RetrogeneDB ID: retro_nleu_2990

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397548.1:396814..397622(+)
• Located in intron of: ENSNLEG00000013362

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSNLEG00000016156
• Aliases: None
• Description: None

Sequence

>retro_nleu_2990
ATGAGGTGGGTGGCCCTGTTCCTGAACCGCAGCCCCAAGAACGGAAAGGTGGTTGCTGTATGTGGAACTTTATCTGATTT
GCTTTCTGTGGCCAGCAGTAAACTCGGCGTAAAAGCCACCAGTGTGTATGATGGGAAAGGTGGACTGATTGATGATCTTG
CTTTGATCAGGGATGATGATGTTTTGTTTGTGTGTGGAGAGCCATTTATTGATACTCAGACAGATTCTAAGTCACCTGAG
GGATTGTCAGGATTCCACACAGACTGGCTAACATTAAATGTTGGAGGGCGGTACTTTACAACAACACAGAGCACTTTAGT
GAATAAAGAACCTGATAGTATGCTGGCCCACATGTTTAAGGACAAAGATGTCTGGGAAATAAGATCACAGAGGAGATTTC
TTAATTGACCAAAGTCCTGAGTACTTTGAACCCATTTTGAACTACTTGTGTCATGGACAGCTTGTTGTAAATGATGGCAT
TAATTTATTGGATATGTTAGAAGCAGCAAGATTTTTTGGTATTGACTCATTGATTGAACACCTAGAAGTGGCAATAAAGA
ATTCTAAACCACCGGAGGATCATTCACCAATATCCTGAAAGGAATTTGTCTGATTTTTGCTAGCAACTCCAATCAAGTCA
GAACTGCGACGCCAAGGTTTGAACTTCAGTGGTGCTGATCTTTCTCATTTGGACCTTTGATACATTAACTTCAAAATGGC
CAGTTTAAACCGCTGCAATCTTGCACATGCAAATCTTTGCTGTGCAAATCTTAAACAAGCTGATCTCTCTGGATCAGTGC
TTGACTGC

Alignment

ORF - retro_nleu_2990 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.71 %
• Parental protein coverage: 69.92 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MRRVTLFLNGSPKNGKVVAVYGTLSDLLSVASSKLGIKATSVYNGKGGLIDDIALIRDDDVLFVCEGEPF
          MR.V.LFLN.SPKNGKVVAV.GTLSDLLSVASSKLG.KATSVY.GKGGLIDD.ALIRDDDVLFVC.GEPF
Retrocopy MRWVALFLNRSPKNGKVVAVCGTLSDLLSVASSKLGVKATSVYDGKGGLIDDLALIRDDDVLFVC-GEPF

Parental  IDPQTDSKPPEGLLGFHTDWLTLNVGGRYFTTTRSTLVNKEPDSMLAHMFKDKGVWGNKQDHRGAFL-ID
          ID.QTDSK.PEGL.GFHTDWLTLNVGGRYFTTT.STLVNKEPDSMLAHMFKDK.VW......R..FL.ID
Retrocopy IDTQTDSKSPEGLSGFHTDWLTLNVGGRYFTTTQSTLVNKEPDSMLAHMFKDKDVWEIRSQRR--FL>ID

Parental  RSPEYFEPILNYLRHGQLIVNDGINLLGVLEEARFFGIDSLIEHLEVAIKNSQPPEDHSPISRKEFVRFL
          .SPEYFEPILNYL.HGQL.VNDGINLL..LE.ARFFGIDSLIEHLEVAIKNS.PPEDHSPIS.KEFV.FL
Retrocopy QSPEYFEPILNYLCHGQLVVNDGINLLDMLEAARFFGIDSLIEHLEVAIKNSKPPEDHSPIS*KEFV*FL

Parental  LATPTKSELRCQGLNFSGADLSRLDLRYINFKMANLSRCNLAHANLCCANLERADLSGSVLDC
          LATP.KSELR.QGLNFSGADLS.LDL.YINFKMA.L.RCNLAHANLCCANL..ADLSGSVLDC
Retrocopy LATPIKSELRRQGLNFSGADLSHLDL*YINFKMASLNRCNLAHANLCCANLKQADLSGSVLDC

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_2990 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 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012157	1 retrocopy	retro_chof_323,
Gorilla gorilla	ENSGGOG00000004480	3 retrocopies	retro_ggor_1309, retro_ggor_2264, retro_ggor_2791,
Macaca mulatta	ENSMMUG00000010151	3 retrocopies	retro_mmul_1083, retro_mmul_1218, retro_mmul_2072,
Nomascus leucogenys	ENSNLEG00000014727	1 retrocopy	retro_nleu_2839,
Nomascus leucogenys	ENSNLEG00000016156	3 retrocopies	retro_nleu_1386, retro_nleu_2499, retro_nleu_2990 ,
Pongo abelii	ENSPPYG00000018452	3 retrocopies	retro_pabe_1527, retro_pabe_2725, retro_pabe_3457,