RetrogeneDB ID: retro_pvam_44

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_1117:100437..100804(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM230
• Ensembl ID: ENSPVAG00000002863
• Aliases: None
• Description: transmembrane protein 230 [Source:HGNC Symbol;Acc:15876]

Sequence

>retro_pvam_44
TGTGGCTGTGTTATGATGTCATCTTCTACCAACCTGGCTACTGGAATCCCCAGTAGTAAAGTGAAATACTCAGGGCTTTC
CAGCACGGAGGATGGCTGCATTAACCTTCAGTTTAAGAAAAGCCCTCCTAAGATCCCATATGAGGCCATTGTGTCTGCTA
TAGTGCTGTTTTTAATTGGCACCTTTTTCATAGGCTCCCAACTGCTTTTGGGCTATACCAGCAAAGAGGGGGGCAGACTG
GGCCATTCTAGTCCTCGTCATTGGCATTCTAATACTCCTGTTGGGATTTTACTTCCTATGCGTCGCCTACTATGTGTCCA
GAGGCTACAGGGGTTACTCCTACAATGACATTCTAGACTTTGATGAC

Alignment

ORF - retro_pvam_44 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.8 %
• Parental protein coverage: 83.22 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  CQCVMMPSRTNLATGIPSSKVKYSRLSSTDDGYIDLQFKKSPPKIPYKAIALATVLFLIGAFLIIIGSLL
          C.CVMM.S.TNLATGIPSSKVKYS.LSST.DG.I.LQFKKSPPKIPY.AI..A.VLFLIG.F...IGS.L
Retrocopy CGCVMMSSSTNLATGIPSSKVKYSGLSSTEDGCINLQFKKSPPKIPYEAIVSAIVLFLIGTF--FIGSQL

Parental  LAGYIS-KGGADRAVPVLIIGILVFLPGFYHLRIAYYASKGYRGYSYDDIPDFDD
          L.GY.S.K.GAD.A..VL.IGIL..L.GFY.L..AYY.S.GYRGYSY.DI.DFDD
Retrocopy LLGYTS>KRGADWAILVLVIGILILLLGFYFLCVAYYVSRGYRGYSYNDILDFDD

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_44 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 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006063	2 retrocopies	retro_btau_1079, retro_btau_147,
Canis familiaris	ENSCAFG00000006039	1 retrocopy	retro_cfam_981,
Dasypus novemcinctus	ENSDNOG00000005724	5 retrocopies	retro_dnov_1004, retro_dnov_2377, retro_dnov_2534, retro_dnov_373, retro_dnov_803,
Myotis lucifugus	ENSMLUG00000023089	2 retrocopies	retro_mluc_1504, retro_mluc_1759,
Ochotona princeps	ENSOPRG00000008611	1 retrocopy	retro_opri_502,
Pteropus vampyrus	ENSPVAG00000002863	1 retrocopy	retro_pvam_44 ,
Ictidomys tridecemlineatus	ENSSTOG00000019378	1 retrocopy	retro_itri_35,