RetrogeneDB ID:

retro_cfam_681

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:15:26354063..26355983(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:ZNF398
Ensembl ID:ENSCAFG00000004429
Aliases:None
Description:zinc finger protein 398 [Source:HGNC Symbol;Acc:18373]


Retrocopy-Parental alignment summary:






>retro_cfam_681
GAGAACAGTAGCCGTGAGACTTCCGAATGGGACTCCGAAGGCCTTACGTCGCTGCAGCCCCTTCCTCTTCGCACGCCCCC
AGCAGCAAATGAGGCACACCTGCAGACTGTGGCCATCTCCCTGTGGACAGTGGTGGCAGCTGTGCAGGCTATCGAGAGGA
AGGTGGAGGTCCACAGCCGGCGACTCTTGCACCTAGAAGGACAGACGGGGACAGCAGAGAAGAAGCTAGCCAGCTGTGAA
AAGACGGTGGCTGACCTTGGGAACCAACTGGAGGGCAAGTGGGCTGTGCTGGGGACCCTGCTGCAGGAGTATGGGCTGCT
GCAGAGGCGGCTGGAGAACTTGGAGGACCTGCTGAGGAACAGGAACTTCTGGATTCTGGGCTGCCACCCGGCATTAGAGG
AGATATCCCGAAGGTGCCTGTGACATTTGATGATATCTCCATCTACTTTTCCACTCCGGAGTGGGAAAAAACTGGAAGAA
TGGCAAAAAGAACTTTACAAGAATATCATGAAGGGCAACTACGAGTCTCTCATCTCCATGGATGATGCCATGAATCAACC
TGATGTCTTATCTCCGATTCAGCCAGAAAGAGAACATACTACAGAGGACCAGGCAGGACCAGAGGAAAGTGAGATTCCCA
CAGACCCCAGTGAAGAGCCTGGCATTTCAACATCAGATATTCTGTCTTGGATCAAACAAGAGGAAGAGCCCCAGGCTGGG
GCCCCACAGGAGACCAAGGACAGTGACATGCACGAGGGCACCTATGCTGATGAAGAACTTGTCCTCAAAGCTGAAAGCCT
TGCCAGAGCCTCCTTGTGCCCAGAGCTTCCGGTCACCTTCTCTTCTCCACCACCAGCAGCAAAGGATACTTTTTCAGATG
TGACTTTCAAAGGTCAGCCCTCTGCATCCATGGCACCTTTCGGGCGTCCGGCTGCCGACCTGGCTGAAGCCTCTGAGGGA
CAAGTGACTTTTACGCAGTTGGGTAGCTACCCCCTGCCACCTCCAGCTGGGGAGCAGGTCTTCTCATGCCACCACTGTGG
CAAGAGCCTCAGCCAAGACATGCTGCTCACCCACCAGTGTAGCCACACGGGTGAGAACCCGTTACCCTGAGCCCAGTGCC
CGAAACACCTCCCCCAGCAGGCCGACCTGGGCAGCAGCTCCCAGCCGCATGCTAGCGAGACGCCCCCCACCTGTCCACAC
TGCGCCAGGACTTTCACTCACCCGTCCAGACTCACCTACCACCTTCGGGTGCATAACAGCACCGAGCGCCCTTTCCCCTG
CCCTGACTGCCCCAAGCGCTTCGCCGACCAGGCCCGGCTCAGCAGCCCCGGCGAGCTCACGCCAGCCAGCGTCCCATGCG
CTGCGCCCGGTGCGGCCGGAGCTTCAGCCTGAAAATCAGCCTCCTGCTCCACCAGCGGGGGCACGCACAGGAGCGGCCCT
TCTCCTGCCCGCAGTGCGGCACTGACTTCGAGGGCCACTCAGCTCCGATCCGCCACCAGACGATCCGCACGGGCGAGCGG
CCAACCCGTGCACTGACTGCAGCAAGAGCTTGGTGCGCAAGGAGCACCTGCTGAACCACCGGCGGCTGCACGCGGGCGAG
CGGCCCTTCCGCTGCGCGCACTGCGGCGAGAGCTTCATCCGCAGGCACCACCTCATGCAGCACCAGCATCCACACGGGCG
AGCGGCCCTACCCCTGCGCCTACTGTGGCAGAAGCTTCCGCTACAAACAGACGCTCAAGGACCACCTGCGCTCCGGCCAC
AGTGGAGGCTGCGGGGGTGACAGCAACCACTCCGGACCGCCAGCCGCCTGACCCGCCGGGGCCCCTCCTAACCGGGCTCG
AAACCTCTGGCCTCGCTGTTAACACCGAAGGTCTAGAGGCCAATCAGTGGTATGGGGAAGGGAGCGGAGGGGGAGTTTTG

ORF - retro_cfam_681 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.22 %
Parental protein coverage: 99.69 %
Number of stop codons detected: 1
Number of frameshifts detected 6


Retrocopy - Parental Gene Alignment:

ParentalEAAPAPTSEWDSECLTSLQPLPLPTPPAANEAHLQTAAISLWTVVAAVQAIERKVEVHSRRLLHLEGRTG
E.....TSEWDSE.LTSLQPLPL.TPPAANEAHLQT.AISLWTVVAAVQAIERKVEVHSRRLLHLEG.TG
RetrocopyENSSRETSEWDSEGLTSLQPLPLRTPPAANEAHLQTVAISLWTVVAAVQAIERKVEVHSRRLLHLEGQTG
ParentalTAEKKLASCEKTVADLGNQLEGKWAVLGTLLQEYGLLQRRLENLENLLRNRNFWILR-LPPGIKGDIPKV
TAEKKLASCEKTVADLGNQLEGKWAVLGTLLQEYGLLQRRLENLE.LLRNRNFWIL..LPPGI.GDIPKV
RetrocopyTAEKKLASCEKTVADLGNQLEGKWAVLGTLLQEYGLLQRRLENLEDLLRNRNFWILG<LPPGIRGDIPKV
ParentalPVTFDDISIYFSTPEWEK-LEEWQKELYKNIMKGNYESLISMDYAMNQPDVLSQIQPEREHTTEDQAGPE
PVTFDDISIYFSTPEWEK.LEEWQKELYKNIMKGNYESLISMD.AMNQPDVLS.IQPEREHTTEDQAGPE
RetrocopyPVTFDDISIYFSTPEWEK>LEEWQKELYKNIMKGNYESLISMDDAMNQPDVLSPIQPEREHTTEDQAGPE
ParentalESEIPTDPSEEIEPGISTSDILSWIKQEEEPQVGAPQETKDSDMHKGTYADEELVIKAESLARASLCPEV
ESEIPTDPSEE..PGISTSDILSWIKQEEEPQ.GAPQETKDSDMH.GTYADEELV.KAESLARASLCPE.
RetrocopyESEIPTDPSEE--PGISTSDILSWIKQEEEPQAGAPQETKDSDMHEGTYADEELVLKAESLARASLCPEL
ParentalPVTFSSPPPAAKDTFSDVTFKGQPSASMAPFGRPAADLAEASEGQVTFTQLGSYPLPPPAGEQVFSCHHC
PVTFSSPPPAAKDTFSDVTFKGQPSASMAPFGRPAADLAEASEGQVTFTQLGSYPLPPPAGEQVFSCHHC
RetrocopyPVTFSSPPPAAKDTFSDVTFKGQPSASMAPFGRPAADLAEASEGQVTFTQLGSYPLPPPAGEQVFSCHHC
ParentalGKSLSQDMLLTHQCSHTGENPLPCAQCPKHFPQQADLGSSSQPHASETPPTCPHCARTFTHPSRLTYHLR
GKSLSQDMLLTHQCSHTGENPLP.AQCPKH.PQQADLGSSSQPHASETPPTCPHCARTFTHPSRLTYHLR
RetrocopyGKSLSQDMLLTHQCSHTGENPLP*AQCPKHLPQQADLGSSSQPHASETPPTCPHCARTFTHPSRLTYHLR
ParentalVHNSTERPFPCPDCPKRFADQARLSS-HRRAHASERPFRCAQCGRSFSLKISLLLHQRGHAQERPFSCPQ
VHNSTERPFPCPDCPKRFADQARLSS..RRAHAS.RP.RCA.CGRSFSLKISLLLHQRGHAQERPFSCPQ
RetrocopyVHNSTERPFPCPDCPKRFADQARLSS<PRRAHASQRPMRCARCGRSFSLKISLLLHQRGHAQERPFSCPQ
ParentalCGIDFNGHSALIRHQMIHTGERP-YPCTDCSKSFMRKEHLLNHRRLHTGERPFSCAHCGKSFIRKHHLMK
CG.DF.GHSA.IRHQ.I.TGERP..PCTDCSKS..RKEHLLNHRRLH.GERPF.CAHCG.SFIR.HHLM.
RetrocopyCGTDFEGHSAPIRHQTIRTGERP<NPCTDCSKSLVRKEHLLNHRRLHAGERPFRCAHCGESFIRRHHLMQ
ParentalHQRIHTGERPYP-CAYCGRSFRYKQTLKDHLRSGHSGGCGGDSNHSGQP-PDPP-GPLLTGLETSGLPVN
HQ..H.G....P.CAYCGRSFRYKQTLKDHLRSGHSGGCGGDSNHSG.P.P..P.GPLLTGLETSGL.VN
RetrocopyHQHPH-GRAALP>CAYCGRSFRYKQTLKDHLRSGHSGGCGGDSNHSGPP>PPDPPGPLLTGLETSGLAVN
ParentalTEGLEANQWYGEGSGGGVL
TEGLEANQWYGEGSGGGVL
RetrocopyTEGLEANQWYGEGSGGGVL

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 .17 RPM 17 .81 RPM
SRP017611_brain 0 .16 RPM 13 .73 RPM
SRP017611_kidney 0 .33 RPM 6 .87 RPM
SRP017611_liver 0 .07 RPM 6 .24 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_681 retrocopy.

TSS - click to see more details

Canis familiaris was not studied using FANTOM5 data.

Lab - click to see more details

retro_cfam_681 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_681 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG00000004429 1 retrocopy
retro_cfam_681 ,


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