RetrogeneDB ID:

retro_pvam_1151

Retrocopy
location
Organism:Megabat (Pteropus vampyrus)
Coordinates:scaffold_3310:3617..4180(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:SSU72
Ensembl ID:ENSPVAG00000017695
Aliases:None
Description:SSU72 RNA polymerase II CTD phosphatase homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:25016]


Retrocopy-Parental alignment summary:






>retro_pvam_1151
TCATCGCCCATGCAGCTGACAGTGGTGTGCTGAGCAACCAGAACTGGAGCAGGGAGGGGCACACTTAGCAAATCAGGATC
CAGTGTCTGGTCCTTTGGAACAGGTATTCACATGAACTTTCCAGGACCGGCACCTGACAAGCCAAATGTTTACGATTTCA
AAACCACCTGTGATCAAATGTACAATGATCTCTTTAGGAAAGACAAAGAACTCTCCACACAAAACGGCATTTTGCATATG
TTAGACAGAAATAAGAGAATCAAGTTCCAGCCAGAAAGGTTCTAGAACTGCAAGAGCCTTTTCTACCTGCCTCTCACCTA
TGAGGAGAGAGTATACAAGCAAATGGTGGAAGATATGAATTCCAGAGAGCAGGAGACTTGCCAGCCGGTGCATTGGATTA
ACATGAACGTCCAGAACAACCACGAAGAGGCCACACTGGGAGTGTTCCTCATCTGTGAGCTCTGCGAGTGCATTCAGCAC
CGGAAGATGTGGAGAATGAGACTGATGAGCTGCTGCAGAAGTTTTAGCAGAAGAGTGGCAAGGCCTTTCTGTGCATCGTC
TGC

ORF - retro_pvam_1151 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 71.73 %
Parental protein coverage: 98.96 %
Number of stop codons detected: 3
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalSLPLRVAVVCSSNQNRSMEAHNILSKRGFSVRSFGTGTHVKLPGPAPDKPNVYDFKTTYDQMYNDLLRKD
S.P....VVC.....R.......LSK.G.SV.SFGTG.H...PGPAPDKPNVYDFKTT.DQMYNDL.RKD
RetrocopySSPMQLTVVC*AT--RTGAGRGTLSKSGSSVWSFGTGIHMNFPGPAPDKPNVYDFKTTCDQMYNDLFRKD
ParentalKELYTQNGILHMLDRNKRIKPRPERFQNCKDLFDLILTCEERVYDQVVEDLNSREQETCQPVHVINVDIQ
KEL.TQNGILHMLDRNKRIK..PERF.NCK.LF.L.LT.EERVY.Q.VED.NSREQETCQPVH.IN...Q
RetrocopyKELSTQNGILHMLDRNKRIKFQPERF*NCKSLFYLPLTYEERVYKQMVEDMNSREQETCQPVHWINMNVQ
ParentalDNHEEATLGAFLICELCQCIQH-TEDMENEIDELLQEFEEKSGRAFLHTVC
.NHEEATLG.FLICELC.CIQH..ED.ENE.DELLQ.F..KSG.AFL..VC
RetrocopyNNHEEATLGVFLICELCECIQH<PEDVENETDELLQKF*QKSGKAFLCIVC

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






Pteropus vampyrus was not studied using RNA-Seq expression data.
Pteropus vampyrus was not studied using ChIP-Seq data.
Pteropus vampyrus was not studied using EST data.
Pteropus vampyrus was not studied using FANTOM5 data.
retro_pvam_1151 was not experimentally validated.

Retrocopy orthology:
Pteropus vampyrus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

Parental genes homology:
Parental genes homology involve 22 parental genes, and 67 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000137363 retrocopies
Canis familiaris ENSCAFG000000192542 retrocopies
Callithrix jacchus ENSCJAG000000109573 retrocopies
Cavia porcellus ENSCPOG000000022382 retrocopies
Dipodomys ordii ENSDORG000000117141 retrocopy
Homo sapiens ENSG000001600758 retrocopies
Gorilla gorilla ENSGGOG000000044211 retrocopy
Loxodonta africana ENSLAFG000000020764 retrocopies
Macropus eugenii ENSMEUG000000151701 retrocopy
Myotis lucifugus ENSMLUG000000165172 retrocopies
Macaca mulatta ENSMMUG000000015511 retrocopy
Monodelphis domestica ENSMODG000000066163 retrocopies
Mustela putorius furoENSMPUG000000143942 retrocopies
Mus musculus ENSMUSG000000290381 retrocopy
Otolemur garnettii ENSOGAG000000244302 retrocopies
Pongo abelii ENSPPYG000000020001 retrocopy
Pan troglodytes ENSPTRG0000000003416 retrocopies
Pteropus vampyrus ENSPVAG00000017695 4 retrocopies
Rattus norvegicus ENSRNOG000000178292 retrocopies
Sus scrofa ENSSSCG000000033482 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000029604 retrocopies
Tursiops truncatus ENSTTRG000000170512 retrocopies



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