RetrogeneDB ID:

retro_cfam_996

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:20:51480442..51481337(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCAFG00000010335
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cfam_996
AAAAGAACTCCATCCATGAAGTCAGGGCAAGACTATCTGGCTGGCCAATCCCAACCTTTATCAGAAGAAGCTAAAGAGAA
ACAGCAGGCTTCTGGTGAACCAAAGTTACCAGGAACCTCAGCAAGTGGGACCAAACAGAAAAGATCTATGAAAGAAGATG
AGGCTTCCTGTTCAGAAAGATGGCCCAAGGCAAGAGTACAAGAGTAAGAATTTGGAAGAAAATCCCAATTCCTCCATTAC
CTTCTAAACTACCACCAGCCAACTTGCTTCACCGAGACATCCTGCGGACCTGGTGCCAAGAATTCAAGCTGAACACCAAA
GGCCAGAAATTAGATGTATATAAGCGAATCTGCGAATATGCTTACCCAGGTCAAAAGAAGAACATTCTTGTCACCACAGA
GGAGACCAAGATTCTCACACAGACACAAAGAAAATTGATAATGGACAAGGGGGAAATGTCTCTGGAAAGTCCTGGAACAA
AGATACCTTCTGGTGGAACCTACCCTCCTGAAGTAGCTGCCCCCCTGAGCGGTCTGATGCTCTCCTGGAGGGGGTCAATA
CTGTTGTTGTGACAACTTCAGCCCCAGATGCCATTGGTGTTTGCCCCCTGGTATAGAATTGCAGCCAGGGCTGGGAAGAT
GAAGACAGTGGCATGGCCACAGGAGGCCCAAGGTGTCAAGTGGTGCATGGTCCATGGGAGAAGTATGTCTGCAGACACCC
AAGGTTGGGTTCACCTGCAATTTCATGCAGGACAAGCCTGGGTGCCTGAAAAGCGGGGGAGAGTAGGTGCCCTCTTCTTG
CTCTCCGCTTGTAACTTTCTACCCCACAGCAGGGGGACAATATGCTGTGCCTCAAATGTGTTCGGAGGAATAAGGTGTTA
ATGAAAAGTCTCCAA

ORF - retro_cfam_996 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 81.85 %
Parental protein coverage: 99.33 %
Number of stop codons detected: 0
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalRRQGSTKSGEDYLAGQSQPVSEEAKEKQQAYGEPKLPGTSASGTKRKRSMKEGKASCSE-KTAQ-ESTRV
.R..S.KSG.DYLAGQSQP.SEEAKEKQQA.GEPKLPGTSASGTK.KRSMKE..ASCSE.K.AQ..STRV
RetrocopyKRTPSMKSGQDYLAGQSQPLSEEAKEKQQASGEPKLPGTSASGTKQKRSMKEDEASCSE<KMAQGKSTRV
ParentalRIRKKIPVPPLPSKLPPANLLHRDILRAWCQELKLSTKGQKLDVYKRICEYAYPDQKTNIPVTAEEAKIL
RI.KKIP.PPLPSKLPPANLLHRDILR.WCQE.KL.TKGQKLDVYKRICEYAYP.QK.NI.VT.EE.KIL
RetrocopyRIWKKIPIPPLPSKLPPANLLHRDILRTWCQEFKLNTKGQKLDVYKRICEYAYPGQKKNILVTTEETKIL
ParentalTQTQRRLMMDKGEMSLESPGTKIPSDGTYPPEVAAPAEG-SDALLEGVNT-VVVTTSAP-DSVFASWSRI
TQTQR.L.MDKGEMSLESPGTKIPS.GTYPPEVAAP..G.SDALLEGVNT.VV.T.......VFA.W.RI
RetrocopyTQTQRKLIMDKGEMSLESPGTKIPSGGTYPPEVAAPLSG<SDALLEGVNTVVVTTSAPD>PLVFAPWYRI
ParentalAARAGKMETVASPQEAHGAKWCVVHGRSMPADTEGWVHLQFHAGQAWVPEKRGRVCALFLLPACNFPP-P
AARAGKM.TVA.PQEA.G.KWC.VHGRSM.ADT.GWVHLQFHAGQAWVPEKRGRV.ALFLL.ACNF.P.P
RetrocopyAARAGKMKTVAWPQEAQGVKWCMVHGRSMSADTQGWVHLQFHAGQAWVPEKRGRVGALFLLSACNFLP<P
ParentalQLEDNMLCPKCVRRNKVLMKSLQ
Q..DNMLC.KCVRRNKVLMKSLQ
RetrocopyQQGDNMLCLKCVRRNKVLMKSLQ

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 .00 RPM 0 .00 RPM
SRP017611_brain 0 .00 RPM 0 .00 RPM
SRP017611_kidney 0 .00 RPM 0 .00 RPM
SRP017611_liver 0 .00 RPM 0 .00 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_996 retrocopy.

TSS - click to see more details

Canis familiaris was not studied using FANTOM5 data.

Lab - click to see more details

retro_cfam_996 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_996 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 19 parental genes, and 37 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG00000010335 5 retrocopies
retro_cfam_1332, retro_cfam_1540, retro_cfam_1905, retro_cfam_1934, retro_cfam_996 ,
Callithrix jacchus ENSCJAG000000201712 retrocopies
retro_cjac_1334, retro_cjac_1491,
Echinops telfairi ENSETEG000000027221 retrocopy
retro_etel_312,
Homo sapiens ENSG000001215701 retrocopy
retro_hsap_893,
Gorilla gorilla ENSGGOG000000151212 retrocopies
retro_ggor_1970, retro_ggor_723,
Loxodonta africana ENSLAFG000000168041 retrocopy
retro_lafr_456,
Myotis lucifugus ENSMLUG000000164231 retrocopy
retro_mluc_973,
Macaca mulatta ENSMMUG000000169011 retrocopy
retro_mmul_1515,
Monodelphis domestica ENSMODG000000180833 retrocopies
retro_mdom_1057, retro_mdom_1478, retro_mdom_999,
Mustela putorius furoENSMPUG000000102061 retrocopy
retro_mputfur_800,
Mus musculus ENSMUSG000000585503 retrocopies
retro_mmus_1907, retro_mmus_2085, retro_mmus_3656,
Nomascus leucogenys ENSNLEG000000040303 retrocopies
retro_nleu_2888, retro_nleu_3018, retro_nleu_388,
Oryctolagus cuniculus ENSOCUG000000164351 retrocopy
retro_ocun_114,
Pongo abelii ENSPPYG000000135653 retrocopies
retro_pabe_2316, retro_pabe_2349, retro_pabe_770,
Pan troglodytes ENSPTRG000000152002 retrocopies
retro_ptro_1923, retro_ptro_616,
Pteropus vampyrus ENSPVAG000000106771 retrocopy
retro_pvam_1237,
Rattus norvegicus ENSRNOG000000254044 retrocopies
retro_rnor_2750, retro_rnor_2996, retro_rnor_861, retro_rnor_862,
Sarcophilus harrisii ENSSHAG000000173981 retrocopy
retro_shar_542,
Tursiops truncatus ENSTTRG000000095081 retrocopy
retro_ttru_1772,


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