RetrogeneDB ID: retro_ggor_1875

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 3:113267545..113268132(+)
• Located in intron of: ENSGGOG00000009490

Retrocopy information

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

Parental gene information

• Parental gene symbol: VPS26A
• Ensembl ID: ENSGGOG00000010433
• Aliases: None
• Description: None

Sequence

>retro_ggor_1875
AATGTTTCAGGGAAGGTAAATGTAGCCTTTAAGCAACCTGGGTAGAAGCTAGAGCACCAAGGAATTAGAATTGAATTTAT
AGGTCAAATGGAACTTTACAATGACAAGAGTAATGCTCATGAATTTATAAACCTAATGAAAGAACTAGCCTTACCTGGAG
AACTGACTCAGAGAAGAAGTTATGATTCTGAGTTTATGCAAGTTAAAAAGCCATATGCATCTGACATCGGTGCCAGTGTT
CACTTGAGGTATTTTCTTAAAGTGACAATAGTGAGAAGACTGACAGATTTAGTAAAAGAATGTGATCTTATTGTTTACCA
GCTTGCCACCTGTCCTGATGTTAACAACTGTATTAAGATAGAAGTGGGCATTGAAGATTGTCTACATATATAATTTGAAT
ATAGTAAGTCAAAGTATCATTTAAAGCATGTAATTGTTGGAAAAATTTACTTCTTAGTAGTAAGAATAAAAATACAACAT
ATGGAGTTACAACTGATCAAAAAAGAGATCACAGGAATTGGACCCAGTACCACAGCAGAAACAGAAACATCACCAAATAT
GAAATAATGGATGGTGCACCAGTAAAA

Alignment

ORF - retro_ggor_1875 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.28 %
• Parental protein coverage: 80.99 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SVSGKVNLAFKQPGKRLEHQGIRIEFVGQIELFNDKSNTHEFVNLVKELALPGELTQSRSYDFEFMQVEK
          .VSGKVN.AFKQPG..LEHQGIRIEF.GQ.EL.NDKSN.HEF.NL.KELALPGELTQ.RSYD.EFMQV.K
Retrocopy NVSGKVNVAFKQPG*KLEHQGIRIEFIGQMELYNDKSNAHEFINLMKELALPGELTQRRSYDSEFMQVKK

Parental  PYESYIGANVRLRYFLKVTIVRRLTDLVKEYDLIVHQLATYPDVNNSIKMEVGIEDCLHIEFEYNKSKYH
          PY.S.IGA.V.LRYFLKVTIVRRLTDLVKE.DLIV.QLAT.PDVNN.IK.EVGIEDCLHI.FEY.KSKYH
Retrocopy PYASDIGASVHLRYFLKVTIVRRLTDLVKECDLIVYQLATCPDVNNCIKIEVGIEDCLHI*FEYSKSKYH

Parental  LKDVIVGKIYFLLVRIKIQHMELQLIKKEITGIGPSTTTETET-IAKYEIMDGAPVK
          LK.VIVGKIYFL.VRIKIQHMELQLIKKEITGIGPSTT.ETET.I.KYEIMDGAPVK
Retrocopy LKHVIVGKIYFLVVRIKIQHMELQLIKKEITGIGPSTTAETET<ITKYEIMDGAPVK

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	0.38 RPM	4.94 RPM
SRP007412_cerebellum	0.83 RPM	5.40 RPM
SRP007412_heart	0.03 RPM	0.91 RPM
SRP007412_kidney	0.45 RPM	7.65 RPM
SRP007412_liver	0.34 RPM	2.95 RPM
SRP007412_testis	1.76 RPM	19.37 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_1875 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1875 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2688
Pan troglodytes	retro_ptro_1815
Pongo abelii	retro_pabe_2293

---

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,