RetrogeneDB ID:

retro_pvam_873

Retrocopy
location
Organism:Megabat (Pteropus vampyrus)
Coordinates:scaffold_1429:34916..35418(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:LAPTM4A
Ensembl ID:ENSPVAG00000002909
Aliases:None
Description:lysosomal protein transmembrane 4 alpha [Source:HGNC Symbol;Acc:6924]


Retrocopy-Parental alignment summary:






>retro_pvam_873
GTCATTGACCATTACTATTTGTCTGAGAAGATGGCTGATAATGCCTGTGTTCTTTTTGCTTTCTCTTTTCTTATATCTAT
AATCAGTTCAATGCTGGTATATGGAGCAATTTTTATCAAGTAGGTTGGCTTATTCCATTTTTCTGTTAAGAACTTTTTAA
CTTAGTTCTCAGTTGCCTAGTAGCTATCAGTTCTCTCATTAATTTGCCAAGAATCAAAGAATATCTGGATCAATTACTTG
ATTTTTTCCTGTAATGATGACCTCTTGGCATTGGACCTTAACCTCCTGTTCCTTGTTCTTGTGTTCTTTGCCTTATTTAT
CATTTTTGAAGGCTTACCTAATCAACTTTGTTTGAAAATATAATAAATACATCAACAACAGAAACACAGCAGAGATTGCT
CTATACCCTGCCTTTGAAGCACCTCCACAGTATGTTTTGGCCAATTTATGAAATGGCAGTGAAGATGCCTGAAAAAGACC
ACCGCCTCCTTACATACCTGCC

ORF - retro_pvam_873 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78.61 %
Parental protein coverage: 72.1 %
Number of stop codons detected: 2
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalVIGNYYSSERMADNACVLFAVSVLMFIISSMLVYGAIS-YQVGWLIPFFCYRLFDFVLSCLVAISSLTYL
VI..YY.SE.MADNACVLFA.S.L..IISSMLVYGAI..YQVGWLIPFFC..LF..VLSCLVAISSL..L
RetrocopyVIDHYYLSEKMADNACVLFAFSFLISIISSMLVYGAIF<YQVGWLIPFFC*ELFNLVLSCLVAISSLINL
ParentalPRIKEYLDQLPD-FPYKDDLLALDSSCLLFIVLVFFALFIIF-KAYLINCVWNCYKYINNRNTPEIAVYP
PRIKEYLDQL.D.F...DDLLALD...LLF.VLVFFALFIIF.KAYLIN.V....KYINNRNT.EIA.YP
RetrocopyPRIKEYLDQLLD>FSCNDDLLALDLN-LLFLVLVFFALFIIF>KAYLINFV*KYNKYINNRNTAEIALYP
ParentalAFEAPPQYVL-PTYEMAVKMPEKE-PPPPYIPA
AFEAPPQYVL.P.YEMAVKMPEK..PPPPYIPA
RetrocopyAFEAPPQYVL>PIYEMAVKMPEKD<PPPPYIPA

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_873 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 7 parental genes, and 11 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000208941 retrocopy
Choloepus hoffmanni ENSCHOG000000112002 retrocopies
Callithrix jacchus ENSCJAG000000074331 retrocopy
Echinops telfairi ENSETEG000000025691 retrocopy
Mustela putorius furoENSMPUG000000137141 retrocopy
Ochotona princeps ENSOPRG000000124012 retrocopies
Pteropus vampyrus ENSPVAG00000002909 3 retrocopies
retro_pvam_779, retro_pvam_847, retro_pvam_873 ,



Copyright © RetrogeneDB 2014-2017