RetrogeneDB ID:

retro_mmus_3301

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:9:102551631..102553133(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Kpna7
Ensembl ID:ENSMUSG00000038770
Aliases:Kpna7, AW146299, Gm1055
Description:karyopherin alpha 7 (importin alpha 8) [Source:MGI Symbol;Acc:MGI:2141165]


Retrocopy-Parental alignment summary:






>retro_mmus_3301
ATTGCTACCTCAGAGTCTCCCAAAAAGAGGCTGAAGAAATATAAGTACCAAGGCAAAGAAATGTCTTTGCAGTGACGACA
GAGGATTGTTTCCAGCCTACAATTCTGGAAGACCAGGAAAGATGAGCAGGTGCTGAAGAGAAGAAATATCAATCTATTCC
CCAGGGACGTGGTTTCTCAAGCACTAGTCAAAGAGGCCGCTTCACTTTGGATGACGTCATCCAAGGGGTGAATAGTTCAG
ATATGATCCTGTGTTTCCTGGCCACCCAGGCTGCCAGGGAAATGCAATCTCAGGACAGGAAAATAACCCTCCTTTAAAGT
TGATTACTGAGGCAGGGCTCATTCCCAAGCTGGTGGACTTCCTGAAGGTGACACCTCTCCCTAACTTGCAGTTTGAGGCC
GCGTGGACGCTCGCCAACATTGCCTCAGGAACTTCAGAGCAGACCCGAGCTGTTGTGAAAGGGGTTGCCATTCAGCCCCT
GCTTGAACTCTTCCGTTCCCCAGACCTGACCGTGTCTGAGCAGGCAGTGTGGGTCCCTGGGAATATAGCTGGTGACTGTG
CAGAATTCAGAGACAATGTCATTTCCAATAATGCCATCCCACACCTTATCAACCTTATTTCAACAAACATACCAATCACA
TTTCTTCGGAACATCACATTGACTTTGTCCAACGTATGCCGAAACAAAAATCCACACCCTGTGAGGATGCCTCCATGAGG
CAGATGCTACCTGCTCTCTGTCAGCTCCCACTGGATCATGGTAATGAGATTCTCTCAGATACCTGCTGGGCCCTGGCCTA
CCTGACTGAGGGCAGCAAAGAGTATATCCATCATGTGGTGACCACCGGCATCCTGCCCGGGCTTGTAGAACTTAAGACCA
GCTCAGAACTCAGTGTCTTGACCCCTTGTCTCCACACTATGGGCTGCATTGTGGCTGGAACAGATGAACAGACCCAAATG
GCCATCGATGCTGGCATGCTAAAGGTGTTGGGCCAGGTCCTGAAGCACCCAAAGTTCTCCATCCAGAAGCTGGCGGCCAG
GACCGTGAGCAACACAGCCGCTGGGCCCAGGCACCACATCTAACAGCTGATTTTGTAACTTGCTGCCTGTCTTGGTAGAC
CTACTGAGGAATGTGGAATTAAAAATCCAAAAAGAGGTTGTGTGCACCATGGCTAACATGGCAACAGGGGCCTCTCAGTG
CCAGCTGACTCTGCTTGCCCACTCGGGAATCTTGGAACCAATGCTGAGTCTGCTCACTGCCCCAGACATGGAGGTTGTCA
TTGTTGGCCTTGACATCATTTCTTATCTCCTCCAGATAGACCACCTACAGGAGAAGAAAAGGCTGTGTTTTCAGACAGAG
GAAGTTGGTGGCTTTTAAAAAGTTGAGTCCCTACAGCACCACCACAACACTTAACATCAGCAATGGTGCTCTGGACATCA
TTGAGAAATATTTATGTGAGGATGAAGACAACGACAGTCTGCCCAGGCCTGGACTGAGAGTG

ORF - retro_mmus_3301 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 75.94 %
Parental protein coverage: 100. %
Number of stop codons detected: 5
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalMATSKAPKERLKNYKYRGKEMSLPRQQRIASSLQLRKTRKDEQVLKRRNIDLFSSDMVSQALVKEV-NFT
.ATS..PK.RLK.YKY.GKEMSL...QRI.SSLQ..KTRKDEQVLKRRNI.LF..D.VSQALVKE...FT
RetrocopyIATSESPKKRLKKYKYQGKEMSLQ*RQRIVSSLQFWKTRKDEQVLKRRNINLFPRDVVSQALVKEA<RFT
ParentalLDDIIQAVNSSDPILHFRATRAAREMISQENTPPL--NLIIEAGLIP-KLVDFLKATPHPKLQFEAAWVL
LDD.IQ.VNSSD.IL.F.AT.AAREM.SQ.....L........G..P.KLVDFLK.TP.P.LQFEAAW.L
RetrocopyLDDVIQGVNSSDMILCFLATQAAREMQSQDRKITLL*S*LLRQGSFP<KLVDFLKVTPLPNLQFEAAWTL
ParentalTNIASGTSEQTRAVVKEGAIQPLIELLCSPHLTVSEQAVWALGNIAGDCAEFRDCVISNNAIPHLINLIS
.NIASGTSEQTRAVVK..AIQPL.EL..SP.LTVSEQAVW..GNIAGDCAEFRD.VISNNAIPHLINLIS
RetrocopyANIASGTSEQTRAVVKGVAIQPLLELFRSPDLTVSEQAVWVPGNIAGDCAEFRDNVISNNAIPHLINLIS
ParentalKGIPITFLRNISWTLSNLCRNKDPY-PSESA-VRQMLPPLCQLLLHRDNEILADTCWALSYLTKGGKEYI
..IPITFLRNI..TLSN.CRNK.P..P.E.A..RQMLP.LCQL.L...NEIL.DTCWAL.YLT.G.KEYI
RetrocopyTNIPITFLRNITLTLSNVCRNKNPH<PCEDASMRQMLPALCQLPLDHGNEILSDTCWALAYLTEGSKEYI
ParentalHHVVTTGILPRLVELMTSSELSISIPCLHTIGNIVAGTDEQTQMAIDAGMLKVLGQVLKHPKTSIQVLAA
HHVVTTGILP.LVEL.TSSELS...PCLHT.G.IVAGTDEQTQMAIDAGMLKVLGQVLKHPK.SIQ.LAA
RetrocopyHHVVTTGILPGLVELKTSSELSVLTPCLHTMGCIVAGTDEQTQMAIDAGMLKVLGQVLKHPKFSIQKLAA
ParentalWTMSNVAAGPRHQVEQLL-CNLLPILVDLLRNAELKVQKEVVCTVINIATGASQDQLTLLAHSGILEPML
.T.SN.AAGPRH...QL..CNLLP.LVDLLRN.ELK.QKEVVCT..N.ATGASQ.QLTLLAHSGILEPML
RetrocopyRTVSNTAAGPRHHI*QLI>CNLLPVLVDLLRNVELKIQKEVVCTMANMATGASQCQLTLLAHSGILEPML
ParentalSLLSAPDLEVVIIVLDIISYLLQHIDNLQEKKRLYFQIEKFGGFEKIECLQHHHN-ISISNSALDIIEKY
SLL.APD.EVVI..LDIISYLLQ.ID.LQEKKRL.FQ.E..GGF.K.E.LQHHHN...ISN.ALDIIEKY
RetrocopySLLTAPDMEVVIVGLDIISYLLQ-IDHLQEKKRLCFQTEEVGGF*KVESLQHHHN>LNISNGALDIIEKY
ParentalFCEDGDGDSLPGPGLRV
.CED.D.DSLP.PGLRV
RetrocopyLCEDEDNDSLPRPGLRV

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
SRP007412_brain 0 .00 RPM 0 .02 RPM
SRP007412_cerebellum 0 .00 RPM 0 .00 RPM
SRP007412_heart 0 .00 RPM 0 .00 RPM
SRP007412_kidney 0 .00 RPM 0 .02 RPM
SRP007412_liver 0 .00 RPM 0 .00 RPM
SRP007412_testis 0 .00 RPM 2 .93 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_3301 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_3301 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_mmus_3301 retrocopy 5' end.

Lab - click to see more details

retro_mmus_3301 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_3301 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 15 parental genes, and 24 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000151252 retrocopies
retro_cfam_459, retro_cfam_861,
Choloepus hoffmanni ENSCHOG000000042431 retrocopy
retro_chof_805,
Callithrix jacchus ENSCJAG000000159431 retrocopy
retro_cjac_2964,
Equus caballus ENSECAG000000005541 retrocopy
retro_ecab_981,
Echinops telfairi ENSETEG000000000961 retrocopy
retro_etel_1548,
Homo sapiens ENSG000001854671 retrocopy
retro_hsap_3337,
Mus musculus ENSMUSG000000183621 retrocopy
retro_mmus_229,
Mus musculus ENSMUSG00000038770 2 retrocopies
retro_mmus_2844, retro_mmus_3301 ,
Nomascus leucogenys ENSNLEG000000108271 retrocopy
retro_nleu_1680,
Otolemur garnettii ENSOGAG000000311063 retrocopies
retro_ogar_1289, retro_ogar_3237, retro_ogar_353,
Ochotona princeps ENSOPRG000000154342 retrocopies
retro_opri_1101, retro_opri_118,
Pongo abelii ENSPPYG000000173691 retrocopy
retro_pabe_2750,
Pan troglodytes ENSPTRG000000194462 retrocopies
retro_ptro_102, retro_ptro_2142,
Tupaia belangeri ENSTBEG000000090073 retrocopies
retro_tbel_1475, retro_tbel_3862, retro_tbel_3962,
Tursiops truncatus ENSTTRG000000029982 retrocopies
retro_ttru_1426, retro_ttru_430,


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