RetrogeneDB ID: retro_nleu_163

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397261.1:6894775..6895807(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PA2G4
• Ensembl ID: ENSNLEG00000017544
• Aliases: None
• Description: None

Sequence

>retro_nleu_163
GGGGACCACATCGCCAACCGGGTACTTTGGTCCTTGGTGGAAGCATCTAGCTCAGGTGTGTCGGTACTGAGCCTGTGTGA
GAAAGGAGATGCCACGATTATGGAAGAAACAGGGAAAATCTTCAAGAAAGAAAAGGAAATGGAGAAAGGTATTGCTTTTC
CCATCAACATTTCAGTAAATAACTGTGTATGTCACTTCTCCCCTTTGAAGAGAGGCCAGGATTATATTCTCAAGGAAGGC
GACTTGGTAAAAATTGAACTTGAGGTCCACGTGGATGGCTTCATCGCTAATGTAGCTCATATTTTTGTGGTTGATGTAGC
TCCGGGGACCCATGTAACAGGGAGGAAAGCAGATGTTATTAAGGCAGCTCACCTTTGTGTTGAAGCTGCCCTATGCCTGG
TCACACCTGGAAATCAGAACACATAAGTGAGAGAAGCCTGGAACAAAGTTGCCCACTCATTTAACTGCATGCCAATAGAA
GGTATGCTGTCACACCAGCTGAAGCAGCGTGTCATCGATGGTGAAAAAAACATTATCCAGAATCCTACAGACCAGCAGAA
GAAGGACCATGAAAAAGCTGAATTTGAGGTACATGAAGTATATGTTGTGGATGTTCTCGTCAGCTCAGGAGAGGGCAAGG
CCAAGGATGCAGGACAGAGAACCACTATTTACAAACGAGACTCCTCTAAACAGTATGGACTGAAGAGGAAAACTTCATGT
GCCTTCTTCAGTGAAGTGGAAAGGCATCTTGATGCCATGCCGTTTACTTTAACAGCATTTGAAGATGAGAAGAAGGCCCC
AATGGATGTGGTGGAGTGCACCAAGCATGGACTGCTGCAACCGTTTAATGTTCTCTATGAGAAGGAGGGTGAATTTGTTG
CCCAGTTTAAATTTACAATTCTGCTCATGCCCAATGGCTCCATGCAGATAACCAGTGGTCCCTTCGAGCCTGACCTCTAC
AGGTCTGAGATGGAGGTCCAGGATGCAGAGCTAAAGGCCCTCCTCCAGAGTTCTGCAAGTCGAGAAACCCAG

Alignment

ORF - retro_nleu_163 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.37 %
• Parental protein coverage: 87.28 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GGDIANRVLRSLVEASSSGVSVLSLCEKGDAMIMEETGKIFKKEKEMKKGIAFPTSISVNNCVCHFSPLK
          G..IANRVL.SLVEASSSGVSVLSLCEKGDA.IMEETGKIFKKEKEM.KGIAFP..ISVNNCVCHFSPLK
Retrocopy GDHIANRVLWSLVEASSSGVSVLSLCEKGDATIMEETGKIFKKEKEMEKGIAFPINISVNNCVCHFSPLK

Parental  SDQDYILKEGDLVKIDLGVHVDGFIANVAHTFVVDVAQGTQVTGRKADVIKAAHLCAEAALRLVKPGNQN
          ..QDYILKEGDLVKI.L.VHVDGFIANVAH.FVVDVA.GT.VTGRKADVIKAAHLC.EAAL.LV.PGNQN
Retrocopy RGQDYILKEGDLVKIELEVHVDGFIANVAHIFVVDVAPGTHVTGRKADVIKAAHLCVEAALCLVTPGNQN

Parental  TQVTEAW-QVAHSFNCTPIEGMLSHQLKQHVIDGEKTIIQNPTDQQKKDHEKAEFEVHEVYAVDVLVSSG
          T.V.EAW..VAHSFNC.PIEGMLSHQLKQ.VIDGEK.IIQNPTDQQKKDHEKAEFEVHEVY.VDVLVSSG
Retrocopy T*VREAWNKVAHSFNCMPIEGMLSHQLKQRVIDGEKNIIQNPTDQQKKDHEKAEFEVHEVYVVDVLVSSG

Parental  EGKAKDAGQRTTIYKRDPSKQYGLKMKTSRAFFSEVERRFDAMPFTLRAFEDEKKARMGVVECAKHELLQ
          EGKAKDAGQRTTIYKRD.SKQYGLK.KTS.AFFSEVER..DAMPFTL.AFEDEKKA.M.VVEC.KH.LLQ
Retrocopy EGKAKDAGQRTTIYKRDSSKQYGLKRKTSCAFFSEVERHLDAMPFTLTAFEDEKKAPMDVVECTKHGLLQ

Parental  PFNVLYEKEGEFVAQFKFTVLLMPNGPMRITSGPFEPDLYKSEMEVQDAELKALLQSSASRKTQ
          PFNVLYEKEGEFVAQFKFT.LLMPNG.M.ITSGPFEPDLY.SEMEVQDAELKALLQSSASR.TQ
Retrocopy PFNVLYEKEGEFVAQFKFTILLMPNGSMQITSGPFEPDLYRSEMEVQDAELKALLQSSASRETQ

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_163 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 8 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007181	2 retrocopies	retro_chof_1089, retro_chof_1847,
Homo sapiens	ENSG00000170515	6 retrocopies	retro_hsap_1930, retro_hsap_2413, retro_hsap_2868, retro_hsap_3646, retro_hsap_4191, retro_hsap_4895,
Macaca mulatta	ENSMMUG00000002164	2 retrocopies	retro_mmul_1168, retro_mmul_2631,
Nomascus leucogenys	ENSNLEG00000017544	6 retrocopies	retro_nleu_1212, retro_nleu_1260, retro_nleu_163 , retro_nleu_3024, retro_nleu_506, retro_nleu_612,
Pongo abelii	ENSPPYG00000025851	7 retrocopies	retro_pabe_1595, retro_pabe_1778, retro_pabe_2375, retro_pabe_2869, retro_pabe_2993, retro_pabe_3430, retro_pabe_3807,
Sus scrofa	ENSSSCG00000000377	1 retrocopy	retro_sscr_338,
Sus scrofa	ENSSSCG00000022666	2 retrocopies	retro_sscr_1143, retro_sscr_337,
Vicugna pacos	ENSVPAG00000009523	1 retrocopy	retro_vpac_2,