RetrogeneDB ID:

retro_fcat_921

Retrocopy
location
Organism:Cat (Felis catus)
Coordinates:B3:89897186..89898277(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:KPNA2
Ensembl ID:ENSFCAG00000001936
Aliases:None
Description:karyopherin alpha 2 (RAG cohort 1, importin alpha 1) [Source:HGNC Symbol;Acc:6395]


Retrocopy-Parental alignment summary:






>retro_fcat_921
ATGTCCACCAATATAAATGCTAATTCACCAGCTGCCTGCCTTAACAGGTTCAAGAACAAGGGGAAAGACAGTACAGAAAT
GAGGTGGCACTGAATAGAAGTTAATGAGGAGCTGAGGAAAGCTAAGGATGACCAGCTGCTGAAAAGGAGAAATGTAAGCT
CATTTCCTGATGGTGCTACTTCTCTACTGCAAGAGAACTGCAACAACCAAGGCACTGTAAGTTGGTCTGTTGATGACATT
GTCCAAGGCATAAATAGCAATTCATTTGGAAAGCTAGCTCCAGGCTACTAAAGCTGATAGGAAACTGCTTTCCAGGGAAA
CACAGCCTCCCATAGACAACATAATCTGGGCTGGTTTTGATTCCAAAATTTGTATACTTCATGGGTAGAACTGATTGTAG
TCCTATTCAGTTTTAATTTGCTTGGGCCCTCACTAACATTGTTTCCAGAACATCAGAACAGACCAAAATTGTGGTAGATG
GAGGTGATACCCCAGCATTCATTTCTCTGTTGGCATCTTCCCATGCCCACATCAGTTAACAAGCTGTAGGGGTGCTAGGA
AGCAATGCAGATGATGGTTCAGTTCCTCAAGACTTGTTTATCAAATATGGTACAGTTGACCTGCTGTTGGCTCTTACAGT
TTCTGATATGTAATCTTTAGAATGTGGTTATTTACATAACCTTCCTTGGACACTTTCAAACCTTTGTCACAACAAGAATC
CTGAATGTCTGTTAGATGCTACTGAGCAGATTCTTCCTACCTTAGTTCATCTCCTGAATCATGATGATCCAGAAGTATTA
TTACATACTTGCTGGGCCATCTCCTATCTTACTGATGGTCCAAATTAATGGACTAAAATGGTCATGAAAATAGGAGTTGT
GCTCCAACTTGTAAAGCTTCTAGGAGCTAGTGAATTGCTCATTGTGACTCCCGTGCTAAAAGCCACAGTAAATATTGTCA
CTGGGGCAGATGAACAGACTCAGGTTGTAATAGATGTAGGAGTACATGTTGTCCTTCCAAGCCTGCTAATGAACCTCAAA
ACTAATATTCAGAAGTAAGCTATATGGACAGTGTCAAACATCATAGCTGGT

ORF - retro_fcat_921 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.66 %
Parental protein coverage: 69.13 %
Number of stop codons detected: 7
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalMSTNENANSPAARLNRFKNKGKDSTEMRRRRIEVNVELRKAKKDDQMLKRRNVSSFPDDATSPLQENRNN
MSTN.NANSPAA.LNRFKNKGKDSTEMR...IEVN.ELRKAK.DDQ.LKRRNVSSFPD.ATS.LQEN.NN
RetrocopyMSTNINANSPAACLNRFKNKGKDSTEMRWH*IEVNEELRKAK-DDQLLKRRNVSSFPDGATSLLQENCNN
ParentalQGTVNWSVDDIVKGINSNN-LESQLQATQAARKLLSREKQPPIDNIIRAG-LIPKFVSFLGRTDCSPIQF
QGTV.WSVDDIV.GINSN..LES.LQAT.A.RKLLSRE.QPPIDNII.AG.LIPKFV.F.GRTDCSPIQF
RetrocopyQGTVSWSVDDIVQGINSNS>LES*LQATKADRKLLSRETQPPIDNIIWAG>LIPKFVYFMGRTDCSPIQF
ParentalESAWALTNIASGTSEQTKAVVDGGAIPAFISLLASSHAHISEQAVWALGNIAGDGSVFRDLVIKYGAVDP
..AWALTNI.S.TSEQTK.VVDGG..PAFISLLASSHAHIS.QAV..LG..A.DGSV..DL.IKYG.VD.
Retrocopy*FAWALTNIVSRTSEQTKIVVDGGDTPAFISLLASSHAHIS*QAVGVLGSNADDGSVPQDLFIKYGTVDL
ParentalLLALLAVPDMSSLACGYLRNLTWTLSNLCRNKNPAPPLDAVEQILPTLVRLLHHDDPEVLADTCWAISYL
LLAL..V.DM.SL.CGYL.NL.WTLSNLC.NKNP...LDA.EQILPTLV.LL.HDDPEVL..TCWAISYL
RetrocopyLLAL-TVSDM*SLECGYLHNLPWTLSNLCHNKNPECLLDATEQILPTLVHLLNHDDPEVLLHTCWAISYL
ParentalTDGPNERIEMVVKTGVVPQLVKLLGATELPIVTPALRAIGNIVTGTDEQTQVVIDAGALAVFPSLLTNPK
TDGPN....MV.K.GVV.QLVKLLGA.EL.IVTP.L.A..NIVTG.DEQTQVVID.G...V.PSLL.N.K
RetrocopyTDGPN*WTKMVMKIGVVLQLVKLLGASELLIVTPVLKATVNIVTGADEQTQVVIDVGVHVVLPSLLMNLK
ParentalTNIQKEATWTMSNITAG
TNIQK.A.WT.SNI.AG
RetrocopyTNIQK*AIWTVSNIIAG

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 15 .04 RPM
SRP017611_kidney 0 .00 RPM 11 .03 RPM
SRP017611_liver 0 .00 RPM 8 .59 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_921 retrocopy.

TSS - click to see more details

Felis catus was not studied using FANTOM5 data.

Lab - click to see more details

retro_fcat_921 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 23 parental genes, and 70 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000184113 retrocopies
retro_amel_1161, retro_amel_1318, retro_amel_440,
Bos taurus ENSBTAG000000122251 retrocopy
retro_btau_1830,
Canis familiaris ENSCAFG000000115982 retrocopies
retro_cfam_648, retro_cfam_90,
Cavia porcellus ENSCPOG000000263181 retrocopy
retro_cpor_46,
Dasypus novemcinctus ENSDNOG000000191516 retrocopies
retro_dnov_1184, retro_dnov_1811, retro_dnov_2161, retro_dnov_2279, retro_dnov_379, retro_dnov_693,
Equus caballus ENSECAG000000205732 retrocopies
retro_ecab_1017, retro_ecab_1123,
Echinops telfairi ENSETEG000000044452 retrocopies
retro_etel_346, retro_etel_347,
Felis catus ENSFCAG00000001936 2 retrocopies
retro_fcat_1176, retro_fcat_921 ,
Homo sapiens ENSG000001824811 retrocopy
retro_hsap_2950,
Gorilla gorilla ENSGGOG000000275352 retrocopies
retro_ggor_2044, retro_ggor_2609,
Myotis lucifugus ENSMLUG000000279467 retrocopies
retro_mluc_1034, retro_mluc_1258, retro_mluc_1414, retro_mluc_288, retro_mluc_50, retro_mluc_52, retro_mluc_993,
Macaca mulatta ENSMMUG000000182563 retrocopies
retro_mmul_1140, retro_mmul_1635, retro_mmul_1947,
Monodelphis domestica ENSMODG000000038971 retrocopy
retro_mdom_271,
Mus musculus ENSMUSG000000183621 retrocopy
retro_mmus_229,
Nomascus leucogenys ENSNLEG000000017493 retrocopies
retro_nleu_1052, retro_nleu_1634, retro_nleu_208,
Oryctolagus cuniculus ENSOCUG000000159134 retrocopies
retro_ocun_1765, retro_ocun_1916, retro_ocun_426, retro_ocun_690,
Otolemur garnettii ENSOGAG000000276727 retrocopies
retro_ogar_1044, retro_ogar_1142, retro_ogar_1757, retro_ogar_2008, retro_ogar_464, retro_ogar_477, retro_ogar_936,
Pongo abelii ENSPPYG000000085691 retrocopy
retro_pabe_3501,
Pteropus vampyrus ENSPVAG000000049762 retrocopies
retro_pvam_1321, retro_pvam_1333,
Rattus norvegicus ENSRNOG000000153291 retrocopy
retro_rnor_42,
Sarcophilus harrisii ENSSHAG000000113911 retrocopy
retro_shar_165,
Tupaia belangeri ENSTBEG0000000627414 retrocopies
retro_tbel_1635, retro_tbel_2077, retro_tbel_2672, retro_tbel_2792, retro_tbel_290, retro_tbel_3638, retro_tbel_4120, retro_tbel_4358, retro_tbel_4414, retro_tbel_4435, retro_tbel_4558, retro_tbel_810, retro_tbel_97, retro_tbel_976,
Vicugna pacos ENSVPAG000000018553 retrocopies
retro_vpac_124, retro_vpac_162, retro_vpac_163,


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