RetrogeneDB ID: retro_pabe_2293

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:18893499..18894349(-)
• Located in intron of: ENSPPYG00000013534

Retrocopy information

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

Parental gene information

• Parental gene symbol: VPS26A
• Ensembl ID: ENSPPYG00000002386
• Aliases: None
• Description: vacuolar protein sorting-associated protein 26A [Source:RefSeq peptide;Acc:NP_001127000]

Sequence

>retro_pabe_2293
ATGAGTTTTCTTGAAGGCTTTTTTGGTCCAATTTGTGAGATCAATATTGTCTTTAATGATGGGGAAGCCAGGAAAATGAC
AGAAATGAAAACTGAAGATGGCAAAGTAGAAAAACACCATCTCTTTATAATGGAGAATCTGTTTCAGGAAAGGTAAAAGT
AGCCTTTAAGCAACCTGGATAGAGGCTAGAGCACCAAGGAATTAGAATTGAATTTGTAGGTCAAATGAAACTTTACAATG
ACAAGAGTAATGCTCATGAATTTATAAACCTAATGAAAGAACTAGCCTTACCTGGAGAACTGACTCAGAGAGGAAGTTAT
GATTCTGAATTTATGCAAGTTGAAAAGCCATATGCATCTGACATCGGTGCCAATGTTCACTTGAGGTATTTTCTTAAAGT
GACAATAGTGAGAAGACTGACAGATTTTAGTAAAAGAATATGATCTTATTGTTCACCAGCTTGCCACCTGTCCTGATGTT
GACAACTATACTAAGATAGAAGTGGGCATTGAAGATTGTCTACATATATAATTTGAATATAATAAGTCAAAGTATCATTT
AAAGCATGTAATTGTTGGAAAAATTTACTTCTTAGTAGTAAGAATAAAAATACAACATATGGAGTTACAACTGATCAAAA
AACAGATCACAGGAATTGTACCACAGCAGAAACAGAAACAATCGCCAAATACGAAATAATGGATGGTGCACCAGTAAAAG
GTGAATCAATTCCAATGAGACTATTTTTAGCGGGATATGACCCTACTCCAACAATCAGAGAGATGTGAACAAAAAAGTTT
CAGTAAGGTACTTTTTGAATTTCGTGTTTGTTGATGAGGAAGACTGAAGG

Alignment

ORF - retro_pabe_2293 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.76 %
• Parental protein coverage: 87.16 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MSFLGGFFGPICEIDIVLNDGETRKMAEMKTEDGKVEKHYLF-YDGESVSGKVNLAFKQPGKRLEHQGIR
          MSFL.GFFGPICEI.IV.NDGE.RKM.EMKTEDGKVEKH.LF.Y.GESVSGKV..AFKQPG.RLEHQGIR
Retrocopy MSFLEGFFGPICEINIVFNDGEARKMTEMKTEDGKVEKHHLF<YNGESVSGKVKVAFKQPG*RLEHQGIR

Parental  IEFVGQIELFNDKSNTHEFVNLVKELALPGELTQSRSYDFEFMQVEKPYESYIGANVRLRYFLKVTIVRR
          IEFVGQ..L.NDKSN.HEF.NL.KELALPGELTQ..SYD.EFMQVEKPY.S.IGANV.LRYFLKVTIVRR
Retrocopy IEFVGQMKLYNDKSNAHEFINLMKELALPGELTQRGSYDSEFMQVEKPYASDIGANVHLRYFLKVTIVRR

Parental  LTD-LVKEYDLIVHQLATYPDVNNSIKMEVGIEDCLHIEFEYNKSKYHLKDVIVGKIYFLLVRIKIQHME
          LTD.LVKEYDLIVHQLAT.PDV.N..K.EVGIEDCLHI.FEYNKSKYHLK.VIVGKIYFL.VRIKIQHME
Retrocopy LTD>LVKEYDLIVHQLATCPDVDNYTKIEVGIEDCLHI*FEYNKSKYHLKHVIVGKIYFLVVRIKIQHME

Parental  LQLIKKEITGIGP-STTTETETIAKYEIMDGAPVKGESIPIRLFLAGYDPTPTMRDV-NKKF-SVRYFLN
          LQLIKK.ITGI.P....TE..TIAKYEIMDGAPVKGESIP.RLFLAGYDPTPT.R....KKF.SVRYFLN
Retrocopy LQLIKKQITGIVP<TAETE--TIAKYEIMDGAPVKGESIPMRLFLAGYDPTPTIREM*TKKF<SVRYFLN

Parental  LVLVDEEDRR
          .V.VDEED.R
Retrocopy FVFVDEED*R

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	24.99 RPM
SRP007412_cerebellum	0.24 RPM	35.02 RPM
SRP007412_heart	0.00 RPM	17.70 RPM
SRP007412_kidney	0.07 RPM	29.60 RPM
SRP007412_liver	0.00 RPM	16.98 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2293 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2293 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2293 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2688
Pan troglodytes	retro_ptro_1815
Gorilla gorilla	retro_ggor_1875

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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,