RetrogeneDB ID: retro_pvam_579

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_3874:1272708..1273091(-)
• Located in intron of: ENSPVAG00000012277

Retrocopy information

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

Parental gene information

• Parental gene symbol: CMTM3
• Ensembl ID: ENSPVAG00000013762
• Aliases: None
• Description: CKLF-like MARVEL transmembrane domain containing 3 [Source:HGNC Symbol;Acc:19174]

Sequence

>retro_pvam_579
GTCTCGCTCATCTTCTTCATCACCTACCTGATGTCCTTGCCAGCTACCTTCCTCCCCGGACCAGGCCGGAGTTTCTGCTG
GCCTTCTACTTCCTCTTTATTGATGCCATGCATCTGAAAGACACATGCCAGAGCTTGTGCTAGGCCATGAGGGACGTCTT
GCCTTGTGTCATGGCAGCCCTCATCTGCTTCACCATCTCCACCACCGCGATTGCCAAATCCTCAGACGGAGCTTCTAAAG
CAACAGGAGTATTGGATTTCTTTGCTGCCATCATGTTTGCAACTGACTTCTACCTGACTTTGAAGAATAAGGCCAAATTC
CTCCAATGAGGGGTCTCTGCAGGCGACACCATAGCAGACAAGGTAGAAGGAAAGAATTCTGAC

Alignment

ORF - retro_pvam_579 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.81 %
• Parental protein coverage: 96.24 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LSFITFVCYVASSASAFLTAP-LLEFLLALFFLFADAMQLNDKWQGLCWPMMDFLRCVTAALIYFAISIT
          .S.I.F..Y..S....FL..P...EFLLA..FLF.DAM.L.D..Q.LC..M.D.L.CV.AALI.F.IS.T
Retrocopy VSLIFFITYLMSLPATFLPGP<RPEFLLAFYFLFIDAMHLKDTCQSLC*AMRDVLPCVMAALICFTISTT

Parental  AVAKYSDGASKAAGVFGFFATIVFAIDFYLIFNDVAKFLKQGDSTDETTANKAEEENSD
          A.AK.SDGASKA.GV..FFA.I.FA.DFYL.....AKFL..G.S...T.A.K.E..NSD
Retrocopy AIAKSSDGASKATGVLDFFAAIMFATDFYLTLKNKAKFLQ*GVSAGDTIADKVEGKNSD

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_579 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000047654	1 retrocopy	retro_btau_1771,
Pteropus vampyrus	ENSPVAG00000011770	2 retrocopies	retro_pvam_1214, retro_pvam_810,
Pteropus vampyrus	ENSPVAG00000013762	1 retrocopy	retro_pvam_579 ,