RetrogeneDB ID: retro_nleu_1725

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397306.1:1874000..1874445(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ISCA1
• Ensembl ID: ENSNLEG00000005129
• Aliases: None
• Description: iron-sulfur cluster assembly 1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:28660]

Sequence

>retro_nleu_1725
AGGCCTAAGTGCACCGTGTGCCGGAGCTTGTGGCATCAATGGGCCTGCTGTGTCCAAAGAAAGAGGCTGAGGCGGCCGAG
CTCCAGCCTGAAGCACCTGGGCACCCAGACAACAAAGAGGTCGGCTTCCTTAGTCCGGAGGACTGTCCGGACTGTGAGCA
AGAGGAAGCTGCAGCCCACGAGGGCCACCCACAGCCTGACACCTTCAGCAGTAAACAAGATAAAATAACTTCTTCAAGAT
AAGCCTGAGCATTAGGTGTAAGAGTTGGTGTCTGAACCAGGGCCTGTAATGACCTTTCTTATAGTCTAGAATAAACGAAG
ACAAAGGAGATTTCAATGAATAAGTTATTCAAGATGGAGTCAGAGTGTTCATCGAAAAGAAAGCACAACTAACACTTTTA
GGAACAGAAATAGACCATGCTGAAGACAAATTATCCAGTGAGTTT

Alignment

ORF - retro_nleu_1725 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.86 %
• Parental protein coverage: 93.71 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RPEGSVRRSLWRQCARRVHGERLRRPTSGPRHRGAGTAKMSASLVRATVRAVSKRKLQPTRAALTLTPSA
          RP...V.RSLW.Q.A..V...RLRRP.S...H.G..T.K.SASLVR.TVR.VSKRKLQPTRA...LTPSA
Retrocopy RPKCTVCRSLWHQWACCVQRKRLRRPSSSLKHLGTQTTKRSASLVRRTVRTVSKRKLQPTRATHSLTPSA

Parental  VNKIKQLLKDKPEH-VGVKVGVRTRGCNGLSYTLEYTKT-KGDSDEEVIQDGVRVFIEKKAQLTLLGTEM
          VNKIK.LL.DKPEH..GV.VGV.TR.CN.LSY.LE.TKT.KGD..E.VIQDGVRVFIEKKAQLTLLGTE.
Retrocopy VNKIK*LLQDKPEH<LGVRVGV*TRACNDLSYSLE*TKT<KGDFNE*VIQDGVRVFIEKKAQLTLLGTEI

Parental  DYVEDKLSRLF
          D..EDKLS..F
Retrocopy DHAEDKLSSEF

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_1725 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 10 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000046526	2 retrocopies	retro_btau_1787, retro_btau_506,
Dasypus novemcinctus	ENSDNOG00000010652	5 retrocopies	retro_dnov_1162, retro_dnov_142, retro_dnov_1956, retro_dnov_431, retro_dnov_95,
Echinops telfairi	ENSETEG00000016537	1 retrocopy	retro_etel_1857,
Gorilla gorilla	ENSGGOG00000007518	2 retrocopies	retro_ggor_1182, retro_ggor_92,
Monodelphis domestica	ENSMODG00000003559	1 retrocopy	retro_mdom_583,
Mus musculus	ENSMUSG00000044792	1 retrocopy	retro_mmus_278,
Nomascus leucogenys	ENSNLEG00000005129	5 retrocopies	retro_nleu_1674, retro_nleu_1725 , retro_nleu_2330, retro_nleu_2618, retro_nleu_2782,
Pongo abelii	ENSPPYG00000019339	5 retrocopies	retro_pabe_1287, retro_pabe_2043, retro_pabe_2744, retro_pabe_2745, retro_pabe_367,
Rattus norvegicus	ENSRNOG00000018343	4 retrocopies	retro_rnor_1177, retro_rnor_1805, retro_rnor_2254, retro_rnor_2956,
Tarsius syrichta	ENSTSYG00000012826	2 retrocopies	retro_tsyr_1060, retro_tsyr_1698,