RetrogeneDB ID:

retro_cfam_1513

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:32:37832775..37833648(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCAFG00000012393
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:VDAC3
Ensembl ID:ENSCAFG00000005502
Aliases:None
Description:Canis lupus familiaris voltage-dependent anion channel 3 (VDAC3), transcript variant 1, mRNA. [Source:RefSeq mRNA;Acc:NM_001251965]


Retrocopy-Parental alignment summary:






>retro_cfam_1513
GAGATAGGCCCTCTGGTTGGAGAGATGTATAACACACCGACTTACTGAGACCTAGGAAAGGCCGCCAAGGATTTCTTCAA
TAAAGGACATGGATTCAGCATGGTCAAAATAGATCTGAGAACCAAGTCTTGTAGTAGGAGTAGAATTTTCTACTTCTGGT
CATGCTTACACTGATACAGGGAAAGCATCAGGCAACCTAGAGACCAAATATAAGGTCTGTAACTATGGACTTACTTTCAC
CCAGAAATGGAACACAGACAATACTCTTGGAACAGAAATCTCTTTGGAGAATAAGTTGGCTGAAGGGTTGAAACTGACTC
TTGATACCATATTTGTACCGAACACAGGAAAGAAGAGTGGAAAATTGAAGGCCTCCTATAAACGAGGTTGTTTCATATTG
ACAGTAATGTTGATATAGATTTTTCTGGACCAACCATCTATGGTTGGGCTGTGTTATCCTTTGAAGGTTGGCTTGTTGGC
TATCAGATGAATTTTGACACAACCAAATCCAAACTGTCACAGGATAATTTCGCCCTGGGTTACAAGGTTGCAGACTTCCA
GCTGCACACTAATGTGAATGATGGCGCTGAATTTGGAGGGTCTATCTACCAGAAGGTTAATGGGAAGATTGAAACATCAA
TAAACCTTGCTTGGACAGCCAGCAGTAACAATACCCGTTTTGGCATGGCTGCTAAATACAAGCTAGATTATAGAACTTCT
CTAACTGCTAAAGTCAATAATGCCAGCCTAATTGGACTGGGTTATACTCAGACCCTTCAACCAGGAATCAAACTGACCCT
ATCAGCTTTAATCAACAGAAAAAACTTCAGTGCAGGAGGTCACAAAGTTGGGTTGGGATTTGAACTAGAAGCT

ORF - retro_cfam_1513 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.4 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 1
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalEYSPIFEEMCNTPTYCDLGKAAKDVFNKGYGFGMVKIDLRTKSCS-GVEFSTSGHAYTDTGKASGNLETK
E..P...EM.NTPTY.DLGKAAKD.FNKG.GF.MVKIDLRTKSCS.GVEFSTSGHAYTDTGKASGNLETK
RetrocopyEIGPLVGEMYNTPTY*DLGKAAKDFFNKGHGFSMVKIDLRTKSCS>GVEFSTSGHAYTDTGKASGNLETK
ParentalYKVCNYGLTFTQKWNTDNTLGTEISLENKLAEGLKLTLDTIFVPNTGKKSGKLKASYKRDCF-SVGSNVD
YKVCNYGLTFTQKWNTDNTLGTEISLENKLAEGLKLTLDTIFVPNTGKKSGKLKASYKR.CF....SNVD
RetrocopyYKVCNYGLTFTQKWNTDNTLGTEISLENKLAEGLKLTLDTIFVPNTGKKSGKLKASYKRGCF<HIDSNVD
ParentalIDFSGPTIYGWAVLAFEGWLAGYQMSFDTAKSKLSQNNFALGYKAADFQLHTHVNDGTEFGGSIYQKVNE
IDFSGPTIYGWAVL.FEGWL.GYQM.FDT.KSKLSQ.NFALGYK.ADFQLHT.VNDG.EFGGSIYQKVN.
RetrocopyIDFSGPTIYGWAVLSFEGWLVGYQMNFDTTKSKLSQDNFALGYKVADFQLHTNVNDGAEFGGSIYQKVNG
ParentalKIETSINLAWTAGSNNTRFGIAAKYKLDCRTSLSAKVNNASLIGLGYTQTLRPGVKLTLSALIDGKNFNA
KIETSINLAWTA.SNNTRFG.AAKYKLD.RTSL.AKVNNASLIGLGYTQTL.PG.KLTLSALI..KNF.A
RetrocopyKIETSINLAWTASSNNTRFGMAAKYKLDYRTSLTAKVNNASLIGLGYTQTLQPGIKLTLSALINRKNFSA
ParentalGGHKVGLGFELEA
GGHKVGLGFELEA
RetrocopyGGHKVGLGFELEA

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 70 .43 RPM
SRP017611_brain 0 .00 RPM 47 .32 RPM
SRP017611_kidney 0 .00 RPM 69 .80 RPM
SRP017611_liver 0 .00 RPM 20 .01 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_1513 retrocopy.

TSS - click to see more details

Canis familiaris was not studied using FANTOM5 data.

Lab - click to see more details

retro_cfam_1513 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_1513 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 24 parental genes, and 53 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000050951 retrocopy
retro_amel_729,
Bos taurus ENSBTAG000000140684 retrocopies
retro_btau_1537, retro_btau_1607, retro_btau_365, retro_btau_685,
Canis familiaris ENSCAFG000000009851 retrocopy
retro_cfam_1728,
Canis familiaris ENSCAFG00000005502 5 retrocopies
retro_cfam_1513 , retro_cfam_2146, retro_cfam_258, retro_cfam_665, retro_cfam_713,
Canis familiaris ENSCAFG000000153981 retrocopy
retro_cfam_376,
Choloepus hoffmanni ENSCHOG000000073691 retrocopy
retro_chof_16,
Dasypus novemcinctus ENSDNOG000000138851 retrocopy
retro_dnov_1753,
Equus caballus ENSECAG000000004381 retrocopy
retro_ecab_799,
Felis catus ENSFCAG000000100752 retrocopies
retro_fcat_1985, retro_fcat_599,
Homo sapiens ENSG000000786681 retrocopy
retro_hsap_1375,
Gallus gallus ENSGALG000000037551 retrocopy
retro_ggal_11,
Gorilla gorilla ENSGGOG000000019322 retrocopies
retro_ggor_1071, retro_ggor_3043,
Microcebus murinus ENSMICG000000102351 retrocopy
retro_mmur_1361,
Monodelphis domestica ENSMODG000000155265 retrocopies
retro_mdom_1130, retro_mdom_1331, retro_mdom_1869, retro_mdom_420, retro_mdom_669,
Mus musculus ENSMUSG000000088922 retrocopies
retro_mmus_110, retro_mmus_1505,
Nomascus leucogenys ENSNLEG000000128901 retrocopy
retro_nleu_2593,
Otolemur garnettii ENSOGAG000000161634 retrocopies
retro_ogar_2770, retro_ogar_2870, retro_ogar_589, retro_ogar_995,
Pongo abelii ENSPPYG000000185548 retrocopies
retro_pabe_1145, retro_pabe_1960, retro_pabe_2304, retro_pabe_3163, retro_pabe_3665, retro_pabe_3791, retro_pabe_819, retro_pabe_971,
Pan troglodytes ENSPTRG000000202052 retrocopies
retro_ptro_2548, retro_ptro_945,
Pteropus vampyrus ENSPVAG000000148222 retrocopies
retro_pvam_637, retro_pvam_907,
Rattus norvegicus ENSRNOG000000192771 retrocopy
retro_rnor_1596,
Sarcophilus harrisii ENSSHAG000000179531 retrocopy
retro_shar_658,
Tupaia belangeri ENSTBEG000000074204 retrocopies
retro_tbel_1801, retro_tbel_2150, retro_tbel_2261, retro_tbel_884,
Tarsius syrichta ENSTSYG000000071121 retrocopy
retro_tsyr_918,


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