RetrogeneDB ID: retro_ptro_945

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 14:99638780..99639562(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VDAC3
• Ensembl ID: ENSPTRG00000020205
• Aliases: VDAC3, VDAC1P5, VDAC5P
• Description: Voltage-dependent anion channel 3 [Source:UniProtKB/TrEMBL;Acc:K7CAB0]

Sequence

>retro_ptro_945
ATGTGTAACACACCAACTTACTGTGACCTGGGAAAGGCTGCTGAGGATGTCTTCAACAAAGGATATGGCTTTGGCATGGG
GAAGATAGACCTGAAAACCAAGTCCTGTAGTGCAGTGGAATTTTCTACTTCTGGTCATGCTTACACTGATACAGGGAAAG
CATCAGGCAACCTAGAACCCAAATGTAAGGTCTGTAACTATGGACTTACCTTCACTCAAAAACGGAACACAGACAATACT
CTTGGGACAGAAATCTCTTTGGAGAATAAGCTGGCTAAAGGGTTGAAACTGAGTCTTGATACCATATTGGTACCAAACAC
AGGAGAGAAGAGCGGGGAATTGAAGGCCTCCTATAAATGGGATTGTTTTAGTGTTGGCAGTAATGTTGATCTAGATTTTT
CCGGACCAACCATCTATGGCTGGGCTGTGTTGGTCTTTGAAGGGTGGCTTGCCGGCTATCAGATGAGTTTTGACACAGCC
AAATCCAAATTGTCACAGAATAATTTCGCCCTGGGTTACGAGGCTGCAGACTTCCAGCTGCACACACATGTGAACGATGG
CACTGAATTTGGAGGTTCTATCTACCAGAAGGTTAATGGGATTGAAATGTCAATAAACCTTGCTTGGGCGGCTGGAGTAA
CAACACCCATTTTGGCATTGCTACTAAGTACAAGCTGGATTGTAGAACTTCTCTCTCTGCTAAAGTAAATAATGCCAGCC
TGATTGGACTGGGTTATACTCAGACCCTTCGACCCGGAGTCAAGTTGACCCTTTATCAGCTT

Alignment

ORF - retro_ptro_945 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.77 %
• Parental protein coverage: 92.61 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MCNTPTYCDLGKAAKDVFNKGYGFGMVKIDLKTKSCSGVQEFSTSGHAYTDTGKASGNLETKYKVCNYGL
          MCNTPTYCDLGKAA.DVFNKGYGFGM.KIDLKTKSCS.V.EFSTSGHAYTDTGKASGNLE.K.KVCNYGL
Retrocopy MCNTPTYCDLGKAAEDVFNKGYGFGMGKIDLKTKSCSAV-EFSTSGHAYTDTGKASGNLEPKCKVCNYGL

Parental  TFTQKWNTDNTLGTEISWENKLAEGLKLTLDTIFVPNTGKKSGKLKASYKRDCFSVGSNVDIDFSGPTIY
          TFTQK.NTDNTLGTEIS.ENKLA.GLKL.LDTI.VPNTG.KSG.LKASYK.DCFSVGSNVD.DFSGPTIY
Retrocopy TFTQKRNTDNTLGTEISLENKLAKGLKLSLDTILVPNTGEKSGELKASYKWDCFSVGSNVDLDFSGPTIY

Parental  GWAVLAFEGWLAGYQMSFDTAKSKLSQNNFALGYKAADFQLHTHVNDGTEFGGSIYQKVNEKIETSINLA
          GWAVL.FEGWLAGYQMSFDTAKSKLSQNNFALGY.AADFQLHTHVNDGTEFGGSIYQKVN..IE.SINLA
Retrocopy GWAVLVFEGWLAGYQMSFDTAKSKLSQNNFALGYEAADFQLHTHVNDGTEFGGSIYQKVN-GIEMSINLA

Parental  WTAG-SNNTRFGIAAKYMLDCRTSLSAKVNNASLIGLGYTQTLRPGVKLTLSAL
          W.AG.SNNT.FGIA.KY.LDCRTSLSAKVNNASLIGLGYTQTLRPGVKLTL..L
Retrocopy WAAG<SNNTHFGIATKYKLDCRTSLSAKVNNASLIGLGYTQTLRPGVKLTLYQL

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.25 RPM	101.85 RPM
SRP007412_cerebellum	2.51 RPM	75.17 RPM
SRP007412_heart	2.42 RPM	132.59 RPM
SRP007412_kidney	0.18 RPM	62.22 RPM
SRP007412_liver	0.07 RPM	40.85 RPM
SRP007412_testis	0.84 RPM	159.76 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_945 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_945 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_945 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1375
Gorilla gorilla	retro_ggor_1071
Pongo abelii	retro_pabe_1145
Macaca mulatta	retro_mmul_2200

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Parental genes homology:

Parental genes homology involve 23 parental genes, and 63 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	ENSPTRG00000017235	12 retrocopies	retro_ptro_1593, retro_ptro_1900, retro_ptro_249, retro_ptro_2905, retro_ptro_3138, retro_ptro_3215, retro_ptro_3246, retro_ptro_345, retro_ptro_588, retro_ptro_682, retro_ptro_84, retro_ptro_861,
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,