RetrogeneDB ID: retro_nleu_2273

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397340.1:127889..128818(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HSD17B12
• Ensembl ID: ENSNLEG00000017959
• Aliases: None
• Description: None

Sequence

>retro_nleu_2273
ATGGAGAGCGCTCTCCCCACCGCCAGCTTCCTGTACTGGGTGGGCACGGGCACCGTGGCCAACCTAACCCTGCACATCTG
TTACTCGCTCTTCACCTCTGGGTCAGGGGAGTGGGGAATGAGTTGGAGGTCGGCCCAGGGCTTGGGGAATGGGCAGTTGT
CACAGGTAGTACTGATGCAATTGGAAAATCATATGCAGAAGAGTTAGCAAAGCGTGGGATGATGGTTGTCCTTATCAGCA
GATTACAGGATAAACTTGACCAGGTTTCTAGGGAAATAAAAGAAAAATTCAAAGTGGAGGCAAGAACCATTGCTGTTGAC
TTTGCATCAGAAGATATTTATGATAAAATTAAAACAGGCTTGGCTGGTCTTGAAATCGGTGTCTTAGTGAACAACGTGGG
AATGTCATATGAGGATCCCAAATACTTTTTGGACATTCCTGACTTGGACAATATGATCAAGAAAATGATAAATATTAATA
TTCTTTCTGTTTGTAAGATGACACAATTGGTGCACCTGGCATGATGGAAAGATCTAAAGGGGCAAATCTGAACCTCTCAG
CAGGCAGAGGCATGTTCCCTGTCCCACTGTTGACCATCTGTTCTGCAACCAAGACTTTTGTTGATTTCTTCTCTCAGTGC
CTCCATGGGGAGTATAGGAGCAAGAGCATCTTTGTGCAGAGTGTCCTGCCATATTTCGTAGCTACAAAACTGGCTAAAAT
CCGAAAGCCGACTTTGGATGAGCCCTCTTTGGAGACATTTTGAACTCTGCAATTAAAACAGTAGGCCTGCAATCCCAAAC
CAATGGATACCTGAGCCATGCTCTTAAGGGCTTGATAATCTCAATCCTGCCGTCTTGGATTTATTTTAAAATAACCATGG
CTATGAAAAGTCTACACGGGATCACTATTTGAGGAAAAACAAGAAGAAC

Alignment

ORF - retro_nleu_2273 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.81 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MESAHPAAGFLYWVGAGTVAYLALRISYSLFTA-LRVWGVG-NEAGVGPGLGEWAVVTGSTDGIGKSYAE
          MESA.P.A.FLYWVG.GTVA.L.L.I.YSLFT.....WG....E.G.G..LGEWAVVTGSTD.IGKSYAE
Retrocopy MESALPTASFLYWVGTGTVANLTLHICYSLFTSGSGEWGMS<LEVGPG--LGEWAVVTGSTDAIGKSYAE

Parental  ELAKRGMKVVLISRSQDKLDQLSSEIKEKFKVETRTIAVDFASEDIYDKIKTGLAGLEIGILVNNVGMSY
          ELAKRGM.VVLISR.QDKLDQ.S.EIKEKFKVE.RTIAVDFASEDIYDKIKTGLAGLEIG.LVNNVGMSY
Retrocopy ELAKRGMMVVLISRLQDKLDQVSREIKEKFKVEARTIAVDFASEDIYDKIKTGLAGLEIGVLVNNVGMSY

Parental  EYPEYFLDVPDLDNVIKKMININILSVCKMTQLV-LPGMVERSKGAILNISSGSGMLPVPLLTIYSATKT
          E.P.YFLD.PDLDN.IKKMININILSVCKMTQLV..PGM.ERSKGA.LN.S.G.GM.PVPLLTI.SATKT
Retrocopy EDPKYFLDIPDLDNMIKKMININILSVCKMTQLV<APGMMERSKGANLNLSAGRGMFPVPLLTICSATKT

Parental  FVDFFSQCLHEEYRSKGVFVQSVLPYFVATKLAKIRKPTLDKPSPETF-VKSAIRTVGLQSRTNGYLIHA
          FVDFFSQCLH.EYRSK..FVQSVLPYFVATKLAKIRKPTLD.PS.ETF...SAI.TVGLQS.TNGYL.HA
Retrocopy FVDFFSQCLHGEYRSKSIFVQSVLPYFVATKLAKIRKPTLDEPSLETF<LNSAIKTVGLQSQTNGYLSHA

Parental  LMGSIFSNLPSWIYLKIAMNM-NKSTRAHYLKKTKKN
          L.G.I.S.LPSWIY.KI.M.M..KSTR.HYL.K.KKN
Retrocopy LKGLIISILPSWIYFKITMAM<EKSTRDHYLRKNKKN

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Nomascus leucogenys was not studied using RNA-Seq expression data.

ChIP-Seq

Nomascus leucogenys was not studied using ChIP-Seq data.

EST

Nomascus leucogenys was not studied using EST data.

TSS

Nomascus leucogenys was not studied using FANTOM5 data.

Lab

retro_nleu_2273 was not experimentally validated.

Homology

Retrocopy orthology:

Nomascus leucogenys does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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,