RetrogeneDB ID: retro_nleu_2746

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397418.1:1476187..1476985(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDK8
• Ensembl ID: ENSNLEG00000014010
• Aliases: None
• Description: None

Sequence

>retro_nleu_2746
TTAGCAGATTTGGATCCAGTGATTGTTACATTCTGGTACTGAGCCCCTGAATTACTTCTTTGAGTAAGGCATTATACCAA
AGCTATTGATATTTGGGCTTATAGGGTGTATGTTTGAAGAACTACTAATGTCAAAACCAATATTTCACGGTCGACAAGAG
GACATCAAAATTGGTAATCCTTATCACCATGACTGGCTGGACAGAATACTCAATGTAATGGGATTTCCTGCAAACAAAGA
TTGGGAAGATGTAAAAAAGATGCCTGAACATTCAACATTAATGAAAGATTTCAGAAGAAATATTCATACTAACTGCAGCC
TTATCAAGTATATGGAAAAACACAAAGTTAAACCAGATAGTAAAGCATTCCACTTGCTTCAGAAGTTTCTTACTATGGAC
CCAATAAAGTGAATTACCTCAGAACAGGATCCCTACTTCTTAGAAGACCCACTTCCTACATCAGACGTTTTTGCCAGTTG
TCAAATCCCTTACCCAAAATGAGAATTTTTAACAGAAGAACCTGATGACAAAGGAGACAAAAAGAACCACCACCAGCAGC
AGGGCAATAATGGAACTGGCCACCCAGGAATCAAGACAACGGTCACACACAGGGACCCCCGTTGAAGAAAGTGAGGCTTG
TTCCTCCTACCACTACCTCAGGTGGACTTTTCATAGCCTCAGACTATCCGCATTCCAATCCACATGCTGCCTATATCCCA
ACCCTGGACCAAGCACATCACAGCCGAAGAGCAGCATGGGATACTCAGCTACCTCCCAGCAGGCTCCACAGTACTCAC

Alignment

ORF - retro_nleu_2746 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.7 %
• Parental protein coverage: 59.48 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LADLDPVVVTFWYRAPELLLGARHYTKAIDIWA-IGCIFAELLTSEPIFHCRQEDIKTSNPYHHDQLDRI
          LADLDPV.VTFWY.APELLL..RHYTKAIDIWA.IGC.F.ELL.S.PIFH.RQEDIK..NPYHHD.LDRI
Retrocopy LADLDPVIVTFWY*APELLL*VRHYTKAIDIWA>IGCMFEELLMSKPIFHGRQEDIKIGNPYHHDWLDRI

Parental  FNVMGFPADKDWEDIKKMPEHSTLMKDFRRNTYTNCSLIKYMEKHKVKPDSKAFHLLQKLLTMDPIKRIT
          .NVMGFPA.KDWED.KKMPEHSTLMKDFRRN..TNCSLIKYMEKHKVKPDSKAFHLLQK.LTMDPIK.IT
Retrocopy LNVMGFPANKDWEDVKKMPEHSTLMKDFRRNIHTNCSLIKYMEKHKVKPDSKAFHLLQKFLTMDPIK*IT

Parental  SEQAMQDPYFLEDPLPTSDVFAGCQIPYPKREFLTEEEPDDKGDKKNQQQQQGNNHTNGTGHPG-NQDSS
          SEQ...DPYFLEDPLPTSDVFA.CQIPYPK.EFLT.EEPDDKGDKKN..QQQGNN...GTGHPG.NQD..
Retrocopy SEQ---DPYFLEDPLPTSDVFASCQIPYPK*EFLT-EEPDDKGDKKNHHQQQGNN---GTGHPG<NQDNG

Parental  HTQGPPLKKVRVVPPTTTSGGLIMTSDYQRSNPHAAYPNPGPSTSQPQSSMGYSATSQQPPQYSHQTH
          HTQGPPLKKVR.VPPTTTSGGL...SDY..SNPHAAY....P...Q...S.......Q.PP...H.TH
Retrocopy HTQGPPLKKVRLVPPTTTSGGLFIASDYPHSNPHAAYI---PTLDQAHHSRRAAWDTQLPPSRLHSTH

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_2746 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001443	1 retrocopy	retro_chof_1102,
Homo sapiens	ENSG00000132964	1 retrocopy	retro_hsap_2147,
Myotis lucifugus	ENSMLUG00000009176	1 retrocopy	retro_mluc_112,
Macaca mulatta	ENSMMUG00000014841	1 retrocopy	retro_mmul_1010,
Mus musculus	ENSMUSG00000029635	1 retrocopy	retro_mmus_1200,
Nomascus leucogenys	ENSNLEG00000014010	1 retrocopy	retro_nleu_2746 ,