RetrogeneDB ID: retro_ptro_1815

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:117249206..117250186(+)
• Located in intron of: ENSPTRG00000015236

Retrocopy information

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

Parental gene information

• Parental gene symbol: VPS26A
• Ensembl ID: ENSPTRG00000002567
• Aliases: None
• Description: None

Sequence

>retro_ptro_1815
ATGAGTTTTCTTGAAGGCTTTTTTGGTCCAGTTTGTGAGATTGATATGTCTTTAATGATGGGGAAGCCAGGAAAATGACA
GAAATGAAAACTGAAGATGGCAAAGTAGAAAAACACCATCTCTTTATAATGGAGAATCTGTTTCAGGGAAGGTAAATGTA
GCCTTTAAGCAACCTGGAGGGAGACTAGAACACCAAGGAATTAGAATTGAATTTATAGGTCAAATGGAACTTTACAATGA
CAAGAGTAATGCTCATGAATTTATAAACCTAATGAAAGAACTAGCCTTACCTGGAGAACTGACTCAGAGAAGAAGTTATG
ATTCTGAGTTTATGCAAGTTAAAAAGCCATATGCATCTGACATCGGTGCCAGTGTTCACTTGAGGTATTTTCTTTAAGTG
ACAATAGTGAGAAGACTGACAGATTTAGTAAAAGAATGTGATCTTATTGTTCACCAGCTTGCCACCTGTCCTGATGTTAA
CAACTGTATTAAGATAGAAGTGGGCATTGAAGATTGTCTACATATATAATTTGAATATAGTAAGTCAAAGTATCATTTAA
AGCATGTAATTGTTGGAAAAATTTACTTCTTAGTAGTAAGAATAAAAATACAACATATGGAGTTACAACTGATCAAAAAA
GAGATCACAGGAATTGGACCCAGTACCACAGCAGAAACAGAAACATCACCAAATATGAAATAATGGATGGTGCACCAGTA
AAAGGTGAATCAATTCCAATGAGACTGTTTTTAGTGGGATATGACCCTACTCCAACAATCAGAGAGATGTGAACCAAAAA
GTTTCAGTAAGGTACTTTTTGAATTTAGTGTTTGTTGATGAGGAAGACTGAAGGTACTTCAAACAGCAGGAGATCATTTT
ATGAAGAAAAGCTCCTGAAAAACTGAGGAAACAGAGAAAAAACTTTCACCAGTGATTTGAATCTCCAGAATCACAGGCAT
CTGCTAAACAGCCTGAAATG

Alignment

ORF - retro_ptro_1815 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.64 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MSFLGGFFGPICEIDI-VLNDGETRKMAEMKTEDGKVEKHYLF-YDGESVSGKVNLAFKQPGKRLEHQGI
          MSFL.GFFGP.CEID..V.NDGE.RKM.EMKTEDGKVEKH.LF.Y.GESVSGKVN.AFKQPG.RLEHQGI
Retrocopy MSFLEGFFGPVCEIDM<VFNDGEARKMTEMKTEDGKVEKHHLF<YNGESVSGKVNVAFKQPGGRLEHQGI

Parental  RIEFVGQIELFNDKSNTHEFVNLVKELALPGELTQSRSYDFEFMQVEKPYESYIGANVRLRYFLKVTIVR
          RIEF.GQ.EL.NDKSN.HEF.NL.KELALPGELTQ.RSYD.EFMQV.KPY.S.IGA.V.LRYFL.VTIVR
Retrocopy RIEFIGQMELYNDKSNAHEFINLMKELALPGELTQRRSYDSEFMQVKKPYASDIGASVHLRYFL*VTIVR

Parental  RLTDLVKEYDLIVHQLATYPDVNNSIKMEVGIEDCLHIEFEYNKSKYHLKDVIVGKIYFLLVRIKIQHME
          RLTDLVKE.DLIVHQLAT.PDVNN.IK.EVGIEDCLHI.FEY.KSKYHLK.VIVGKIYFL.VRIKIQHME
Retrocopy RLTDLVKECDLIVHQLATCPDVNNCIKIEVGIEDCLHI*FEYSKSKYHLKHVIVGKIYFLVVRIKIQHME

Parental  LQLIKKEITGIGPSTTTETET-IAKYEIMDGAPVKGESIPIRLFLAGYDPTPTMRDV-NKKF-SVRYFLN
          LQLIKKEITGIGPSTT.ETET.I.KYEIMDGAPVKGESIP.RLFL.GYDPTPT.R....KKF.SVRYFLN
Retrocopy LQLIKKEITGIGPSTTAETET<ITKYEIMDGAPVKGESIPMRLFLVGYDPTPTIREM*TKKF<SVRYFLN

Parental  LVLVDEEDRRYFKQQEIILWRKAPEKLRKQRTNFHQRFESPESQASAEQPEM
          LV.VDEED.RYFKQQEIIL.RKAPEKLRKQR.NFHQ.FESPESQASA.QPEM
Retrocopy LVFVDEED*RYFKQQEIIL*RKAPEKLRKQRKNFHQ*FESPESQASAKQPEM

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	0.02 RPM	21.41 RPM
SRP007412_cerebellum	0.00 RPM	16.31 RPM
SRP007412_heart	0.00 RPM	8.69 RPM
SRP007412_kidney	0.05 RPM	18.02 RPM
SRP007412_liver	0.03 RPM	8.51 RPM
SRP007412_testis	0.00 RPM	30.67 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1815 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1815 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1815 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2688
Gorilla gorilla	retro_ggor_1875
Pongo abelii	retro_pabe_2293

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013827	1 retrocopy	retro_cfam_1133,
Choloepus hoffmanni	ENSCHOG00000007324	5 retrocopies	retro_chof_1303, retro_chof_1663, retro_chof_1796, retro_chof_2352, retro_chof_242,
Callithrix jacchus	ENSCJAG00000012907	1 retrocopy	retro_cjac_1420,
Equus caballus	ENSECAG00000009507	1 retrocopy	retro_ecab_17,
Homo sapiens	ENSG00000122958	1 retrocopy	retro_hsap_2688,
Gorilla gorilla	ENSGGOG00000010433	1 retrocopy	retro_ggor_1875,
Microcebus murinus	ENSMICG00000014940	1 retrocopy	retro_mmur_1070,
Mustela putorius furo	ENSMPUG00000004519	1 retrocopy	retro_mputfur_146,
Nomascus leucogenys	ENSNLEG00000011548	1 retrocopy	retro_nleu_1187,
Pongo abelii	ENSPPYG00000002386	1 retrocopy	retro_pabe_2293,
Pan troglodytes	ENSPTRG00000002567	3 retrocopies	retro_ptro_1815 , retro_ptro_2245, retro_ptro_4,
Tupaia belangeri	ENSTBEG00000015348	1 retrocopy	retro_tbel_1425,
Vicugna pacos	ENSVPAG00000000630	1 retrocopy	retro_vpac_385,