RetrogeneDB ID: retro_pvam_853

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_13634:26527..26889(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPVAG00000017134
• Aliases: None
• Description: None

Sequence

>retro_pvam_853
GTGAAGCTGCTCACCCACAACCTGCTGAGCTCACATGTGTAGGAGGTGGGGCCCGTGGTTTTCCTCTGTACTTCCAGGCT
ACTGAGTTTTGCATCAACTCTGTGGAGTTCAGTCCTGACTTTGTGAAATGTATAATGCCCCAGGTGGAGTGAGCAGCACT
TCTAAAGGTGGCCAACACCTTGCATCTGGCTGAGGTGTCCAAAGGGAGAATCCACAGGTATAATAGCGAAGAGAAATTTC
TGAAGATGTGCCACATACTGCAGGAGGCAGATGTGTTAGAGACAGTGCCCCAAGTCTGATGTCTGTTCCCCATCAGCTGC
AGGATTCCCAACATGCTACTGAGTGATGAGGAAATTAAGACT

Alignment

ORF - retro_pvam_853 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.73 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MKLLTHNLLSSHVRGVGP-RGFPLRLQATEVRVNPVEFNPDFVARMIPKVEWAVLLEAADTLHLIEVPKE
          .KLLTHNLLSSHV..VGP.RGFPL..QATE...N.VEF.PDFV....P.VE.A.LL..A.TLHL.EV.K.
Retrocopy VKLLTHNLLSSHV*EVGP<RGFPLYFQATEFCINSVEFSPDFVKCIMPQVE*AALLKVANTLHLAEVSKG

Parental  PIQGYEQDETFLRKMHHVLLEVDVVEGTLQCPESGRVFPISRGIPNMLLSEEETET
          .I..Y...E.FL.KM.H.L.E.DV.E.....P.....FPIS..IPNMLLS.EE..T
Retrocopy RIHRYNSEEKFL-KMCHILQEADVLE---TVPQV*CLFPISCRIPNMLLSDEEIKT

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_853 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 11 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017965	3 retrocopies	retro_amel_125, retro_amel_1748, retro_amel_295,
Bos taurus	ENSBTAG00000008646	1 retrocopy	retro_btau_410,
Callithrix jacchus	ENSCJAG00000018026	1 retrocopy	retro_cjac_2995,
Equus caballus	ENSECAG00000016960	1 retrocopy	retro_ecab_103,
Homo sapiens	ENSG00000173113	4 retrocopies	retro_hsap_1853, retro_hsap_2847, retro_hsap_2974, retro_hsap_86,
Gorilla gorilla	ENSGGOG00000001334	3 retrocopies	retro_ggor_1669, retro_ggor_2157, retro_ggor_2867,
Macaca mulatta	ENSMMUG00000019647	2 retrocopies	retro_mmul_1267, retro_mmul_2181,
Nomascus leucogenys	ENSNLEG00000004991	4 retrocopies	retro_nleu_1599, retro_nleu_2137, retro_nleu_2169, retro_nleu_556,
Pongo abelii	ENSPPYG00000025906	5 retrocopies	retro_pabe_1510, retro_pabe_2357, retro_pabe_3062, retro_pabe_3332, retro_pabe_3496,
Pteropus vampyrus	ENSPVAG00000017134	1 retrocopy	retro_pvam_853 ,
Ictidomys tridecemlineatus	ENSSTOG00000019857	1 retrocopy	retro_itri_208,