RetrogeneDB ID: retro_ggor_2491

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 6:158468735..158469500(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGGOG00000024408
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HSD17B12
• Ensembl ID: ENSGGOG00000002003
• Aliases: None
• Description: None

Sequence

>retro_ggor_2491
TCAGGTAGTACTGATGGAACTGGAAAATCGTATGCAGAAGAGTTAGCAAAACATGAAATGGCGGTTGTCCTTATCAGCAG
ATTACAGGATAAACTTGACCAGGTTTCCAGGGAAATAAAAGAAAACTTCAAAGTGGAGACAAGACCATTGCTGTTGACTG
CATCAGAAGATATTTATGATAAAATTAAAACAGGCTTGGCTGGTCTTGAAATCGGCGTCTTAGTGAACAACGTGGGAATG
TCATATGAATATCCCAAATACTTTTTGGACATTCCTGACTTGGACAATATGATCAAGAAAATGATAAATATTAATATTCT
CTCTGTTTGTAAGATGACACAATTGGTGCACCTGGCATGATGGAAAGATCTAAAGGGGTGAATCTGAACCTCTCCGCTGG
CAGAGGCATGTTCCCCGTCCCACTGTTGACGATCTGTTCTGCAACCAAGACTTTTGTTGATTTCTTCTCTCAGTGCCTCC
GTGGGGAGTATAGGAGCAAGGGCATCTTTGTGCAGAGTGTCCTGCCATACTTCGTAGCTATAAAACTGGCTAAAATCCGA
AAGCCAACTTTGGATAAGCCCTCTTCGGGGACATTTTGAAGTCTGCAATTAAAACAGTAGGCCTGCAATCCCAAACCAAT
GGATACTTGATCCATGCTCTTATGGGCTTGATAATCTCAATCCTGCCGTCTTGGATTTATTTTAAAATAATCATGGCTAT
GAAAAGTCTACACGGGATCGCTATTTGAAAAAAACCAAGAAGAAC

Alignment

ORF - retro_ggor_2491 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.54 %
• Parental protein coverage: 82.37 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TGSTDGIGKSYAEELAKHGMKVVLISRSKDKLDQVSSEIKEKFKVETRTIAVDFASEDIYDKIKTGLAGL
          .GSTDG.GKSYAEELAKH.M.VVLISR..DKLDQVS.EIKE.FKVETR......ASEDIYDKIKTGLAGL
Retrocopy SGSTDGTGKSYAEELAKHEMAVVLISRLQDKLDQVSREIKENFKVETRPLLLT-ASEDIYDKIKTGLAGL

Parental  EIGILVNNVGMSYEYPEYFLDVPDLDNVIKKMININILSVCKMTQLV-LPGMVERSKGAILNISSGSGML
          EIG.LVNNVGMSYEYP.YFLD.PDLDN.IKKMININILSVCKMTQLV..PGM.ERSKG..LN.S.G.GM.
Retrocopy EIGVLVNNVGMSYEYPKYFLDIPDLDNMIKKMININILSVCKMTQLV<APGMMERSKGVNLNLSAGRGMF

Parental  PVPLLTIYSATKTFVDFFSRCLHEEYRSKGVFVQSVLPYFVATKLAKIRKPTLDKPSPEMF-VKSAIKTV
          PVPLLTI.SATKTFVDFFS.CL..EYRSKG.FVQSVLPYFVA.KLAKIRKPTLDKPS...F..KSAIKTV
Retrocopy PVPLLTICSATKTFVDFFSQCLRGEYRSKGIFVQSVLPYFVAIKLAKIRKPTLDKPSSGTF<LKSAIKTV

Parental  GLQSRTNGYLIHALMGSIISNLPSWIYLKIVMNM-NKSTRAHYLKKTKKN
          GLQS.TNGYLIHALMG.IIS.LPSWIY.KI.M.M..KSTR..YLKKTKKN
Retrocopy GLQSQTNGYLIHALMGLIISILPSWIYFKIIMAM<EKSTRDRYLKKTKKN

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	0.05 RPM	36.45 RPM
SRP007412_cerebellum	0.24 RPM	24.90 RPM
SRP007412_heart	0.00 RPM	6.44 RPM
SRP007412_kidney	0.00 RPM	61.54 RPM
SRP007412_liver	0.00 RPM	66.84 RPM
SRP007412_testis	0.10 RPM	41.54 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_2491 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2491 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2499
Pongo abelii	retro_pabe_3021

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000011325	1 retrocopy	retro_cjac_2489,
Dipodomys ordii	ENSDORG00000004834	1 retrocopy	retro_dord_561,
Homo sapiens	ENSG00000149084	1 retrocopy	retro_hsap_3684,
Gorilla gorilla	ENSGGOG00000002003	1 retrocopy	retro_ggor_2491 ,
Nomascus leucogenys	ENSNLEG00000017959	1 retrocopy	retro_nleu_2273,
Oryctolagus cuniculus	ENSOCUG00000016351	1 retrocopy	retro_ocun_1335,
Otolemur garnettii	ENSOGAG00000009102	1 retrocopy	retro_ogar_3391,
Pongo abelii	ENSPPYG00000003343	1 retrocopy	retro_pabe_3021,
Pan troglodytes	ENSPTRG00000003522	1 retrocopy	retro_ptro_2499,
Ictidomys tridecemlineatus	ENSSTOG00000005473	1 retrocopy	retro_itri_1099,
Tursiops truncatus	ENSTTRG00000005103	1 retrocopy	retro_ttru_772,