RetrogeneDB ID:

retro_cfam_1024

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:21:45556443..45558768(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:DDX21
Ensembl ID:ENSCAFG00000013791
Aliases:None
Description:DEAD (Asp-Glu-Ala-Asp) box helicase 21 [Source:HGNC Symbol;Acc:2744]


Retrocopy-Parental alignment summary:






>retro_cfam_1024
ATGCCGGGGAAAATCATTAGTGATGTGGGTTTGGACTCCGAGACCTCCATGGAAGAAGTGGAGACACCACGGAAGCAGAA
TGAGAAGAAAGGTAGAAAGGAGAAACCAAAATCTATTAAGACTGAAGAGGCAACAGAAGTAAAAGAAGAAATTCCTTCCC
CTAAAGCTAAAAAAGTTAAAAAGAAAGTTGAGTCTAATGAGGTTGACATGAATTCTCCTAAATCTAAAAAGGCAAAAAAG
AAAGAGGGGACATCTCAGGATGACATAATTTGTCCTAAAACCAAAAGTGTGAAAAAAACAAAGGAGTTCTTTGAAAAGAA
AGTTGTTTCTCCTAAAACAAAAAAAGTAATAAAAAGTGAAGAACCTTCTGAAGAAGAGATAAGTGCTCCTAAGCCCAAGA
AGATGAAGAAAGAAAAGGAAATGAATGGAGAAATTGGAGAGAAAAGCCCCAAACTGAAGAATGGATTCTCTCATTCTGGA
CTTGTCTCTAACACCAGTGAAACCCTAGGGGAAGAATGTAACAGTGAGTTAGAGCAGGAAATACCTGTGGAACAGAAAGA
AGGAGCTTTCTCTAATTTCCCCATATCTGAAGAGACTAATTAAAGTTCTCAAAGCCTGTGGGGTGACCTTCCTGTCTCCT
ATACAAGCAAAGACATTTTACCATGTCTATAGTGGAAAGGACTTAATTGCACAGGCACGGACAGGAACTGGGAAGACATT
CTCCTTTGCCATCCCTTTGATTGCGAAGCTCCAGGGAGAACTGCAAGACAGGAGAAGAGGTCGTGCCCCTCAGGTACTGG
TTCTTGCACCCATGAGGGAGTTGGCAAATCAAGTAAGCAGAGACTTCAGTGACATCACATGAAAGCTGGCGGTGGCTTGT
TTTTATGGTGGAACTCCCTATGGAGGTCAAATTGGACGCATGCGGAATGGGATTGATATCCGGGTTGGGACCCCAGGTCG
TATCAAAGACCACCTTCAGAATGGCAAGCTAGATCTCGCCAAACTTAAGCATGTTGTCCTGGATGAAGTCGACCAGATGT
TAGATATGGGGTTTGCTGATCAAGTGGAAGAGATTTTAAGTGTGGCATACAAAAAAGATTCAGAAGATAATCCCCAAGCA
TTGCTTTTTTCGCAACTTGCCCTCATTGGGTATATAATGTTGCTAAGAAATACATGAAATCTACATATGAACAGGTGGAC
CTGATTGGTAAAAAGACCCAGAAAACGGCAATAACCGTGGAGCACCTGGCTATCAAGTGCCACTGGACTCAAAGGGCAGC
AGTTATTGGGGATGTGATCCGAGTATATAGTGGTTTTCATGGGCGTACCATTATCTTCTTTGAAACCAAGAAAGAAGCCC
AGGAGTTGTCACAGAATGTGTCCATAAGGCAGGATGCCCAGTCATTGCATGGAGATATTCCCCAGAAGCAGAGAGAAATC
ACTCTGAAAGGTTTTAGAAATGGTGATTTTGGAGTTTTGGTTGCAACTAATGTTGCTGCTCGTGGGTTAGACATCCCTGA
GGTTGATCTGGTGATACAGAGTTCTCCACCAAAGGATGTGGAGTCCTATGTTCATCACTCTGGGAGGACGGGCAGAGCTG
GAAGGACAGGGATTTGCATCTGCTTTTATCAGCACAAGGAGGAGTATCAGTTAGCACAAGTGGAGCAAAAAGCGGGAATT
AAATTTAAACGAATAGGTGTCCCGTCTGCAACAGAGATCATAAAAGCTTCCAGCAAAGATGCCATCAGGCTTTTGGAATT
TGTGCCTCCCACTGCCATTAGTCATTTCAAGCAGTCAGCGGAGAAACTAATAGAGGAGAAAGGAGCTGTGGAAGCCCTGG
CAGCAGCCTTGGCCCATATTTCAGGTGCCACATCAGTAGACCAGCACTCTCTGATCAACTCAGATGCGGGCTTTGTGACC
ATGACCTTACGATGCTCAATTGAAATGCCAAACATTAGTTATGCTTGGAAAGAACTTAAAGAGCAGCTGGGAGAGGATAT
TGATTCCAAAGTGAAAGGAATGTTTTTTCTCAAAGGAAAGCAGGGGGTTTGCTTCGATGTCCCTACTGCAGCAGTAACAG
AAATACAGGAAAAATGGCATGATTCGTGTCGCTGGCAGCTCTCTGTGGCCACGGAGCAACCAGAGCTGGAAGGACCTCGG
GAAGGATATCGAAACTTCTGTGGACAGCAGGAAGGCAGTCAAGGATTTAGAGGACAGCGGGAGGGAAATCGAAGCTTCAG
AGGACAGCGATCAGGAGGTGGCAACAAAAATAACAGATTCCAAAACAAAGGCCAGAAGAGGAGTTTCAGTAAAGCATTTG
GGCAG

ORF - retro_cfam_1024 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.1 %
Parental protein coverage: 98.73 %
Number of stop codons detected: 1
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalMPGKLLSDAGLDSETAMEEVETPRKQNEKKGRKEKPKSIKTEEATEVKEEIPSPKAKKVKKKAESNEVDM
MPGK..SD.GLDSET.MEEVETPRKQNEKKGRKEKPKSIKTEEATEVKEEIPSPKAKKVKKK.ESNEVDM
RetrocopyMPGKIISDVGLDSETSMEEVETPRKQNEKKGRKEKPKSIKTEEATEVKEEIPSPKAKKVKKKVESNEVDM
ParentalNSPKSKKAKKKEEPSQDDIISPKTKSVKKTKESFEKKVVSPKTKKVIKSEEPSEEEISAPKPKKMKKEKE
NSPKSKKAKKKE..SQDDII.PKTKSVKKTKE.F...............EEPSEEEISAPKPKKMKKEKE
RetrocopyNSPKSKKAKKKEGTSQDDIICPKTKSVKKTKEFFXXXXXXXXXXXXXXXEEPSEEEISAPKPKKMKKEKE
ParentalMNGEIGEKSPKLKNGFPHSGLVSNTSETLGEESSSELEQEIPVEQKEGAFSNFPISEET-IKLLKARGVT
MNGEIGEKSPKLKNGF.HSGLVSNTSETLGEE..SELEQEIPVEQKEGAFSNFPISEET.IK.LKA.GVT
RetrocopyMNGEIGEKSPKLKNGFSHSGLVSNTSETLGEECNSELEQEIPVEQKEGAFSNFPISEET>IKVLKACGVT
ParentalFLFPIQAKTFYHVYSGKDLIAQARTGTGKTFSFAIPLIVKLQGELQDRKRGRAPQVLVLAPTRELANQVS
FL.PIQAKTFYHVYSGKDLIAQARTGTGKTFSFAIPLI.KLQGELQDR.RGRAPQVLVLAP.RELANQVS
RetrocopyFLSPIQAKTFYHVYSGKDLIAQARTGTGKTFSFAIPLIAKLQGELQDRRRGRAPQVLVLAPMRELANQVS
ParentalRDFSDITRKLAVACFYGGTPYGGQIERMRNGIDILVGTPGRIKDHLQNGKLDLTKLKHVVLDEVDQMLDM
RDFSDIT.KLAVACFYGGTPYGGQI.RMRNGIDI.VGTPGRIKDHLQNGKLDL.KLKHVVLDEVDQMLDM
RetrocopyRDFSDIT*KLAVACFYGGTPYGGQIGRMRNGIDIRVGTPGRIKDHLQNGKLDLAKLKHVVLDEVDQMLDM
ParentalGFADQVEEILSVAYKKDSEDNPQTLLFS-ATCPHWVYNVAKKYMKSTYEQVDLIGKKTQKTAITVEHLAI
GFADQVEEILSVAYKKDSEDNPQ.LLFS.ATCPHWVYNVAKKYMKSTYEQVDLIGKKTQKTAITVEHLAI
RetrocopyGFADQVEEILSVAYKKDSEDNPQALLFS<ATCPHWVYNVAKKYMKSTYEQVDLIGKKTQKTAITVEHLAI
ParentalKCHWTQRAAVIGDVIRVYSGFHGRTIIFCETKKEAQELSQNVSIRQDAQSLHGDIPQKQREITLKGFRNG
KCHWTQRAAVIGDVIRVYSGFHGRTIIF.ETKKEAQELSQNVSIRQDAQSLHGDIPQKQREITLKGFRNG
RetrocopyKCHWTQRAAVIGDVIRVYSGFHGRTIIFFETKKEAQELSQNVSIRQDAQSLHGDIPQKQREITLKGFRNG
ParentalDFGVLVATNVAARGLDIPEVDLVIQSSPPKDVESYIHRSGRTGRAGRTGICICFYQHKEEYQLAQVEQKA
DFGVLVATNVAARGLDIPEVDLVIQSSPPKDVESY.H.SGRTGRAGRTGICICFYQHKEEYQLAQVEQKA
RetrocopyDFGVLVATNVAARGLDIPEVDLVIQSSPPKDVESYVHHSGRTGRAGRTGICICFYQHKEEYQLAQVEQKA
ParentalGIKFKRIGVPSATEIIKASSKDAIRLLDSVPPTAISHFKQSAEKLIEEKGAVEALAAALAHISGATSVDQ
GIKFKRIGVPSATEIIKASSKDAIRLL..VPPTAISHFKQSAEKLIEEKGAVEALAAALAHISGATSVDQ
RetrocopyGIKFKRIGVPSATEIIKASSKDAIRLLEFVPPTAISHFKQSAEKLIEEKGAVEALAAALAHISGATSVDQ
ParentalRSLINSDAGFVTMILRCSIEMPNISYAWKELKEQLGEDIDSKVKGMVFLKGKQGVCFDVPTAALTEIQQE
.SLINSDAGFVTM.LRCSIEMPNISYAWKELKEQLGEDIDSKVKGM.FLKGKQGVCFDVPTAA.TEI.QE
RetrocopyHSLINSDAGFVTMTLRCSIEMPNISYAWKELKEQLGEDIDSKVKGMFFLKGKQGVCFDVPTAAVTEI-QE
ParentalKWHDSRRWQLSVATEQPELEGPREGYRNFRGQREGSRGSRGQREGSRGFRGQREGNRSFRGQRSRGGNKN
KWHDS.RWQLSVATEQPELEGPREGYRNF.GQ.EGS.G.RGQREG.R.FRGQR.G...........G.K.
RetrocopyKWHDSCRWQLSVATEQPELEGPREGYRNFCGQQEGSQGFRGQREGNRSFRGQRSGGGNKNNRFQNKGQKR
ParentalNRFQNKGQ
......GQ
RetrocopySFSKAFGQ

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
SRP012049_cerebellum 0 .08 RPM 20 .29 RPM
SRP017611_brain 0 .00 RPM 8 .89 RPM
SRP017611_kidney 0 .07 RPM 20 .47 RPM
SRP017611_liver 0 .15 RPM 19 .14 RPM

ChIP-Seq - click to see more details

Canis familiaris was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_cfam_1024 retrocopy.

TSS - click to see more details

Canis familiaris was not studied using FANTOM5 data.

Lab - click to see more details

retro_cfam_1024 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_1024 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 8 parental genes, and 11 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG00000013791 2 retrocopies
retro_cfam_1024 , retro_cfam_1925,
Callithrix jacchus ENSCJAG000000128761 retrocopy
retro_cjac_1912,
Macropus eugenii ENSMEUG000000105861 retrocopy
retro_meug_1383,
Microcebus murinus ENSMICG000000151121 retrocopy
retro_mmur_95,
Mus musculus ENSMUSG000000200752 retrocopies
retro_mmus_582, retro_mmus_662,
Procavia capensis ENSPCAG000000166971 retrocopy
retro_pcap_346,
Pongo abelii ENSPPYG000000023891 retrocopy
retro_pabe_3816,
Tupaia belangeri ENSTBEG000000023102 retrocopies
retro_tbel_1590, retro_tbel_4454,


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