RetrogeneDB ID: retro_ptro_2245

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:35671661..35672642(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000039087
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_ptro_2245
ATGAGTTTTCTTGGAGGCTTTTTTGGTCCAATTTGTGAGATCGATATTGTTCTTAATGATGGGGAAACCAGGAAAATGGC
AGAAATGAAAACTGAAGATGGCAAAGTAGAAAAACACTATCTCTTCTATGACGGAGAATCTGTTTCAGGAAAGGTAAACC
TAGCCTTTAAGCAACCTGGAAAGAGGCTAGAACACCAAGGAATTAGAATTGAATTTGTAGGTCAAATTGAACTTTTCAAT
GACAAGAGTAATACTCATGAATTTGTAAACCTAGTGAAAGAACTAGCCTTACCTGGAGAACTGACTCAGAGCAGAAGTTA
TGATTTTGAATTTATGCAAGTTGAAAAGCCATATGAATCTTACATCGGTGCCAATGTCCGCTTGAGGTATTTTCTTAAAG
TGACAATAGTGAGAAGACTGACAGATTTGGTAAAAGAGTATGATCTTATTGTTCACCAGCTTGCCACCTATCCTGATGTT
AACAACTCTATTAAGATGGAAGTGGGCATTGAAGATTGTCTACATATAGAATTTGAATATAATAAATCAAAGTATCATTT
AAAGGATGTGATTGTTGGAAAAATTTACTTCTTATTAGTAAGAATAAAAATACAACATATGGAGTTACAGCTGATCAAAA
AAGAGATCACAGGAATTGGACCCAGTACCACAACAGAAACAGAAACAATCGCCAAATATGAAATAATGGATGGTGCACCA
GTAAAAGGTGAATCAATTCCAATAAGGCTATTTTTAGCAGGATATGACCCAACTCCAACAATGAGAGATGTGAACAAAAA
ATTTTCAGTAAGGTACTTTTTGAATTTAGTGCTTGTTGATGAGGAAGACCGGAGGTACTTCAAACAGCAGGAGATAATTT
TATGGAGAAAAGCTCCTGAAAAACTGAGGAAACAGAGAACAAACTTTCACCAGCGATTTGAATCTCCAGAATCACAGGCA
TCTGCCGAACAGCCTGAAATG

Alignment

ORF - retro_ptro_2245 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100.0 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSFLGGFFGPICEIDIVLNDGETRKMAEMKTEDGKVEKHYLFYDGESVSGKVNLAFKQPGKRLEHQGIRI
          MSFLGGFFGPICEIDIVLNDGETRKMAEMKTEDGKVEKHYLFYDGESVSGKVNLAFKQPGKRLEHQGIRI
Retrocopy MSFLGGFFGPICEIDIVLNDGETRKMAEMKTEDGKVEKHYLFYDGESVSGKVNLAFKQPGKRLEHQGIRI

Parental  EFVGQIELFNDKSNTHEFVNLVKELALPGELTQSRSYDFEFMQVEKPYESYIGANVRLRYFLKVTIVRRL
          EFVGQIELFNDKSNTHEFVNLVKELALPGELTQSRSYDFEFMQVEKPYESYIGANVRLRYFLKVTIVRRL
Retrocopy EFVGQIELFNDKSNTHEFVNLVKELALPGELTQSRSYDFEFMQVEKPYESYIGANVRLRYFLKVTIVRRL

Parental  TDLVKEYDLIVHQLATYPDVNNSIKMEVGIEDCLHIEFEYNKSKYHLKDVIVGKIYFLLVRIKIQHMELQ
          TDLVKEYDLIVHQLATYPDVNNSIKMEVGIEDCLHIEFEYNKSKYHLKDVIVGKIYFLLVRIKIQHMELQ
Retrocopy TDLVKEYDLIVHQLATYPDVNNSIKMEVGIEDCLHIEFEYNKSKYHLKDVIVGKIYFLLVRIKIQHMELQ

Parental  LIKKEITGIGPSTTTETETIAKYEIMDGAPVKGESIPIRLFLAGYDPTPTMRDVNKKFSVRYFLNLVLVD
          LIKKEITGIGPSTTTETETIAKYEIMDGAPVKGESIPIRLFLAGYDPTPTMRDVNKKFSVRYFLNLVLVD
Retrocopy LIKKEITGIGPSTTTETETIAKYEIMDGAPVKGESIPIRLFLAGYDPTPTMRDVNKKFSVRYFLNLVLVD

Parental  EEDRRYFKQQEIILWRKAPEKLRKQRTNFHQRFESPESQASAEQPEM
          EEDRRYFKQQEIILWRKAPEKLRKQRTNFHQRFESPESQASAEQPEM
Retrocopy EEDRRYFKQQEIILWRKAPEKLRKQRTNFHQRFESPESQASAEQPEM

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	0.61 RPM	21.41 RPM
SRP007412_cerebellum	0.18 RPM	16.31 RPM
SRP007412_heart	0.09 RPM	8.69 RPM
SRP007412_kidney	0.08 RPM	18.02 RPM
SRP007412_liver	0.07 RPM	8.51 RPM
SRP007412_testis	0.32 RPM	30.67 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2245 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2245 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2245 has 0 orthologous retrocopies within eutheria group .

---

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,