RetrogeneDB ID: retro_ptro_2499

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:159106621..159107227(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HSD17B12
• Ensembl ID: ENSPTRG00000003522
• Aliases: None
• Description: None

Sequence

>retro_ptro_2499
GCATCAGAAGATATTTATGATAAAATTAAAACAGGCTTGGCTGGTCTTGAAATCGGCGTCTTAGTGAACAACGTGGGAAT
GTCATATGAGTATCCCAAATACTTTTTGGACATTCCTGACTTGGACAATATGATCAAGAAAATGATAAATATTAATATTC
TCTCTGTTTGTAAGATGGCACAATTGGTGCACCTGGCATAATGGAAAGATCTAAAGGGGTGAATCTGAACCTCTCCGCTG
GCAGAGGCATGTTCCCCGTCCCACTGTTGACGATCTGTTCTGCAACCAAGACTTTTGTTGATTTCTTCTCTCAGTACCTC
CATGGGGAGTATAGGAGCAAGGGCATCTTTGTGCAGAGTGTCCTGCCATACTTCGTAGCTATAAAACTGGCTAAAATCCG
AAAGCCAACTTTGGATAAGCCCTCTTCGGGGACATTTTGAAGTCTGCAATTAAAACAGTAGGCCTGCAATCCCAAAACAA
TGGATACCTGATCCATGCTCTTATGGGCTTGATAATCTCAATCCTGCCATCTTGGATTTATTTTAAAATAATCATGGCTA
TGAAAAGTCTACACGGGATCGCTATTTGAAAAAAACCAAGAAGAAC

Alignment

ORF - retro_ptro_2499 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.52 %
• Parental protein coverage: 65.06 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ASEDIYDKIKTALAGLEIGILVNNVGMSYEYPEYFLDVPDLDNVIKKMININILSVCKMTQLV-LPGMVE
          ASEDIYDKIKT.LAGLEIG.LVNNVGMSYEYP.YFLD.PDLDN.IKKMININILSVCKM.QLV..PG..E
Retrocopy ASEDIYDKIKTGLAGLEIGVLVNNVGMSYEYPKYFLDIPDLDNMIKKMININILSVCKMAQLV<APGIME

Parental  RSKGAILNISSGSGMLPVPLLTIYSATKTFVDFFSQCLHEEYRSKGVFVQSVLPYFVATKLAKIRKPTLD
          RSKG..LN.S.G.GM.PVPLLTI.SATKTFVDFFSQ.LH.EYRSKG.FVQSVLPYFVA.KLAKIRKPTLD
Retrocopy RSKGVNLNLSAGRGMFPVPLLTICSATKTFVDFFSQYLHGEYRSKGIFVQSVLPYFVAIKLAKIRKPTLD

Parental  KPSPETF-VKSAIKTVGLQSRTNGYLIHALMGSIISNLPSWIYLKIVMNM-NKSTRAHYLKKTKKN
          KPS..TF..KSAIKTVGLQS..NGYLIHALMG.IIS.LPSWIY.KI.M.M..KSTR..YLKKTKKN
Retrocopy KPSSGTF<LKSAIKTVGLQSQNNGYLIHALMGLIISILPSWIYFKIIMAM<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	0.00 RPM	34.41 RPM
SRP007412_cerebellum	0.14 RPM	25.70 RPM
SRP007412_heart	0.00 RPM	25.62 RPM
SRP007412_kidney	0.00 RPM	60.80 RPM
SRP007412_liver	0.00 RPM	40.00 RPM
SRP007412_testis	0.00 RPM	22.13 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2499 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2499 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2499 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_2491
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,