RetrogeneDB ID:

retro_btau_365

Retrocopy
location
Organism:Cow (Bos taurus)
Coordinates:10:20993730..20994575(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:VDAC5P
Ensembl ID:ENSBTAG00000014068
Aliases:VDAC3, VDAC1P5, VDAC5P
Description:Voltage-dependent anion-selective channel protein 3 [Source:UniProtKB/Swiss-Prot;Acc:Q9MZ13]


Retrocopy-Parental alignment summary:






>retro_btau_365
ATGTGTAACACACCGACTTACTGTGACCTAGGAAAGGCTGCCAAAGATGTCTTCAACAAAGCATATGGATTTGGCGTGGT
CAAAATAGACCTGAGAACCAAATCATGTAGTGGAATGAAATTCTTTACTTCTGGTCATGCTTACACTGATACGGGGAAAG
CATCAGGTAACCTAGAGACCAAATACAAATCTGTAACTATGGACTGACCTTCATCCAGAAGTGGAACACAGACAATACTC
TTGGGACGGAAATGTCTTGGGAGAATAAGTTGGCTGAAGGCTTGAAACTGACTCTTGATAACATATTTGTACCAAGCACA
GGAAAGAAGGGTGGGAAATTGAAGGCCTCCTATAAACCGGATTGTTTCAGTCTTGGCAGTAATATTGATGTAGATTTTTC
TGGACCAACCATCTATGGCTGGGCTGTGTTGGCCTTTGAAGGTTGGCTTGCTGGCTATCAGATGAGTTTTGACACAGACA
AATGCAAACTGTCACAGAATAATTTCACCCTGGGTTACAAGGCCGCAGACTTCCAGCTGCACACTCATGTGAATGATGGT
GCTGAGTTTGGAGGGTCGATCTACCAGAAGGTGAATGAGAAGATTGAAATGTCAATAAACCTCGCACGGACAGCCAGCAG
TAACAACACCCGCTTCGGCATTGCTGCTAAGTACAAGCTGGACTGTAGAACTTCTCTCTGTGCTAAAGGAAACAATGCCA
GCCTGATTGGACTGGGTTACACTCAGACCCTTTGACCAGGAGTGAAACTGATCCTGTCAACTCTAATCAATGGAAAGAAA
TTTAATGCAGGAGGGCACAAGTTTGGGCTGGGATTTGAACTAGAA

ORF - retro_btau_365 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 89.75 %
Parental protein coverage: 99.65 %
Number of stop codons detected: 1
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalMCNTPTYCDLGKAAKDVFNKGYGFGMVKIDLRTKSCSGVEFSTSGHAYTDTGKASGNLETKYK-ICNYGL
MCNTPTYCDLGKAAKDVFNK.YGFG.VKIDLRTKSCSG..F.TSGHAYTDTGKASGNLETKYK.ICNYGL
RetrocopyMCNTPTYCDLGKAAKDVFNKAYGFGVVKIDLRTKSCSGMKFFTSGHAYTDTGKASGNLETKYK<ICNYGL
ParentalTFTQKWNTDNTLGTEISWENKLAEGLKLTLDTIFVPNTGKKSGKLKASYKRDCFSLGSNVDIDFSGPTIY
TF.QKWNTDNTLGTE.SWENKLAEGLKLTLD.IFVP.TGKK.GKLKASYK.DCFSLGSN.D.DFSGPTIY
RetrocopyTFIQKWNTDNTLGTEMSWENKLAEGLKLTLDNIFVPSTGKKGGKLKASYKPDCFSLGSNIDVDFSGPTIY
ParentalGWAVLAFEGWLAGYQMSFDTAKSKLSQNNFALGYKAADFQLHTHVNDGTEFGGSIYQKVNEKIETSINLA
GWAVLAFEGWLAGYQMSFDT.K.KLSQNNF.LGYKAADFQLHTHVNDG.EFGGSIYQKVNEKIE.SINLA
RetrocopyGWAVLAFEGWLAGYQMSFDTDKCKLSQNNFTLGYKAADFQLHTHVNDGAEFGGSIYQKVNEKIEMSINLA
ParentalWTAGSNNTRFGIAAKYKLDCRTSLSAKVNNASLIGLGYTQTLRPGVKLTLSALIDGKNFNAGGHKVGLGF
.TA.SNNTRFGIAAKYKLDCRTSL.AK.NNASLIGLGYTQTL.PGVKL.LS.LI.GK.FNAGGHK.GLGF
RetrocopyRTASSNNTRFGIAAKYKLDCRTSLCAKGNNASLIGLGYTQTL*PGVKLILSTLINGKKFNAGGHKFGLGF
ParentalELE
ELE
RetrocopyELE

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
ERP005899_liver 0 .14 RPM 57 .53 RPM
ERP005899_muscle 0 .00 RPM 212 .11 RPM
SRP017611_brain 0 .00 RPM 100 .81 RPM
SRP017611_kidney 0 .00 RPM 126 .49 RPM
SRP017611_liver 0 .00 RPM 42 .28 RPM
SRP030211_testis 0 .05 RPM 361 .25 RPM

ChIP-Seq - click to see more details

Bos taurus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_btau_365 retrocopy.

TSS - click to see more details

Bos taurus was not studied using FANTOM5 data.

Lab - click to see more details

retro_btau_365 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_btau_365 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 25 parental genes, and 58 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000050951 retrocopy
retro_amel_729,
Bos taurus ENSBTAG000000129752 retrocopies
retro_btau_1252, retro_btau_1389,
Bos taurus ENSBTAG00000014068 4 retrocopies
retro_btau_1537, retro_btau_1607, retro_btau_365 , retro_btau_685,
Canis familiaris ENSCAFG000000055025 retrocopies
retro_cfam_1513, retro_cfam_2146, retro_cfam_258, retro_cfam_665, retro_cfam_713,
Choloepus hoffmanni ENSCHOG000000073691 retrocopy
retro_chof_16,
Dasypus novemcinctus ENSDNOG000000138851 retrocopy
retro_dnov_1753,
Equus caballus ENSECAG000000004381 retrocopy
retro_ecab_799,
Echinops telfairi ENSETEG000000026522 retrocopies
retro_etel_1456, retro_etel_1487,
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,
Tursiops truncatus ENSTTRG000000096813 retrocopies
retro_ttru_1201, retro_ttru_1254, retro_ttru_634,


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