RetrogeneDB ID: retro_nleu_2529

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397367.1:1165303..1166342(-)
• Located in intron of: ENSNLEG00000010902

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRPF3
• Ensembl ID: ENSNLEG00000009841
• Aliases: None
• Description: None

Sequence

>retro_nleu_2529
AAGACAGTGAAGAGGGTGCTGGGTTTCTCAGAGCCTACAGTGGTCACAGCAGCATTGAACTGTGTGGGGAAGAGCATGGA
CAAGAAGAAGGCAGCCGATCATCTGAAACCTTTTCTTGATGATTCTACTCCCCGATTTGTGGACAAACTGAGGCTGTAGG
AGGAAGGCAGAAGCTCTAGGCATTCCAAGTCTAGCAGTGACGGAAGCAGAAAACGAAAGCTAAAGAAGGTGTTTGGTGAT
GACTCTTGAGATCTCCAAGGAATCATCAGGAGTAAAGAAGCAGCAAATACCCCGTTTTGAGGAGGTGGAAGAAGAGCCAG
AGGTGATCCCTGGGCCTCCATCAGAGAGTCCTGGCATGCTGACTAAGCTCCACATCAAACAGATGATGGACGCAGCAAAA
TGACAAATCGAGGAGAGGAAAAAACAGCTGCGCTTCATTAGCCCCCCTACACCTCAGCCAAAGACTCCTTCTTCCTCCCA
ACCAGAGCGACTTCCAATTGGCCACACTATTCAGCCCTCCCAGGCTGCCACTTTCATGAATGATGCCATTGAGAAAGCAA
GGAAAGCAGCTGAACTATAAGCTCGACTCCAAGCCCGGCTGGCACTGAAGCCAGGACTCATCAGCAATGTCAACATGGTG
GGCCCAGCTAATCTTCACTGACATGGGCATTGCTCCCCCAAAGGGGGAGTTAAAAGACCAAATTAAACCTACACCACTGA
TCCTAGATGAGCAAGGGTGCATTGTAGATGCAACAGACAAGGAGATTGAGCTGACACACTGCATGTCTACTCCTGCCAAT
ATTCGTGCTGTTCCCTCTTCAGAGGGAACCATTCAAGCAACAGCTAAAAAAAAGCCATCAGAAGACATGGAGTCCAATGC
CTTTTTTGACCCCGAGTCTCCACTGTCGCTTCCCAGCGCCAGAAACGCACGTTTAAATTCCATTGCAAGGGCAAATTTGA
GAAGATTGCTCAGCGATTAAGGACAAAGGCTCGACTGGAGAAGCTTCAGGCAGAGATTTCACAAGCAGCTCAAAAAACA

Alignment

ORF - retro_nleu_2529 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.48 %
• Parental protein coverage: 56.17 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KTVKRVLGFSEPTVVTAALNCVGKGMDKKKAADHLKPFLDDSTLRFVDKLFEAVEEGRSSRHSKSSSDRS
          KTVKRVLGFSEPTVVTAALNCVGK.MDKKKAADHLKPFLDDST.RFVDKL....EEGRSSRHSKSSSD.S
Retrocopy KTVKRVLGFSEPTVVTAALNCVGKSMDKKKAADHLKPFLDDSTPRFVDKL-RL*EEGRSSRHSKSSSDGS

Parental  RKRELKEVFGDDS-EISKESSGVKKRRIPRFEEVEEEPEVIPGPPSESPGMLTKLQIKQMMEAATRQIEE
          RKR.LK.VFGDDS.EISKESSGVKK..IPRFEEVEEEPEVIPGPPSESPGMLTKL.IKQMM.AA..QIEE
Retrocopy RKRKLKKVFGDDS>EISKESSGVKKQQIPRFEEVEEEPEVIPGPPSESPGMLTKLHIKQMMDAAK*QIEE

Parental  RKKQLSFISPPTPQPKTPSSSQPERLPIGNTIQPSQAATFMNDAIEKARKAAELQARIQAQLALKPGLIG
          RKKQL.FISPPTPQPKTPSSSQPERLPIG.TIQPSQAATFMNDAIEKARKAAEL.AR.QA.LALKPGLI.
Retrocopy RKKQLRFISPPTPQPKTPSSSQPERLPIGHTIQPSQAATFMNDAIEKARKAAEL*ARLQARLALKPGLIS

Parental  NANMVGLANLH-AMGIAPPKVELKDQTKPTPLILDEQGRTVDATGKEIELTHRMPTLKANIRAVKREQ--
          N.NMVG.ANLH..MGIAPPK.ELKDQ.KPTPLILDEQG..VDAT.KEIELTH.M.T..ANIRAV......
Retrocopy NVNMVGPANLH>DMGIAPPKGELKDQIKPTPLILDEQGCIVDATDKEIELTHCMST-PANIRAVPSSEGT

Parental  FKQQLKEKPSEDMESNTFFD-PRVSIAPSQRQRRTFKFHDKGKFEKIAQRLRTKAQLEKLQAEISQAARK
          ........PSEDMESN.FFD.PRVS...SQRQ.RTFKFH.KGKFEKIAQRLRTKA.LEKLQAEISQAA.K
Retrocopy IQATAXXXPSEDMESNAFFD<PRVSTVASQRQKRTFKFHCKGKFEKIAQRLRTKARLEKLQAEISQAAQK

Parental  T
          T
Retrocopy T

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_2529 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 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009926	1 retrocopy	retro_cjac_1499,
Macaca mulatta	ENSMMUG00000016301	1 retrocopy	retro_mmul_2348,
Nomascus leucogenys	ENSNLEG00000009841	1 retrocopy	retro_nleu_2529 ,
Otolemur garnettii	ENSOGAG00000005352	4 retrocopies	retro_ogar_2360, retro_ogar_3052, retro_ogar_374, retro_ogar_409,
Pan troglodytes	ENSPTRG00000001254	1 retrocopy	retro_ptro_2758,