RetrogeneDB ID:

retro_cfam_489

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:12:39613443..39614693(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:GMPPA
Ensembl ID:ENSCAFG00000015541
Aliases:None
Description:GDP-mannose pyrophosphorylase A [Source:HGNC Symbol;Acc:22923]


Retrocopy-Parental alignment summary:






>retro_cfam_489
CTCAAAGCTGTGATCCTGATTGGAGGTCTCAAAAGAGGACTCTCTTCAGACCTTTGTCTTTTGAGATCCCCAAACCCCTG
TTTCCAGTGGTGGGGGTCCCAATGACACAGTACCACATTGAGGCCTCTGCCCAGGTCTCTGTGATGCAAGAGATTCTGCT
CATTGTCTTCTACCACCCTGATGAACCTCTCACCCAATTTCTAGCGGCTGTCCATTAGGAGTTTAACCTTCCAGTAAGAT
ACCTGCAGGAATTTGCACCCCTCAGCACAAGAGGTAGTCTCTACCATTCCTAGGACCAGATCCTGGCTGGGGTCCTGAGG
CCTTCTTGGTGCTCAATGCTGATGTCTGCTCTGACTTCCCCTTGAGTGATGTGTTGGATGCCTACAGACACCAGCCTCAC
TCTTTCTTGCTCCCTGGCACCACAGCTAATGGGACATAATCCCTCAACTATAGCTGCATCGTAGAGAATCCACAGACACA
CAAGGTCCTACACTATGTGGAGAAATCCAGCATTGTTAGTGACATCATCAACTGTGGTATGTATCTCTTCTCTCTGGGAG
CCCTGAAGCCCCTTGGGGATTTCTTCCAATGTAACCAGCAGGATGGGCAACTGGGGGACTCTTCAGGTCTGTGGCCAGGA
GCGGGCACCATCTACCTGGAACAGGATGTGTTCTAGTCCCTGGTCCAGCAGGGCCAGATCTAGCCATGCCTCACTGATGG
TATCTGGAGTCAGATCAAGTCCACAGGCTCAGCCCTCTATGCCTCCTGCCTCTACCTGGGCCAGCACCCGCTCACTTACC
CAGAACAACCGGCCAAGCACACCCCAGGGGGTCCATAAATCTGAGGAAATGTTTACATCCACCCAATAGCTAAGGTGGCT
CCCTCAGCTGTGCTGGGCCCTAATGTCTCCACTGGGGAGGAGATGACCATAAGCAAGGGTGTGTAGCTCCAAGAGAGTGC
TATTCTCCACAAAGCCATGCTACAGGAGCACACATGTGTTCCACATACCACTATGGGCTAGGGGAGCACTGTAGAGTGTT
AGGCCCATGTGGAGGTACCCCGATGACCCCAATCCCAACAACCTGCAAGTGCACATGAACAGGGAGAGCCTCTTCAAGGG
TGGGAAGCTGCTGTCTGCCATCACCATCCTAGGCTGTTGTGTCCGGATCCCTATTGAGGTGCTTAGCCTGAACTGGATTG
TTCTGTCACACAAGGAGCTAAGCAGCAGCTTCACCAACCAGATTATCCTC

ORF - retro_cfam_489 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 75.65 %
Parental protein coverage: 99.76 %
Number of stop codons detected: 10
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalLKAVILIGG-PQKGTRFRPLSFEVPKPLFPVAGVPMIQHHIEACAQVPGMQEILLIGFYQPDEALTRFLE
LKAVILIGG..QK.T.FRPLSFE.PKPLFPV.GVPM.Q.HIEA.AQV..MQEILLI.FY.PDE.LT.FL.
RetrocopyLKAVILIGG<SQKRTLFRPLSFEIPKPLFPVVGVPMTQYHIEASAQVSVMQEILLIVFYHPDEPLTQFLA
ParentalAAQQEFNLPVRYLQEFVPLGTGGGLYHFRDQILAG-GPEAFFVLNADVCSDFPLSAMLAAYRRQPHPFLL
A...EFNLPVRYLQEF.PL.T.G.LYH..DQILAG.GPEAF.VLNADVCSDFPLS..L.AYR.QPH.FLL
RetrocopyAVH*EFNLPVRYLQEFAPLSTRGSLYHS*DQILAG<GPEAFLVLNADVCSDFPLSDVLDAYRHQPHSFLL
ParentalLGTTANRTQSLNYGCIVENPQTHEVLHYVEKPSTFVSDVINCGIYLFSPEALKPLRDVFQRNQQDGQLED
.GTTAN.T.SLNY.CIVENPQTH.VLHYVEK.S..VSD.INCG.YLFS..ALKPL.D.FQ.NQQDGQL.D
RetrocopyPGTTANGT*SLNYSCIVENPQTHKVLHYVEK-SSIVSDIINCGMYLFSLGALKPLGDFFQCNQQDGQLGD
ParentalSSGLWPGAGTIRLEQDVFSALAGQGQIYVHLTDGIWSQIKSAGSALYASRLYLGQYQLTHPERLAKHTPG
SSGLWPGAGTI.LEQDVF..L..QGQI...LTDGIWSQIKS.GSALYAS.LYLGQ..LT.PE..AKHTPG
RetrocopySSGLWPGAGTIYLEQDVF*SLVQQGQI*PCLTDGIWSQIKSTGSALYASCLYLGQHPLTYPEQPAKHTPG
ParentalGPRIRGNVYIHPTAKVAPSAVLGPNVSIGEGVTVGEGVRLRESIVLHGATLQEHTCVLHTIVGWGSTVGR
GP.I.GNVYIHP.AKVAPSAVLGPNVS.GE..T...GV.L.ES..LH.A.LQEHTCV.HT..G.GSTV..
RetrocopyGP*I*GNVYIHPIAKVAPSAVLGPNVSTGEEMTISKGV*LQESAILHKAMLQEHTCVPHTTMG*GSTVEC
ParentalWARVE-GT-PNDPNPNDPRAHMDSESLFKDGKLLPAITILGCRVRIPAEVLILNSIVLPHKELSRSFTNQ
.A.VE.GT.P.DPNPN....HM..ESLFK.GKLL.AITILGC.VRIP.EVL.LN.IVL.HKELS.SFTNQ
Retrocopy*AHVE<GT<PDDPNPNNLQVHMNRESLFKGGKLLSAITILGCCVRIPIEVLSLNWIVLSHKELSSSFTNQ
ParentalIIL
IIL
RetrocopyIIL

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 29 .65 RPM
SRP017611_brain 0 .00 RPM 28 .42 RPM
SRP017611_kidney 0 .00 RPM 49 .13 RPM
SRP017611_liver 0 .00 RPM 23 .93 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_489 retrocopy.

TSS - click to see more details

Canis familiaris was not studied using FANTOM5 data.

Lab - click to see more details

retro_cfam_489 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_489 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 ENSCAFG00000015541 1 retrocopy
retro_cfam_489 ,


Copyright © RetrogeneDB 2014-2017