RetrogeneDB ID: retro_nleu_2689

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397398.1:3799576..3800432(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: OBFC1
• Ensembl ID: ENSNLEG00000015282
• Aliases: None
• Description: None

Sequence

>retro_nleu_2689
ACTGGAGTTATAAACTGCATCTGCTAGAAAATATTGAGCAATATCAAGTTTTTATCTGCTGCTCCAAATGCAGCAAGAGA
ACTGAGCTTTACCTCAATACTCAAGAAGCTGCAAGACACCATTGAGCAGAGAACAAAAATTGAAACTGCGGACATGTTCT
GAATCAGAGGCTATGTCTACACGTGCAGAGAAGAGTGAGAAATTTATGCCACTGCTTAATATAAAGTGGACGATCCAGTG
TGGAACATTCAAATTGCAAGGGTGTTTGAGCTGCCCGTTAATCTACAGGAAAGTTTAGACCAAGCCTTTCCATTGCCCAG
ACTTAGAGAAAGAAGAAGCAATCCAAGTGTCCTGGCCTTCACTAGTCTCATGTGTTTGCTGAGTGAAAAAGCCAAAGAAT
TCCCCATGAAGAACAAAGTGCAGACCTTTGACCAGCAGGAGTTGGAAATGGTGAAGCCTTTGCTGTCCCTTGCTAACCAG
CCTGTTACTGACAGTGCCTGCTCTGAACAAGGAAATTTTAAGAAGGATATCACTTTCAAGGCAATTTATAGCATATTTTA
AAATGCTATGCAACAGCTGCAGGAAAAAGGACTCGTCTTCCAGAAAGATGGTGGTTTTGATAACCTATGCTGTGTAATCG
GAAATGACAAAGACCTGCATAGGAAAACCCATGGGATAATTCAGGAAGACTGCCAGAAACCAAATCACCCGAAGAAGGGC
TGCCGCTTCCTGCACATCTTGGCCTGCACTCACCCTGAGCATCTGCCCAGTTCTAGGTAGGGCTATGTTGCAGCAAGTTC
TGGAGCTCCTGGAGGACCAGAGTGACTTCATCAGCACAATGGAGCACCACTACTCC

Alignment

ORF - retro_nleu_2689 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.06 %
• Parental protein coverage: 77.72 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TGVINCICWKKL-NTESVSAAPSAARELSLTSQLKKLQETIEQRTKIEIGDTIRVRGSIRTYREEREIHA
          TGVINCIC.K.L.N....SAAP.AARELS.TS.LKKLQ.TIEQRTKIE..D....RG...T.REE.EI.A
Retrocopy TGVINCIC*KILSNIKFLSAAPNAARELSFTSILKKLQDTIEQRTKIETADMF*IRGYVYTCREE*EIYA

Parental  TAYYKVDDPVWNIQIARMLELPTIYRKVYDQPFRSSALEKEEALSNPGALDLPTLTSLLSEKAKEFLMEN
          TA.YKVDDPVWNIQIAR..ELP.......DQ.F....L...E..SNP..L....L..LLSEKAKEF.M.N
Retrocopy TA*YKVDDPVWNIQIARVFELPVNLQESLDQAFPLPRLR--ERRSNPSVLAFTSLMCLLSEKAKEFPMKN

Parental  RVQSFYQQELEMVESLLSLANQPVIHSACSDQVNFKKDTTSKAIHSIFKNAIQLLQEKGLVFQKDDGFDN
          .VQ.F.QQELEMV..LLSLANQPV..SACS.Q.NFKKD.T.KAI.SIF.NA.Q.LQEKGLVFQKD.GFDN
Retrocopy KVQTFDQQELEMVKPLLSLANQPVTDSACSEQGNFKKDITFKAIYSIF*NAMQQLQEKGLVFQKDGGFDN

Parental  LYYVTREDKDLHRKIHRIIQQDCQKPNHMEKGCHFLHILACAR-LSIRPGLSEAVLQQVLELLEDQSDIV
          L..V...DKDLHRK.H.IIQ.DCQKPNH..KGC.FLHILAC...LSI.P.L..A.LQQVLELLEDQSD..
Retrocopy LCCVIGNDKDLHRKTHGIIQEDCQKPNHPKKGCRFLHILACTH>LSICPVLGRAMLQQVLELLEDQSDFI

Parental  STMEHYYT
          STMEH.Y.
Retrocopy STMEHHYS

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_2689 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018342	1 retrocopy	retro_cjac_1791,
Homo sapiens	ENSG00000107960	1 retrocopy	retro_hsap_3257,
Gorilla gorilla	ENSGGOG00000008979	1 retrocopy	retro_ggor_2219,
Macaca mulatta	ENSMMUG00000015323	1 retrocopy	retro_mmul_2050,
Nomascus leucogenys	ENSNLEG00000015282	1 retrocopy	retro_nleu_2689 ,
Pongo abelii	ENSPPYG00000002628	1 retrocopy	retro_pabe_2701,
Pan troglodytes	ENSPTRG00000002919	1 retrocopy	retro_ptro_2203,