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 symbol: LAPTM4A
• Ensembl ID: ENSPVAG00000002909
• Aliases: None
• Description: lysosomal protein transmembrane 4 alpha [Source:HGNC Symbol;Acc:6924]

Sequence

>retro_pvam_873
GTCATTGACCATTACTATTTGTCTGAGAAGATGGCTGATAATGCCTGTGTTCTTTTTGCTTTCTCTTTTCTTATATCTAT
AATCAGTTCAATGCTGGTATATGGAGCAATTTTTATCAAGTAGGTTGGCTTATTCCATTTTTCTGTTAAGAACTTTTTAA
CTTAGTTCTCAGTTGCCTAGTAGCTATCAGTTCTCTCATTAATTTGCCAAGAATCAAAGAATATCTGGATCAATTACTTG
ATTTTTTCCTGTAATGATGACCTCTTGGCATTGGACCTTAACCTCCTGTTCCTTGTTCTTGTGTTCTTTGCCTTATTTAT
CATTTTTGAAGGCTTACCTAATCAACTTTGTTTGAAAATATAATAAATACATCAACAACAGAAACACAGCAGAGATTGCT
CTATACCCTGCCTTTGAAGCACCTCCACAGTATGTTTTGGCCAATTTATGAAATGGCAGTGAAGATGCCTGAAAAAGACC
ACCGCCTCCTTACATACCTGCC

Alignment

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:

Parental  VIGNYYSSERMADNACVLFAVSVLMFIISSMLVYGAIS-YQVGWLIPFFCYRLFDFVLSCLVAISSLTYL
          VI..YY.SE.MADNACVLFA.S.L..IISSMLVYGAI..YQVGWLIPFFC..LF..VLSCLVAISSL..L
Retrocopy VIDHYYLSEKMADNACVLFAFSFLISIISSMLVYGAIF<YQVGWLIPFFC*ELFNLVLSCLVAISSLINL

Parental  PRIKEYLDQLPD-FPYKDDLLALDSSCLLFIVLVFFALFIIF-KAYLINCVWNCYKYINNRNTPEIAVYP
          PRIKEYLDQL.D.F...DDLLALD...LLF.VLVFFALFIIF.KAYLIN.V....KYINNRNT.EIA.YP
Retrocopy PRIKEYLDQLLD>FSCNDDLLALDLN-LLFLVLVFFALFIIF>KAYLINFV*KYNKYINNRNTAEIALYP

Parental  AFEAPPQYVL-PTYEMAVKMPEKE-PPPPYIPA
          AFEAPPQYVL.P.YEMAVKMPEK..PPPPYIPA
Retrocopy AFEAPPQYVL>PIYEMAVKMPEKD<PPPPYIPA

Legend:

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

Expression

RNA-Seq

Pteropus vampyrus was not studied using RNA-Seq expression data.

ChIP-Seq

Pteropus vampyrus was not studied using ChIP-Seq data.

EST

Pteropus vampyrus was not studied using EST data.

TSS

Pteropus vampyrus was not studied using FANTOM5 data.

Lab

retro_pvam_873 was not experimentally validated.

Homology

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.

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020894	1 retrocopy	retro_btau_575,
Choloepus hoffmanni	ENSCHOG00000011200	2 retrocopies	retro_chof_1916, retro_chof_2320,
Callithrix jacchus	ENSCJAG00000007433	1 retrocopy	retro_cjac_839,
Echinops telfairi	ENSETEG00000002569	1 retrocopy	retro_etel_591,
Mustela putorius furo	ENSMPUG00000013714	1 retrocopy	retro_mputfur_657,
Ochotona princeps	ENSOPRG00000012401	2 retrocopies	retro_opri_356, retro_opri_474,
Pteropus vampyrus	ENSPVAG00000002909	3 retrocopies	retro_pvam_779, retro_pvam_847, retro_pvam_873 ,