RetrogeneDB ID: retro_ptro_2548

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 7:81687378..81687900(+)
• 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_2548
AAATGCGGAAAACTGAAGGCTTCCTCTACATGTGAATAAGTAAGTCTTGGCAGTATTACTGCTGGAGATTTTTCTAGACC
AACGCTTTATGGTTGGGCTCTGCTGGCCTTCGAACTTTGCCTTGATGGGTGTCAGATGATTTCTGACACAAGCAAATCCA
AACTATCAGAGAATCATTTCACCCTTGTTCACAAAGCTGCACACCTCTAGCTGTAATCTCATGTGAATGATGGCACTGAA
CTTGAAAGTTTTGTATGCAAGAAGGTTAATGAGAAAATTGAAACTCCAAAAAATCTTGTTTGGAGAGCTGGTAGTGACAA
CACCCGATTTTGCTTTACTACAGTATACAAGCTGGATTATAGATCTTCTGCATTTGGTAGAGTAACTCATGCCAGTCTGA
ATGCACACGGGTATACTCAAACCTTTCCATCAGGAGTCAAAGTGATCCTGTCAGCTTAAACTGATGGGAAAAACTTCCAT
GCAGAAGGTTATAAGGTCGGGTTAAGATTTGAACTGGAAGCT

Alignment

ORF - retro_ptro_2548 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.62 %
• Parental protein coverage: 61.27 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KSGKLKASYKRDCFSVGSNVDIDFSGPTIYGWAVLAFEGWLAGYQMSFDTAKSKLSQNNFALGYKAADFQ
          K.GKLKAS......S.GS....DFS.PT.YGWA.LAFE..L.G.QM..DT.KSKLS.N.F.L..KAA...
Retrocopy KCGKLKASSTCE*VSLGSITAGDFSRPTLYGWALLAFELCLDGCQMISDTSKSKLSENHFTLVHKAAHL*

Parental  LHTHVNDGTEFGGSIYQKVNEKIETSINLAWTAGSNNTRFGIAAKYMLDCRTSLSAKVNNASLIGLGYTQ
          L..HVNDGTE.......KVNEKIET..NL.W.AGS.NTRF.....Y.LD.R.S....V..ASL...GYTQ
Retrocopy L*SHVNDGTELESFVCKKVNEKIETPKNLVWRAGSDNTRFCFTTVYKLDYRSSAFGRVTHASLNAHGYTQ

Parental  TLRPGVKLTLSALIDGKNFSAGGHKVGLGFELEA
          T...GVK..LSA..DGKNF.A.G.KVGL.FELEA
Retrocopy TFPSGVKVILSA*TDGKNFHAEGYKVGLRFELEA

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	0.00 RPM	101.85 RPM
SRP007412_cerebellum	0.00 RPM	75.17 RPM
SRP007412_heart	0.00 RPM	132.59 RPM
SRP007412_kidney	0.00 RPM	62.22 RPM
SRP007412_liver	0.00 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_2548 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2548 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2548 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_3163
Equus caballus	retro_ecab_799

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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,