballus ENSECAG000000203632 retrocopies
retro_ecab_66, retro_ecab_93,
Equus caballus ENSECAG000000222601 retrocopy
retro_ecab_802,
Erinaceus europaeus ENSEEUG000000003423 retrocopies
retro_eeur_407, retro_eeur_492, retro_eeur_625,
Felis catus ENSFCAG00000030977 14 retrocopies
retro_fcat_1021, retro_fcat_1388, retro_fcat_1569, retro_fcat_1683 , retro_fcat_1825, retro_fcat_184, retro_fcat_1915, retro_fcat_220, retro_fcat_221, retro_fcat_334, retro_fcat_515, retro_fcat_566, retro_fcat_688, retro_fcat_737,
Homo sapiens ENSG0000015650827 retrocopies
retro_hsap_1093, retro_hsap_1181, retro_hsap_1567, retro_hsap_1671, retro_hsap_190, retro_hsap_2302, retro_hsap_2455, retro_hsap_2637, retro_hsap_2712, retro_hsap_278, retro_hsap_283, retro_hsap_2896, retro_hsap_2920, retro_hsap_2967, retro_hsap_2983, retro_hsap_3239, retro_hsap_3291, retro_hsap_3314, retro_hsap_363, retro_hsap_3701, retro_hsap_3706, retro_hsap_3758, retro_hsap_3825, retro_hsap_3917, retro_hsap_4220, retro_hsap_4730, retro_hsap_989,
Loxodonta africana ENSLAFG000000280811 retrocopy
retro_lafr_651,
Myotis lucifugus ENSMLUG0000001353724 retrocopies
retro_mluc_110, retro_mluc_1252, retro_mluc_1392, retro_mluc_1430, retro_mluc_1558, retro_mluc_1628, retro_mluc_1644, retro_mluc_1853, retro_mluc_1901, retro_mluc_1910, retro_mluc_2071, retro_mluc_2148, retro_mluc_2154, retro_mluc_2277, retro_mluc_2355, retro_mluc_2358, retro_mluc_2359, retro_mluc_2391, retro_mluc_441, retro_mluc_470, retro_mluc_677, retro_mluc_950, retro_mluc_956, retro_mluc_966,
Monodelphis domestica ENSMODG000000185334 retrocopies
retro_mdom_1053, retro_mdom_1146, retro_mdom_311, retro_mdom_792,
Mustela putorius furoENSMPUG000000038166 retrocopies
retro_mputfur_1514, retro_mputfur_1643, retro_mputfur_220, retro_mputfur_502, retro_mputfur_844, retro_mputfur_862,
Mustela putorius furoENSMPUG0000000427110 retrocopies
retro_mputfur_1179, retro_mputfur_1276, retro_mputfur_1351, retro_mputfur_1394, retro_mputfur_284, retro_mputfur_355, retro_mputfur_474, retro_mputfur_678, retro_mputfur_920, retro_mputfur_973,
Mus musculus ENSMUSG0000003774215 retrocopies
retro_mmus_1349, retro_mmus_1518, retro_mmus_1667, retro_mmus_1783, retro_mmus_1816, retro_mmus_1849, retro_mmus_1850, retro_mmus_1864, retro_mmus_1909, retro_mmus_2363, retro_mmus_2583, retro_mmus_2902, retro_mmus_3249, retro_mmus_480, retro_mmus_483,
Oryctolagus cuniculus ENSOCUG000000084813 retrocopies
retro_ocun_1102, retro_ocun_187, retro_ocun_71,
Ochotona princeps ENSOPRG000000166856 retrocopies
retro_opri_1049, retro_opri_1076, retro_opri_1197, retro_opri_298, retro_opri_325, retro_opri_383,
Sus scrofa ENSSSCG000000044894 retrocopies
retro_sscr_169, retro_sscr_492, retro_sscr_612, retro_sscr_758,
Ictidomys tridecemlineatus ENSSTOG000000076874 retrocopies
retro_itri_1509, retro_itri_1740, retro_itri_1816, retro_itri_195,
Tursiops truncatus ENSTTRG0000000011419 retrocopies
retro_ttru_1020, retro_ttru_1150, retro_ttru_1196, retro_ttru_1349, retro_ttru_1351, retro_ttru_1368, retro_ttru_1384, retro_ttru_1810, retro_ttru_1861, retro_ttru_1876, retro_ttru_384, retro_ttru_390, retro_ttru_401, retro_ttru_523, retro_ttru_664, retro_ttru_698, retro_ttru_844, retro_ttru_941, retro_ttru_998,
Drosophila melanogaster FBgn00005571 retrocopy
retro_dmel_9,


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