RetrogeneDB ID: retro_ptro_4

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 9:117646443..117647454(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000004494
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

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

Sequence

>retro_ptro_4
ATGAGCTTCTTCGGCTTCGGGCAGAGCGTGGAGGTGGAAATCCTTCTGAACGATGCAGAGAGTAGGAAGCGGGCCGAGCA
CAAGACGGAGGACGGGAAGAAGGAGAAATATTTCCTCTTCTACAACGGGGAGACGGTCTCCGGGAAGGTGAGCCTTGCCC
TCAAGAACCCCAACAAGCGGCTGGAGCACCAGGGCATCAAGATCGAGTTCATCGGGCAGATCGAACTCTACTACGATCGC
GGGAACCACCATGAATTTGTGTCCCTGGTGAAGGACCTGGCCCGGCCTGGAGAGATCACCCAGTCGCAGGCCTTCGACTT
TGAGTTTACCCACGTGGAGAAGCCGTATGAGTCCTACACAGGGCAGAATGTGAAGCTACGCTATTTCCTTCGAGCTACCA
TCAGCCGCCGCCTCAATGATGTTGTCAAAGAGATGGACATTGTAGTTCACACACTCAGCACATACCCGGAGCTGAACTCT
TCCATCAAGATGGAGGTTGGGATTGAGGACTGTCTGCACATTGAATTTGAGTACAATAAATCCAAATACCACTTGAAAGA
TGTCATTGTAGGGAAGATATACTTCCTGCTAGTGAGAATCAAAATCAAGCACATGGAGATAGACATCATCAAGCGAGAAA
CGACGGGTACAGGCCCCAACGTGTACCATGAGAACGACACGATAGCCAAGTACGAGATCATGGACGGGGCACCAGTGCGA
GGAGAGTCCATCCCGATCCGGCTCTTCCTGGCCGGGTATGAGCTCACGCCCACCATGCGGGACATCAACAAGAAGTTCTC
TGTGCGCTATTACCTCAACCTGGTGCTGATAGACGAGGAGGAGCGGCGCTACTTCAAGCAGCAGGAAGTGGTGTTGTGGC
GGAAGGGTGACATCGTACGGAAGAGCATGTCCCACCAGGCGGCCATCGCCTCACAGCGCTTTGAGGGCACCACCTCCCTG
GGTGAGGTGCGGACCCCCAGCCAGCTGTCTGACAACAACTGCAGGCAGTAG

Alignment

ORF - retro_ptro_4 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.51 %
• Parental protein coverage: 99.39 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSFLGGFFGPICEIDIVLNDGETRKMAEMKTEDGKVEKHYLFYDGESVSGKVNLAFKQPGKRLEHQGIRI
          MSF.G..FG...E..I.LND.E.RK.AE.KTEDGK.EK..LFY.GE.VSGKV.LA.K.P.KRLEHQGI.I
Retrocopy MSFFG--FGQSVEVEILLNDAESRKRAEHKTEDGKKEKYFLFYNGETVSGKVSLALKNPNKRLEHQGIKI

Parental  EFVGQIELFNDKSNTHEFVNLVKELALPGELTQSRSYDFEFMQVEKPYESYIGANVRLRYFLKVTIVRRL
          EF.GQIEL..D..N.HEFV.LVK.LA.PGE.TQS...DFEF..VEKPYESY.G.NV.LRYFL..TI.RRL
Retrocopy EFIGQIELYYDRGNHHEFVSLVKDLARPGEITQSQAFDFEFTHVEKPYESYTGQNVKLRYFLRATISRRL

Parental  TDLVKEYDLIVHQLATYPDVNNSIKMEVGIEDCLHIEFEYNKSKYHLKDVIVGKIYFLLVRIKIQHMELQ
          .D.VKE.D..VH.L.TYP..N.SIKMEVGIEDCLHIEFEYNKSKYHLKDVIVGKIYFLLVRIKI.HME..
Retrocopy NDVVKEMDIVVHTLSTYPELNSSIKMEVGIEDCLHIEFEYNKSKYHLKDVIVGKIYFLLVRIKIKHMEID

Parental  LIKKEITGIGPSTTTETETIAKYEIMDGAPVKGESIPIRLFLAGYDPTPTMRDVNKKFSVRYFLNLVLVD
          .IK.E.TG.GP....E..TIAKYEIMDGAPV.GESIPIRLFLAGY..TPTMRD.NKKFSVRY.LNLVL.D
Retrocopy IIKRETTGTGPNVYHENDTIAKYEIMDGAPVRGESIPIRLFLAGYELTPTMRDINKKFSVRYYLNLVLID

Parental  EEDRRYFKQQEIILWRKAP---EKLRKQRTNFHQRFESPESQASAEQP
          EE.RRYFKQQE..LWRK..........Q.....QRFE...S......P
Retrocopy EEERRYFKQQEVVLWRKGDIVRKSMSHQAAIASQRFEGTTSLGEVRTP

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	19.23 RPM	21.41 RPM
SRP007412_cerebellum	11.29 RPM	16.31 RPM
SRP007412_heart	3.47 RPM	8.69 RPM
SRP007412_kidney	4.86 RPM	18.02 RPM
SRP007412_liver	6.25 RPM	8.51 RPM
SRP007412_testis	3.37 RPM	30.67 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_4 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_4 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_4 has 0 orthologous retrocopies within eutheria group .

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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,