RetrogeneDB ID: retro_nleu_1575

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397300.1:3670469..3671184(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDCL3
• Ensembl ID: ENSNLEG00000014393
• Aliases: None
• Description: None

Sequence

>retro_nleu_1575
ATGCAGGACCCCAACGCAGACACTGAGTGGAATGACATCTTACCAAAAAGGGTATCTTGCCCCCCAAGGAAAGTCTGAAA
GAATTGGAAAAGGAGGTGGAAGAGGAGCAACGCATCCTCCAGCAGTCAGTGGTGATAACATATAAAGATAGAACTTTGAA
AGAGCTGGAGGATCATGAAGATGAGTTTAATGAGGAGGATGAATGTGCTATTGAAATGTACACATGGCAGAGACTGGTTG
AGTGGAAGCATCTAAACGGAAGAATACATTTGGAGAAGTTTTGGAGATCTCAGGGAAGGATCATATTCAAGAAGTTGCCA
AAGCTGATGAGGGCTCGTGGGTCATCTTGCACCTTTACAAACGAGGAATTCCTCTCAGTGCCCTGATAAACCAGCACCTC
AGTGGACTTGCCAGGAAGTTTCCTGATGTCAAATTTATCAAAGCCATTTCAACAACCTGCATACCCAATTATCCTGACAG
GAATCTGCCCACGATATTTGTTTTCCTGGAAGGAGATATTAAGGCTCAGTTTTATCGTCCTCTGGTGTTTGGCGGCACAC
ACCTGACAAGAGATGAGTTGGAGCGGAAACTGTCTGAATCTGGAGCAATTAAGATGGACCTGGAGGAAAACCTTAAGAAG
CCGATTGAAGACATGTTGCTGTCCTCACTGCGGCGCTCTGTCCCCATGAGGAGGGACAGCGATTCCAAGGGTGAC

Alignment

ORF - retro_nleu_1575 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.65 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MQDPNADTEWNDIL-RKKGILPPKESLKELEEEAEEEQRILQQSVVKTYEDMTLEELEDHEDEFNEEDER
          MQDPNADTEWNDIL..KKGILPPKESLKELE.E.EEEQRILQQSVV.TY.D.TL.ELEDHEDEFNEEDE.
Retrocopy MQDPNADTEWNDIL<TKKGILPPKESLKELEKEVEEEQRILQQSVVITYKDRTLKELEDHEDEFNEEDEC

Parental  AIEMYRRQRLAEWK-ATKLKNKFGEVLEISGKDYVQEVTKAGEGLWVILHLYKQGIPLCALINQHLSGLA
          AIEMY..QRL.EWK.A.K.KN.FGEVLEISGKD..QEV.KA.EG.WVILHLYK.GIPL.ALINQHLSGLA
Retrocopy AIEMYTWQRLVEWK<ASKRKNTFGEVLEISGKDHIQEVAKADEGSWVILHLYKRGIPLSALINQHLSGLA

Parental  RKFPDVKFIKAISTTCIPNYPDRNLPTIFVYLEGDIKAQFIGPLVFGGMNLTRDELEWKLSESGAIMTDL
          RKFPDVKFIKAISTTCIPNYPDRNLPTIFV.LEGDIKAQF..PLVFGG..LTRDELE.KLSESGAI..DL
Retrocopy RKFPDVKFIKAISTTCIPNYPDRNLPTIFVFLEGDIKAQFYRPLVFGGTHLTRDELERKLSESGAIKMDL

Parental  EENPKKPIEDVLLSSVRRSVLMRRHSDSEGD
          EEN.KKPIED.LLSS.RRSV.MRR.SDS.GD
Retrocopy EENLKKPIEDMLLSSLRRSVPMRRDSDSKGD

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_1575 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 13 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000002226	1 retrocopy	retro_cfam_1740,
Callithrix jacchus	ENSCJAG00000010160	3 retrocopies	retro_cjac_1486, retro_cjac_1599, retro_cjac_2055,
Dipodomys ordii	ENSDORG00000012397	1 retrocopy	retro_dord_702,
Erinaceus europaeus	ENSEEUG00000000224	1 retrocopy	retro_eeur_506,
Homo sapiens	ENSG00000115539	7 retrocopies	retro_hsap_1132, retro_hsap_151, retro_hsap_2684, retro_hsap_2757, retro_hsap_3535, retro_hsap_3961, retro_hsap_4102,
Myotis lucifugus	ENSMLUG00000016446	1 retrocopy	retro_mluc_1443,
Monodelphis domestica	ENSMODG00000001489	1 retrocopy	retro_mdom_734,
Mus musculus	ENSMUSG00000026078	1 retrocopy	retro_mmus_2284,
Nomascus leucogenys	ENSNLEG00000014393	8 retrocopies	retro_nleu_1499, retro_nleu_1575 , retro_nleu_2741, retro_nleu_2891, retro_nleu_538, retro_nleu_571, retro_nleu_778, retro_nleu_926,
Oryctolagus cuniculus	ENSOCUG00000001469	2 retrocopies	retro_ocun_1035, retro_ocun_920,
Otolemur garnettii	ENSOGAG00000015138	2 retrocopies	retro_ogar_1147, retro_ogar_2959,
Ochotona princeps	ENSOPRG00000011600	2 retrocopies	retro_opri_1070, retro_opri_289,
Tursiops truncatus	ENSTTRG00000006242	1 retrocopy	retro_ttru_1184,