RetrogeneDB ID:

retro_cfam_98

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:16:12956940..12958353(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCAFG00000003207
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCAFG00000017071
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cfam_98
ATGCAGAGCAATAAAACCTTTAACTTGGAGAAGCAAAACCATACTCCAAGGAAGCATCATCAGCATCACCACCAGCAGCA
CCACCAGCAGCAACAGCAGCAACCACCACCGCCACCAATACCTGCAAATGGGCAACAAGCCAGCAGCCAAAATGAAGACT
TGACTATTGACCTGAAGAGTTTTAGGAAACCAGGAGAGAAGACCTTCACCCAACGTAGCCGGCTCTTTGTGGGCAATCTT
CCTCCTGATATCACTGAAGAGGAGATGAGGAAACTATTTGAGAAATACGGGAAAGCAGGTGAAGTCTTCATTCATAAGGA
TAAGGGCTTTGGCTTTATCCGCTTGGAAACACGAACCTTAGCGGAGATTGCCAAAGTAGAATTGGACAACATGCCACTTC
GTGGAAAGCAGCTGCGTGTGCGTTTTGCCTGCCATAGTGCATCCCTTACAGTCCGAAACCTTCCTCAGTATGTTTCCAAT
GAACTGCTGGAGGAAGCCTTTTCCGTGTTTGGCCAGGTGGAGAGGGCTGTAGTCATCGTGGATGATCGAGGAAGGCCCTC
AGGAAAAGGCATTGTTGAATTCTCAGGGAAGCCAGCTGCTCGGAAAGCTCTGGACAGGTGCAGTGAAGGCTCTTTCCTGC
TAACCACATTTCCTAGGCCTGTGACTGTGGAGCCCATGGACCAGTTGGATGATGAAGAGGGACTTCCAGAGAAACTGGTT
ATAAAGAATCAGCAATTTCACAAGGAGCGAGAGCAGCCACCCAGATTTGCACAGCCTGGCTCCTCTGAGTATGAGTATGC
CATGCGCTGGAAGGCACTGATTGAGATGGAGAAGCAGCAGCAGGACCAAGTGGACCGCAACATCAAGGAAGCTCGTGAGA
AGCTGGAGATGGAGATGGAGGCTGCTCGCCATGAGCACCAGGTCATGCTAATGAGACAGGATTTGATGAGGCGTCAAGAA
GAACTTAGGAGGATGGAAGAGCTGCATAACCAAGAAGTGCAAAAACGAAAGCAACTGGAGCTCAGGCAAGAGGAGGAGCG
CAGGCGCCGAGAGGAAGAGATGCGGCGGCAACAGGAAGAAATGATGCGGCGACAGCAGGAAGGATTCAAGGGAACATTCC
CTGATGCGAGAGAACAGGAGATACGGATGGGGCAGATGGCTATGGGAGGTGCTATGGGCATAAACAATAGAGGTGCCATG
CCCCCTGCTCCAGTGCCAGCTGGTACCCCAGCTCCTCCAGAACCTGCCACTATGATGCCAGATGGAACCTTGGGATTGAC
CCCACCAACAACTGAATGCTTTGGCCAGGCTGCTACAATGGAAGGAATTGGGGCAATTGGTGGAACCCCTCCTGCATTCA
ACCGTGCAGCTCCTGGAGCTGAATTTGCTCCAAACAAACGTTGCCGATACTAA

ORF - retro_cfam_98 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 98.72 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMQSNKTFNLEKQNHTPRKHHQHHHQQHHQQQQQQPPPPPIPANGQQASSQNEGLTIDLKNFRKPGEKTFT
MQSNKTFNLEKQNHTPRKHHQHHHQQHHQQQQQQPPPPPIPANGQQASSQNE.LTIDLK.FRKPGEKTFT
RetrocopyMQSNKTFNLEKQNHTPRKHHQHHHQQHHQQQQQQPPPPPIPANGQQASSQNEDLTIDLKSFRKPGEKTFT
ParentalQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRV
QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRV
RetrocopyQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRV
ParentalRFACHSASLTVRNLPQYVSNELLEEAFSVFGQVERAVVIVDDRGRPSGKGIVEFSGKPAARKALDRCSEG
RFACHSASLTVRNLPQYVSNELLEEAFSVFGQVERAVVIVDDRGRPSGKGIVEFSGKPAARKALDRCSEG
RetrocopyRFACHSASLTVRNLPQYVSNELLEEAFSVFGQVERAVVIVDDRGRPSGKGIVEFSGKPAARKALDRCSEG
ParentalSFLLTTFPRPVTVEPMDQLDDEEGLPEKLVIKNQQFHKEREQPPRFAQPGSFEYEYAMRWKALIEMEKQQ
SFLLTTFPRPVTVEPMDQLDDEEGLPEKLVIKNQQFHKEREQPPRFAQPGS.EYEYAMRWKALIEMEKQQ
RetrocopySFLLTTFPRPVTVEPMDQLDDEEGLPEKLVIKNQQFHKEREQPPRFAQPGSSEYEYAMRWKALIEMEKQQ
ParentalQDQVDRNIKEAREKLEMEMEAARHEHQVMLMRQDLMRRQEELRRMEELHNQEVQKRKQLELRQEEERRRR
QDQVDRNIKEAREKLEMEMEAARHEHQVMLMRQDLMRRQEELRRMEELHNQEVQKRKQLELRQEEERRRR
RetrocopyQDQVDRNIKEAREKLEMEMEAARHEHQVMLMRQDLMRRQEELRRMEELHNQEVQKRKQLELRQEEERRRR
ParentalEEEMRRQQEEMMRRQQEGFKGTFPDAREQEIRMGQMAMGGAMGINNRGAMPPAPVPAGTPAPPGPATMMP
EEEMRRQQEEMMRRQQEGFKGTFPDAREQEIRMGQMAMGGAMGINNRGAMPPAPVPAGTPAPP.PATMMP
RetrocopyEEEMRRQQEEMMRRQQEGFKGTFPDAREQEIRMGQMAMGGAMGINNRGAMPPAPVPAGTPAPPEPATMMP
ParentalDGTLGLTPPTTERFGQAATMEGIGAIGGTPPAFNRAAPGAEFAPNKRRRY
DGTLGLTPPTTE.FGQAATMEGIGAIGGTPPAFNRAAPGAEFAPNKR.RY
RetrocopyDGTLGLTPPTTECFGQAATMEGIGAIGGTPPAFNRAAPGAEFAPNKRCRY

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 4 .91 RPM 100 .34 RPM
SRP017611_brain 1 .11 RPM 32 .71 RPM
SRP017611_kidney 2 .05 RPM 61 .94 RPM
SRP017611_liver 1 .02 RPM 35 .02 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_98 retrocopy.

TSS - click to see more details

Canis familiaris was not studied using FANTOM5 data.

Lab - click to see more details

retro_cfam_98 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_98 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 22 parental genes, and 32 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000160572 retrocopies
retro_amel_1438, retro_amel_795,
Bos taurus ENSBTAG000000121522 retrocopies
retro_btau_1027, retro_btau_313,
Canis familiaris ENSCAFG000000035951 retrocopy
retro_cfam_198,
Canis familiaris ENSCAFG00000017071 1 retrocopy
retro_cfam_98 ,
Callithrix jacchus ENSCJAG000000367441 retrocopy
retro_cjac_3990,
Equus caballus ENSECAG000000085022 retrocopies
retro_ecab_357, retro_ecab_427,
Felis catus ENSFCAG000000148072 retrocopies
retro_fcat_1219, retro_fcat_147,
Homo sapiens ENSG000001471401 retrocopy
retro_hsap_1699,
Gorilla gorilla ENSGGOG000000061941 retrocopy
retro_ggor_1273,
Microcebus murinus ENSMICG000000002321 retrocopy
retro_mmur_569,
Myotis lucifugus ENSMLUG000000024891 retrocopy
retro_mluc_622,
Mustela putorius furoENSMPUG000000049371 retrocopy
retro_mputfur_937,
Mus musculus ENSMUSG000000313112 retrocopies
retro_mmus_3652, retro_mmus_632,
Nomascus leucogenys ENSNLEG000000012781 retrocopy
retro_nleu_1344,
Oryctolagus cuniculus ENSOCUG000000218482 retrocopies
retro_ocun_1317, retro_ocun_1804,
Otolemur garnettii ENSOGAG000000048343 retrocopies
retro_ogar_1525, retro_ogar_546, retro_ogar_593,
Pongo abelii ENSPPYG000000204511 retrocopy
retro_pabe_1398,
Pan troglodytes ENSPTRG000000220101 retrocopy
retro_ptro_1150,
Pteropus vampyrus ENSPVAG000000165031 retrocopy
retro_pvam_444,
Rattus norvegicus ENSRNOG000000036892 retrocopies
retro_rnor_1178, retro_rnor_1503,
Sorex araneus ENSSARG000000079592 retrocopies
retro_sara_661, retro_sara_663,
Drosophila melanogaster FBgn00042271 retrocopy
retro_dmel_11,


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