RetrogeneDB ID: retro_pvam_907

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_15993:16118..16938(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VDAC3
• Ensembl ID: ENSPVAG00000014822
• Aliases: None
• Description: voltage-dependent anion channel 3 [Source:HGNC Symbol;Acc:12674]

Sequence

>retro_pvam_907
ATGTGTATTCCTCCATCATATGCTGACCTTGGCAAAGCTGCCAGAGATATTTTCAACAAAGGATTTGGTTCTGGGTTGGT
AAAACTGGATATGAAAACAAAGTCATGCAGCGGTGTGGAATTCTCAACATCTGGTTCATCTAATACAGACACTGGAAAAG
TTACTGGGACCTTAGAGACCAAATATAAATGGTGTTGAGTATGGTCTGACTTTCACAGAGAAATGGAACACTGATAACAC
TCTGGGAACAGAAATCGCAATGGAAGACCAGATTTGTCAAGGTTTGAAACACATTTGATACCACCTTTTCACCAAATACA
GGAAAGAAAAGTGGTAAAATCAAGTCTTCTTACAAGAAGAAGTGTATAAACCTTGGTTGCAATGTTGACTTTGATTTTAC
TGGCCCTGCAATCCATGGTTCAGTTGTCTTTGGTTATGAGGGCTGGCTTGCTGGGTACCAGATGACCTTGACAGTGCCAA
ATCAAAGGTGACAAGGAATAACTTTGCAGTGGGCTACAGGACTGGGGACTTCCAGCTACACACTAATGTTAATGATGGGA
CAGAATATGAAGGATCAATTTATCAGAAAATATGTGAAGATCGTGACACTTCAGTAAACCTTGCTTGGACATCAGGTATC
AACTGCACTTGCTTTGGCATTGCAGCTAAATATCAGCTGGATCCCACTGCTTCCATTTCTGCAAAAGTCAACAACTCTAG
TTTAATTGGAGTGGGCTACGCTCAGACTCTGAGGCCTGGTGGGAAGCTTACACTGTCTGGTCTGGTAGAGTGGAAGGGCA
TTAATGCTGGAGGCCACAAA

Alignment

ORF - retro_pvam_907 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.15 %
• Parental protein coverage: 96.82 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MCNTPTYCDLGKAAKDVFNKGYGFGMVKIDLRTKSCSGVEFSTSGHAYTDTGKASGNLETKYKVC-NYGL
          MC..P.Y.DLGKAA.D.FNKG.G.G.VK.D..TKSCSGVEFSTSG...TDTGK..G.LETKYK.C..YGL
Retrocopy MCIPPSYADLGKAARDIFNKGFGSGLVKLDMKTKSCSGVEFSTSGSSNTDTGKVTGTLETKYKWC>EYGL

Parental  TFTQKWNTDNTLGTEIS-WENKLAEGLKLTLDTIFVPNTGKKSGKLKASYKRDCFSLGSNVDIDFSGPTI
          TFT.KWNTDNTLGTEI..W..........T.DT.F.PNTGKKSGK.K.SYK..C..LG.NVD.DF.GP.I
Retrocopy TFTEKWNTDNTLGTEIA>WKTRFVK-V*NTFDTTFSPNTGKKSGKIKSSYKKKCINLGCNVDFDFTGPAI

Parental  YGWAVLALEGWLAGYQMSF-DTAKSKLSQNNFALGYKAADFQLHTHVNDGTEFGGSIYQKVNEKIETSIN
          .G..V...EGWLAGYQM...D.AKSK...NNFA.GY...DFQLHT.VNDGTE..GSIYQK..E...TS.N
Retrocopy HGSVVFGYEGWLAGYQMTL<DSAKSKVTRNNFAVGYRTGDFQLHTNVNDGTEYEGSIYQKICEDRDTSVN

Parental  LAWTAGSNNTRFGIAAKYKLDCRTSLSAKVNNASLIGLGYTQTLRPGVKLTLSALVDGKNFNAGGHK
          LAWT.G.N.T.FGIAAKY.LD...S.SAKVNN.SLIG.GY.QTLRPG.KLTLS.LV..K..NAGGHK
Retrocopy LAWTSGINCTCFGIAAKYQLDPTASISAKVNNSSLIGVGYAQTLRPGGKLTLSGLVEWKGINAGGHK

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_907 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 22 parental genes, and 51 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005095	1 retrocopy	retro_amel_729,
Bos taurus	ENSBTAG00000014068	4 retrocopies	retro_btau_1537, retro_btau_1607, retro_btau_365, retro_btau_685,
Canis familiaris	ENSCAFG00000005502	5 retrocopies	retro_cfam_1513, retro_cfam_2146, retro_cfam_258, retro_cfam_665, retro_cfam_713,
Choloepus hoffmanni	ENSCHOG00000007369	1 retrocopy	retro_chof_16,
Dasypus novemcinctus	ENSDNOG00000013885	1 retrocopy	retro_dnov_1753,
Equus caballus	ENSECAG00000000438	1 retrocopy	retro_ecab_799,
Felis catus	ENSFCAG00000010075	2 retrocopies	retro_fcat_1985, retro_fcat_599,
Homo sapiens	ENSG00000078668	1 retrocopy	retro_hsap_1375,
Gallus gallus	ENSGALG00000003755	1 retrocopy	retro_ggal_11,
Gorilla gorilla	ENSGGOG00000001932	2 retrocopies	retro_ggor_1071, retro_ggor_3043,
Microcebus murinus	ENSMICG00000010235	1 retrocopy	retro_mmur_1361,
Monodelphis domestica	ENSMODG00000015526	5 retrocopies	retro_mdom_1130, retro_mdom_1331, retro_mdom_1869, retro_mdom_420, retro_mdom_669,
Mus musculus	ENSMUSG00000008892	2 retrocopies	retro_mmus_110, retro_mmus_1505,
Nomascus leucogenys	ENSNLEG00000012890	1 retrocopy	retro_nleu_2593,
Otolemur garnettii	ENSOGAG00000016163	4 retrocopies	retro_ogar_2770, retro_ogar_2870, retro_ogar_589, retro_ogar_995,
Pongo abelii	ENSPPYG00000018554	8 retrocopies	retro_pabe_1145, retro_pabe_1960, retro_pabe_2304, retro_pabe_3163, retro_pabe_3665, retro_pabe_3791, retro_pabe_819, retro_pabe_971,
Pan troglodytes	ENSPTRG00000020205	2 retrocopies	retro_ptro_2548, retro_ptro_945,
Pteropus vampyrus	ENSPVAG00000014822	2 retrocopies	retro_pvam_637, retro_pvam_907 ,
Rattus norvegicus	ENSRNOG00000019277	1 retrocopy	retro_rnor_1596,
Sarcophilus harrisii	ENSSHAG00000017953	1 retrocopy	retro_shar_658,
Tupaia belangeri	ENSTBEG00000007420	4 retrocopies	retro_tbel_1801, retro_tbel_2150, retro_tbel_2261, retro_tbel_884,
Tarsius syrichta	ENSTSYG00000007112	1 retrocopy	retro_tsyr_918,