RetrogeneDB ID: retro_nleu_1166

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397283.1:11405947..11406462(-)
• Located in intron of: ENSNLEG00000012801

Retrocopy information

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

Parental gene information

• Parental gene symbol: IMPACT
• Ensembl ID: ENSNLEG00000006582
• Aliases: None
• Description: impact RWD domain protein [Source:HGNC Symbol;Acc:20387]

Sequence

>retro_nleu_1166
GAATTATCTCCGATTGATCATGGCATTTCTGTTACAGACCAAATAAGTACTTTTCAGGCAGACTTTGATCCAGTAGTTTG
TCCCAAACAGGTGAAAATGGTTCTTTCCAACTTGCGTGAGAATAAGAAAATAGCTAGTACCACCCACAGCATCTATGCCT
ACAGAGTATATTGTGAGAATAAACAGACCTTCTTACAGGATTGTGAGGATGATGGGGAAAGAGCAGCTGGTGGGCATCTT
CTTCATCTCATGGAGAGTTTAAATGTGAGGAATATCATGGTGGTGGTATCACGCTGGTATGGAGGGATTCTGTACGACCA
GATCACTGTAAACATAACTGTGCCAGAAACATACTAGTGGAGAAGAACAACACACATTCACCTGAAAATCATCTAAGGCT
TTGGAAAGAAAAACAAAAAATGTTCATCACTGAGTAATGGATTAAGTGAAAATCCAGGGGTATCCACTTGCAGTTATGGG
CTGAGGTGACAATTCTTCCAACATATTTGTTAGCA

Alignment

ORF - retro_nleu_1166 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.77 %
• Parental protein coverage: 50.73 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  ELPPIDHGIPITDRRSTFQAHLAPVVCPKQVKMVLSKLYENKKIASATHNIYAYRIYCEDKQTFLQDCED
          EL.PIDHGI..TD..STFQA...PVVCPKQVKMVLS.L.ENKKIAS.TH.IYAYR.YCE.KQTFLQDCED
Retrocopy ELSPIDHGISVTDQISTFQADFDPVVCPKQVKMVLSNLRENKKIASTTHSIYAYRVYCENKQTFLQDCED

Parental  DGETAAGGRLLHLMEILNVKNVMVVVSRWYGGIL-LGPDRFKHINNCARNILVEKNYTNSPE-ESSKSL-
          DGE.AAGG.LLHLME.LNV.N.MVVVSRWYGGIL...PD..KH..NCARNILVEKN.T.SPE..SSK.L.
Retrocopy DGERAAGGHLLHLMESLNVRNIMVVVSRWYGGIL<VRPDHCKH--NCARNILVEKNNTHSPE<KSSKAL<

Parental  GK-NKKCSS-SNGLSENPGV-IHLQLCAEVIIHPTYLLA
          GK.NKKCSS.SNGLSENPGV.IHLQL.AEV.I.PTYLLA
Retrocopy GKKNKKCSSLSNGLSENPGV<IHLQLWAEVTILPTYLLA

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_1166 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 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013068	1 retrocopy	retro_chof_2523,
Erinaceus europaeus	ENSEEUG00000003962	1 retrocopy	retro_eeur_409,
Homo sapiens	ENSG00000154059	1 retrocopy	retro_hsap_3341,
Macaca mulatta	ENSMMUG00000004664	1 retrocopy	retro_mmul_1041,
Nomascus leucogenys	ENSNLEG00000006582	1 retrocopy	retro_nleu_1166 ,
Pongo abelii	ENSPPYG00000009071	1 retrocopy	retro_pabe_2753,
Pan troglodytes	ENSPTRG00000009927	1 retrocopy	retro_ptro_2141,
Sorex araneus	ENSSARG00000002836	1 retrocopy	retro_sara_719,