RetrogeneDB - Retrocopy retro_dord

                        
>retro_dord_71
ATGGTGTCGAGTGATGGCAACCTGGGGAGTTTATTATACCACCATGTCCAGAGGCCGTGTGGGACACATGGGCAAACATT

GGGAGGGCGGTTGACCTCGCGCTGTTAGGGTGTAAACAATCAATCTTGAATCTCATTACTTAATAATACAAGGAGTTCCT

GCAGTGGGAGCAATGAAGGAATTAGTTGAGCGATTTGCTCTATATGGTGTTATAGAAGAATATAATGCTCTTGGTGAATA

CTCAGCAGGAGACTTTACAGAAGTTTATCTTATTAAGTTTATGAATTTGCAGAGTGCAAGGATAACCAAGGAAAAAAATG

GATGAGCAAAATTTCTTTTGTGGGTTGCTTCATATATGCTAGGCTCCAGAATTTGAGACAGTTGAAGAAACTAAAAAGAA

TAAGAAGAAAGTCAGGCTTATATAGCAAAAGCTACTAAAACTAAAGACTACTACAAGTCAGTGAAGAAACTGGTTCCAGA

ATATAAGCACAGAGATTTTAGATCAGACTTCCACGCAGATAGATCTGGATTTTGTGCAGCTTCTTTGAAGACTAGTGGAA

AGTCAACTCCTTATCTTCCTTATTCTTGTGAATTGCCTTTCTGTTATTTTGCCTCAAAATGTACCTGTTCATCTGGGGAG

CACATGGACAGACCATCAAAATCCTACAAGGATGATAGTAACCATAATGAAACTGTGAAGCATTGTAATCACACTAACTC

TTCACAGAAAGTGCCACTAAACACTTTTAAGAATCCAGTACCTTGCTTGAATGCACAAAAAAACCTTACTTCATCAGAGG

CAGTTGACAGATTTATGCCTAGAACAATATAACTCCAGGAACAGAAAAGAAGAAAAGATGACTGTAAACTTGGAACTTTG

CTTGAAGCAAGCACAAGCAGTAATGAGGTTATGATGAGGCCTAAATTACCAGACATACCTAAAGTGGATTTGCAGGATAA

CTCCTTAAATACAATGGCCAACTTAATTTGGAATAAACTTAAAGAGGTAATTTCATCTGTACCAAAGCCTTCAGATGACA

AGTTGGAAAATTCATGTCCAACTCATCCATTGAAACAAAGAAGA

ORF - retro_dord_71 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	82.29 %
Parental protein coverage:	99.45 %
Number of stop codons detected:	4
Number of frameshifts detected:	4

Retrocopy - Parental Gene Alignment:

                                ParentalMASGDGKLGSLLEHHVQR-AVCDTRA-KYREGRRPRAVKVYTINLESRYLIIQGVPAVGAMKELVERFAL
M.S.DG.LGSLL.HHVQR.AV.DT.A.K..EG..PRAV.V.TINLES.YLIIQGVPAVGAMKELVERFAL
RetrocopyMVSSDGNLGSLLYHHVQR<AVWDTWA<KHWEGG*PRAVRV*TINLESHYLIIQGVPAVGAMKELVERFAL
ParentalYGAIEEYNALDEYPAEDFTEVYLIKFVNLQSARIAK-KKMDEQSFFGGLLHVCYAPEFETVEETRKKL-E
YG.IEEYNAL.EY.A.DFTEVYLIKF.NLQSARI.K.KKMDEQ.FF.GLLH.C.APEFETVEET.K...E
RetrocopyYGVIEEYNALGEYSAGDFTEVYLIKFMNLQSARITK>KKMDEQNFFCGLLHIC*APEFETVEETKKNK<E
ParentalERQAYITRATKTKDYYKSKRKVIPEHKHKDFRSDFHSDRSGFCAASLKTSGNSTTCLPYSCELPLCYFAS
E.QAYI..ATKTKDYYKS..K..PE.KH.DFRSDFH.DRSGFCAASLKTSG.ST..LPYSCELP.CYFAS
RetrocopyESQAYIAKATKTKDYYKSVKKLVPEYKHRDFRSDFHADRSGFCAASLKTSGKSTPYLPYSCELPFCYFAS
ParentalKCTCSSGEHMDRPSNSYKDDSNHNEAVKYCNHTNSSQKVPLNTFKNPVPCLNAQKDLISSEAVDRFMPRT
KCTCSSGEHMDRPS.SYKDDSNHNE.VK.CNHTNSSQKVPLNTFKNPVPCLNAQK.L.SSEAVDRFMPRT
RetrocopyKCTCSSGEHMDRPSKSYKDDSNHNETVKHCNHTNSSQKVPLNTFKNPVPCLNAQKNLTSSEAVDRFMPRT
ParentalTQLQERKRRREDDRKLGTLLETSTSSNEVIIGPKLPDIPKVDLQDDSLNTTANLIRNKLKEVISSVPKPS
..LQE.KRR..DD.KLGTLLE.STSSNEV...PKLPDIPKVDLQD.SLNT.ANLI.NKLKEVISSVPKPS
RetrocopyI*LQEQKRRK-DDCKLGTLLEASTSSNEVMMRPKLPDIPKVDLQDNSLNTMANLIWNKLKEVISSVPKPS
ParentalDDKLEHSCPSRPLKQRR
DDKLE.SCP..PLKQRR
RetrocopyDDKLENSCPTHPLKQRR

                            

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

                        

RNA-Seq - click to see more details

Dipodomys ordii was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Dipodomys ordii was not studied using ChIP-Seq data.

EST - click to see more details

Dipodomys ordii was not studied using EST data.

TSS - click to see more details

Dipodomys ordii was not studied using FANTOM5 data.

Lab - click to see more details

retro_dord_71 was not experimentally validated.

Retrocopy orthology:

Dipodomys ordii 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000007376	1 retrocopy	retro_cpor_683,
Dipodomys ordii	ENSDORG00000005900	1 retrocopy	retro_dord_71 ,

	RetrogeneDB ID:	retro_dord_71
Retrocopy location	Organism:	*Kangaroo rat (Dipodomys ordii)*
	Coordinates:	GeneScaffold_2012:74769..75853(+)
	Located in intron of:	ENSDORG00000014139
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	Rbm48
	Ensembl ID:	ENSDORG00000005900
	Aliases:	None
	Description:	RNA binding motif protein 48 [Source:MGI Symbol;Acc:MGI:2442653]

Parental	MASGDGKLGSLLEHHVQR-AVCDTRA-KYREGRRPRAVKVYTINLESRYLIIQGVPAVGAMKELVERFAL
	M.S.DG.LGSLL.HHVQR.AV.DT.A.K..EG..PRAV.V.TINLES.YLIIQGVPAVGAMKELVERFAL
Retrocopy	MVSSDGNLGSLLYHHVQR<AVWDTWA<KHWEGGPRAVRVTINLESHYLIIQGVPAVGAMKELVERFAL

Parental	YGAIEEYNALDEYPAEDFTEVYLIKFVNLQSARIAK-KKMDEQSFFGGLLHVCYAPEFETVEETRKKL-E
	YG.IEEYNAL.EY.A.DFTEVYLIKF.NLQSARI.K.KKMDEQ.FF.GLLH.C.APEFETVEET.K...E
Retrocopy	YGVIEEYNALGEYSAGDFTEVYLIKFMNLQSARITK>KKMDEQNFFCGLLHIC*APEFETVEETKKNK<E

Parental	ERQAYITRATKTKDYYKSKRKVIPEHKHKDFRSDFHSDRSGFCAASLKTSGNSTTCLPYSCELPLCYFAS
	E.QAYI..ATKTKDYYKS..K..PE.KH.DFRSDFH.DRSGFCAASLKTSG.ST..LPYSCELP.CYFAS
Retrocopy	ESQAYIAKATKTKDYYKSVKKLVPEYKHRDFRSDFHADRSGFCAASLKTSGKSTPYLPYSCELPFCYFAS

Parental	KCTCSSGEHMDRPSNSYKDDSNHNEAVKYCNHTNSSQKVPLNTFKNPVPCLNAQKDLISSEAVDRFMPRT
	KCTCSSGEHMDRPS.SYKDDSNHNE.VK.CNHTNSSQKVPLNTFKNPVPCLNAQK.L.SSEAVDRFMPRT
Retrocopy	KCTCSSGEHMDRPSKSYKDDSNHNETVKHCNHTNSSQKVPLNTFKNPVPCLNAQKNLTSSEAVDRFMPRT

Parental	TQLQERKRRREDDRKLGTLLETSTSSNEVIIGPKLPDIPKVDLQDDSLNTTANLIRNKLKEVISSVPKPS
	..LQE.KRR..DD.KLGTLLE.STSSNEV...PKLPDIPKVDLQD.SLNT.ANLI.NKLKEVISSVPKPS
Retrocopy	I*LQEQKRRK-DDCKLGTLLEASTSSNEVMMRPKLPDIPKVDLQDNSLNTMANLIWNKLKEVISSVPKPS

Parental	DDKLEHSCPSRPLKQRR
	DDKLE.SCP..PLKQRR
Retrocopy	DDKLENSCPTHPLKQRR

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

RetrogeneDB ID:

retro_dord_71