RetrogeneDB - Retrocopy retro_mmus

                        
>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:	100.0 %
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 activity 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	ENSCAFG00000015125	2 retrocopies	retro_cfam_459, retro_cfam_861,
Choloepus hoffmanni	ENSCHOG00000004243	1 retrocopy	retro_chof_805,
Callithrix jacchus	ENSCJAG00000015943	1 retrocopy	retro_cjac_2964,
Equus caballus	ENSECAG00000000554	1 retrocopy	retro_ecab_981,
Echinops telfairi	ENSETEG00000000096	1 retrocopy	retro_etel_1548,
Homo sapiens	ENSG00000185467	1 retrocopy	retro_hsap_3337,
Mus musculus	ENSMUSG00000018362	1 retrocopy	retro_mmus_229,
Mus musculus	ENSMUSG00000038770	2 retrocopies	retro_mmus_2844, retro_mmus_3301 ,
Nomascus leucogenys	ENSNLEG00000010827	1 retrocopy	retro_nleu_1680,
Otolemur garnettii	ENSOGAG00000031106	3 retrocopies	retro_ogar_1289, retro_ogar_3237, retro_ogar_353,
Ochotona princeps	ENSOPRG00000015434	2 retrocopies	retro_opri_1101, retro_opri_118,
Pongo abelii	ENSPPYG00000017369	1 retrocopy	retro_pabe_2750,
Pan troglodytes	ENSPTRG00000019446	2 retrocopies	retro_ptro_102, retro_ptro_2142,
Tupaia belangeri	ENSTBEG00000009007	3 retrocopies	retro_tbel_1475, retro_tbel_3862, retro_tbel_3962,
Tursiops truncatus	ENSTTRG00000002998	2 retrocopies	retro_ttru_1426, retro_ttru_430,

	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]

Parental	MATSKAPKERLKNYKYRGKEMSLPRQQRIASSLQLRKTRKDEQVLKRRNIDLFSSDMVSQALVKEV-NFT
	.ATS..PK.RLK.YKY.GKEMSL...QRI.SSLQ..KTRKDEQVLKRRNI.LF..D.VSQALVKE...FT
Retrocopy	IATSESPKKRLKKYKYQGKEMSLQ*RQRIVSSLQFWKTRKDEQVLKRRNINLFPRDVVSQALVKEA<RFT

Parental	LDDIIQAVNSSDPILHFRATRAAREMISQENTPPL--NLIIEAGLIP-KLVDFLKATPHPKLQFEAAWVL
	LDD.IQ.VNSSD.IL.F.AT.AAREM.SQ.....L........G..P.KLVDFLK.TP.P.LQFEAAW.L
Retrocopy	LDDVIQGVNSSDMILCFLATQAAREMQSQDRKITLLSLLRQGSFP<KLVDFLKVTPLPNLQFEAAWTL

Parental	TNIASGTSEQTRAVVKEGAIQPLIELLCSPHLTVSEQAVWALGNIAGDCAEFRDCVISNNAIPHLINLIS
	.NIASGTSEQTRAVVK..AIQPL.EL..SP.LTVSEQAVW..GNIAGDCAEFRD.VISNNAIPHLINLIS
Retrocopy	ANIASGTSEQTRAVVKGVAIQPLLELFRSPDLTVSEQAVWVPGNIAGDCAEFRDNVISNNAIPHLINLIS

Parental	KGIPITFLRNISWTLSNLCRNKDPY-PSESA-VRQMLPPLCQLLLHRDNEILADTCWALSYLTKGGKEYI
	..IPITFLRNI..TLSN.CRNK.P..P.E.A..RQMLP.LCQL.L...NEIL.DTCWAL.YLT.G.KEYI
Retrocopy	TNIPITFLRNITLTLSNVCRNKNPH<PCEDASMRQMLPALCQLPLDHGNEILSDTCWALAYLTEGSKEYI

Parental	HHVVTTGILPRLVELMTSSELSISIPCLHTIGNIVAGTDEQTQMAIDAGMLKVLGQVLKHPKTSIQVLAA
	HHVVTTGILP.LVEL.TSSELS...PCLHT.G.IVAGTDEQTQMAIDAGMLKVLGQVLKHPK.SIQ.LAA
Retrocopy	HHVVTTGILPGLVELKTSSELSVLTPCLHTMGCIVAGTDEQTQMAIDAGMLKVLGQVLKHPKFSIQKLAA

Parental	WTMSNVAAGPRHQVEQLL-CNLLPILVDLLRNAELKVQKEVVCTVINIATGASQDQLTLLAHSGILEPML
	.T.SN.AAGPRH...QL..CNLLP.LVDLLRN.ELK.QKEVVCT..N.ATGASQ.QLTLLAHSGILEPML
Retrocopy	RTVSNTAAGPRHHI*QLI>CNLLPVLVDLLRNVELKIQKEVVCTMANMATGASQCQLTLLAHSGILEPML

Parental	SLLSAPDLEVVIIVLDIISYLLQHIDNLQEKKRLYFQIEKFGGFEKIECLQHHHN-ISISNSALDIIEKY
	SLL.APD.EVVI..LDIISYLLQ.ID.LQEKKRL.FQ.E..GGF.K.E.LQHHHN...ISN.ALDIIEKY
Retrocopy	SLLTAPDMEVVIVGLDIISYLLQ-IDHLQEKKRLCFQTEEVGGF*KVESLQHHHN>LNISNGALDIIEKY

Parental	FCEDGDGDSLPGPGLRV
	.CED.D.DSLP.PGLRV
Retrocopy	LCEDEDNDSLPRPGLRV

*	Stop codon
>	Forward frameshift by one nucleotide
<	Reverse frameshift by one nucleotide

RetrogeneDB ID:

retro_mmus_3301