RetrogeneDB ID: retro_nleu_1644

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397302.1:5739033..5739706(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC90B
• Ensembl ID: ENSNLEG00000016478
• Aliases: None
• Description: None

Sequence

>retro_nleu_1644
CTGCAGAGAGACTTCTTCAGCACCACAACCAAGGAGGGATATGATAGGCAGCCAGTGGATATAACTCCTTTAAAAGAAAG
GAAATTAACTTTTGATACCCATGCATTGGTTCAGGACTTGGAAACTCATGGATCTGACAAAACACAAGCAGAAACAATAG
TATCAGCATTAACTACTTTATCAAATGTCAGCCCGGATACTACCTACAAAGAGATGGTCACTCAAGCTCAACAGAAAATA
ACAGTACAACAGCTAATGGCTCATTTGGACTCTATCAGGAGAAACATGGTCATCCTGGAGAAAAGTGAATTTGCAAATCT
CAGAGCAGAGAATGAGAAAATGAAAATTGAATTAGACCAAGTTAAGCAACAACTAATACATGAAACCAGTTGAATCAGAG
CAGATAATAAACTGGATATCAGCCTAGAAAGGAGCAGAGTAACAGATATGTTTACAGATCAAGAAAAGCAACTTATGGAA
GCAACTACAGAATTTACAAAAAAAGGATACCCAAAACAAAAGTGTTATTTCAGAGACCAGTAATAAAATTGATGCAGAAA
TTGCTTCCTTAAAAACACTGATGGAGTCTAACAAACTTGAGATAATTCATTATCTTGCAGCCTTGGTGTTTATTTGCTTG
GCAATAGCATTGGGATTTTATAAATTCTGGAAG

Alignment

ORF - retro_nleu_1644 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.33 %
• Parental protein coverage: 88.19 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LRREFFTTTTKEGYDRRPVDITPLEQRKLTFDTHALVQDLETHGFDKTQAETIVSALTTLSNVSLDTIYK
          L.R.FF.TTTKEGYDR.PVDITPL..RKLTFDTHALVQDLETHG.DKTQAETIVSALTTLSNVS.DT.YK
Retrocopy LQRDFFSTTTKEGYDRQPVDITPLKERKLTFDTHALVQDLETHGSDKTQAETIVSALTTLSNVSPDTTYK

Parental  EMVTQAQQEITVQQLMAHLDSIRKDMVILEKSEFANLRAENEKMKIELDQVKQQLVHETSRIRADNKLDI
          EMVTQAQQ.ITVQQLMAHLDSIR..MVILEKSEFANLRAENEKMKIELDQVKQQL.HETS.IRADNKLDI
Retrocopy EMVTQAQQKITVQQLMAHLDSIRRNMVILEKSEFANLRAENEKMKIELDQVKQQLIHETS*IRADNKLDI

Parental  NLERSRVTDMFTDQEKQLMETTTEFT-KKDTQTKSIISETSNKIDAEIASLKTLMESNKLETIRYLAASV
          .LERSRVTDMFTDQEKQLME.TTEFT.KKDTQ.KS.ISETSNKIDAEIASLKTLMESNKLE.I.YLAA.V
Retrocopy SLERSRVTDMFTDQEKQLMEATTEFT>KKDTQNKSVISETSNKIDAEIASLKTLMESNKLEIIHYLAALV

Parental  FTCLAIALGFYRFWK
          F.CLAIALGFY.FWK
Retrocopy FICLAIALGFYKFWK

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_1644 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 15 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010541	2 retrocopies	retro_chof_1396, retro_chof_780,
Callithrix jacchus	ENSCJAG00000014547	1 retrocopy	retro_cjac_219,
Homo sapiens	ENSG00000137500	1 retrocopy	retro_hsap_3050,
Macaca mulatta	ENSMMUG00000020154	2 retrocopies	retro_mmul_1880, retro_mmul_773,
Nomascus leucogenys	ENSNLEG00000000914	1 retrocopy	retro_nleu_2768,
Nomascus leucogenys	ENSNLEG00000016478	1 retrocopy	retro_nleu_1644 ,
Ochotona princeps	ENSOPRG00000004144	2 retrocopies	retro_opri_197, retro_opri_682,
Pongo abelii	ENSPPYG00000003736	1 retrocopy	retro_pabe_2525,
Pan troglodytes	ENSPTRG00000004129	1 retrocopy	retro_ptro_1990,
Pteropus vampyrus	ENSPVAG00000005459	1 retrocopy	retro_pvam_614,
Rattus norvegicus	ENSRNOG00000009462	1 retrocopy	retro_rnor_868,
Tupaia belangeri	ENSTBEG00000014665	2 retrocopies	retro_tbel_3436, retro_tbel_4221,
Tarsius syrichta	ENSTSYG00000011196	1 retrocopy	retro_tsyr_710,
Tursiops truncatus	ENSTTRG00000003998	1 retrocopy	retro_ttru_445,
Vicugna pacos	ENSVPAG00000007753	1 retrocopy	retro_vpac_366,