RetrogeneDB ID: retro_nleu_1125

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397282.1:28629656..28630437(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP2R5C
• Ensembl ID: ENSNLEG00000015727
• Aliases: None
• Description: None

Sequence

>retro_nleu_1125
GAGAGAGCTTTTCCTAAAACCAGCCTTTGCAGAATCTATGGGAAATTCTTAGGCTTGAGAGCTTATATCAGAAAACAAAT
AATATATTTTATAGGTTTATTTATGAAACAGAGCATCATGATGGCATAGCCGAGTTACTAGATATATTGGGAAATATGAT
TAATGGATTTGTTTTACCACTAAAAGAAGATTTTCTTATTCAAGGTGCTATACCTTTGCACAAAGTGAAATCTCTGAGTG
TCTACCATCCCCAGCTGGCATATTGTGTAGTACAGTTTTTAGAAAAGGATAGCACCCTCACTGTATCAATGGTGATGGCA
CTTCTCGAATATGGGCCAGAGTCTTACAGTCCAAAAGAAGTAATTTTCTTAAACAAATTAGAAGAAATTTTAGATATAAT
TGAACCATTGGAATTTGGAAGATCATGGAGCCTCTCTTCTGGCAGCTAGCCAAATGTGTCTCCGGCTCACACTTCCAGGT
GGCAGAGCAGGCACTCTGTTACTGGAATAATGAATACATTATGAGCTTAATCAGTAACAGCACAGCAAAGATTCTGCTGA
TCATGTTTCCATACTTGTACTGCAATTCAAAGACCCATTGGAACAGGACAATACATGGCTTGATATCCAACACACTGAAG
CTCTTCATGCAGATGACACAAAATCTATTTAATGACTGTACCTAACTGTTCAAAGCAGAGAAACTGAAAGAGAAGCTAAA
AATGAAAGAACAGGAAGAAGCATTGGTTAAAATAGAAAATCTAACCAAAGCCAATCACCAG

Alignment

ORF - retro_nleu_1125 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.66 %
• Parental protein coverage: 50.57 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ERDFLKTTLHRIYGKF-LGLRAYIRKQINNIFYRFIYETEHHNGIAELLEILGSIINGFALPLKEEHKIF
          ER.F.KT.L.RIYGKF.L.L.....K..NNIFYRFIYETEHH.GIAELL.ILG..INGF.LPLKE....F
Retrocopy ERAFPKTSLCRIYGKF<LRLESLYQKT-NNIFYRFIYETEHHDGIAELLDILGNMINGFVLPLKED---F

Parental  LLKVLLPLHKVKSLSVYHPQLAYCVVQFLEKDSTLTEPVVMALLKYWPKTHSPKEVMFLNELEEILDVIE
          L.....PLHKVKSLSVYHPQLAYCVVQFLEKDSTLT...VMALL.Y.P...SPKEV.FLN.LEEILD.IE
Retrocopy LIQGAIPLHKVKSLSVYHPQLAYCVVQFLEKDSTLTVSMVMALLEYGPESYSPKEVIFLNKLEEILDIIE

Parental  PSEF-VKIMEPLFRQLAKCVSSPHFQVAERALYYWNNEYIMSLISDNAAKILPIMFPSLYRNSKTHWNKT
          P.EF..KIMEPLF.QLAKCVS..HFQVAE.AL.YWNNEYIMSLIS...AKIL.IMFP.LY.NSKTHWN.T
Retrocopy PLEF<WKIMEPLFWQLAKCVSGSHFQVAEQALCYWNNEYIMSLISNSTAKILLIMFPYLYCNSKTHWNRT

Parental  IHGLIYNALKLFMEMNQKLFDDCTQQFKAEKLKEKLKMKEREEAWVKIENLAKANPQ
          IHGLI.N.LKLFM.M.Q.LF.DCT..FKAEKLKEKLKMKE.EEA.VKIENL.KAN.Q
Retrocopy IHGLISNTLKLFMQMTQNLFNDCT*LFKAEKLKEKLKMKEQEEALVKIENLTKANHQ

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_1125 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000078304	2 retrocopies	retro_hsap_2649, retro_hsap_3796,
Nomascus leucogenys	ENSNLEG00000015727	2 retrocopies	retro_nleu_1125 , retro_nleu_655,
Otolemur garnettii	ENSOGAG00000006274	1 retrocopy	retro_ogar_1944,
Pongo abelii	ENSPPYG00000006152	3 retrocopies	retro_pabe_2322, retro_pabe_2414, retro_pabe_3101,
Pan troglodytes	ENSPTRG00000006734	1 retrocopy	retro_ptro_1784,