RetrogeneDB ID: retro_nleu_903

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397276.1:6288123..6289061(+)
• Located in intron of: ENSNLEG00000004219

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAHD2A
• Ensembl ID: ENSNLEG00000000008
• Aliases: None
• Description: None

Sequence

>retro_nleu_903
ATGCTGGTCTCTGGTAGAAGGTTGCTCACAGCTCTGCTGCAGGCTCAGAAGTGGCCCTTTCAACCCTCCAGAGACATGAG
ACTAGTCCAGTTCCAGGCACCCCACCTGGTGGGGCCTCGCTTGGGCCCAGAGATGGGGAATGGTGGAAGGGTTATCGACC
TCAATGCCTTTGACTCTATGCTCCCCAAAATGATGACACAGTTCCTACAGCAGGGAGAGGCCACCCTCTCAGTGGCAAGA
AGAGCCTTGGGTGCCCAGTTGCCAGTCCTACCATGGTTGGAAGTAACCTCCCTGGCTCCAGCCACGTGGCCAGATAAGGT
GGTGTGTGTGGGCGTGAATTATGTGGACCACTGCAAAGAACAGAATGTGCCCGTGCCCATGGAACCCATCATCTTCAGCA
AGTTTGCCAACTCCATTGTGGAGCCCTATGATGAGATGGTCCTCCCACCAGAGAGCCAGGAGGTAGACTGGGAAGTGGAG
CAGCAGTGGTCATTGGAAAGAAAGGCAAGCACATCAAGGCCACAGATGCCATGGCCCATGTGACTGGCTTCACTGTGGCT
CATAACGTGAGTGCTCAGGACTGGCAAATGAGACATAATGGGAAACAGTAGCTGGTGGGAAAAACCTTCGACACCTTCTG
CCCTCTGGGCCCTGCCTTGGTGACCAACGACAGTGTAGCAGATGCACACATCTTAAAGATCTGCTGCCAAGTGAATGGGG
AAGTGGTCCAGAGCAACAACACCAACCAGATGGTGGTCAAGACAGAGGAGCGGATAGCCTGGGTCTTCCAGTTTGTCACC
TTTTGCCCAGGGGATGTCATCCTGACCGGGACCTCCCCAGGTGTCAGTGTATTCAGGAAACCTCCTGTCTTTCTCAAGAA
GGGAGATGAAGTCCAGTGTGAAATTGAAGAACTAGGTGTCATCATCAGCAAGGTGGTG

Alignment

ORF - retro_nleu_903 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.71 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MLVSCRRRLLTALLQAQKWPFQPSRDMRLVQFQAPHLLGPHLGLETGNGGGVINLNAFDPTLPKTMTQFL
          MLVS..RRLLTALLQAQKWPFQPSRDMRLVQFQAPHL.GP.LG.E.GNGG.VI.LNAFD..LPK.MTQFL
Retrocopy MLVS-GRRLLTALLQAQKWPFQPSRDMRLVQFQAPHLVGPRLGPEMGNGGRVIDLNAFDSMLPKMMTQFL

Parental  EQGEATLSVARRALAAQLPVLPRSEVTFLAPVTRPDKVVCVGMNYVDHCKEQNVPVPKEPIIFSKFASSI
          .QGEATLSVARRAL.AQLPVLP..EVT.LAP.T.PDKVVCVG.NYVDHCKEQNVPVP.EPIIFSKFA.SI
Retrocopy QQGEATLSVARRALGAQLPVLPWLEVTSLAPATWPDKVVCVGVNYVDHCKEQNVPVPMEPIIFSKFANSI

Parental  VGPYDEVVLPPQSQEVDWEVE-LAVVIGKKGKHIKATDAMAHVAGFTVAHDVSARDWQMRRNGKQWLLGK
          V.PYDE.VLPP.SQEVDWEVE..AVVIGKKGKHIKATDAMAHV.GFTVAH.VSA.DWQMR.NGKQ.L.GK
Retrocopy VEPYDEMVLPPESQEVDWEVE<AAVVIGKKGKHIKATDAMAHVTGFTVAHNVSAQDWQMRHNGKQ*LVGK

Parental  TFDTFCPLGPALVTKDSVADPHNLKICCRVNGEVVQSSNTNQMVFKTEDLIAWVSQFVTFYPGDVILTGT
          TFDTFCPLGPALVT.DSVAD.H.LKICC.VNGEVVQS.NTNQMV.KTE..IAWV.QFVTF.PGDVILTGT
Retrocopy TFDTFCPLGPALVTNDSVADAHILKICCQVNGEVVQSNNTNQMVVKTEERIAWVFQFVTFCPGDVILTGT

Parental  PPGVGVFRKPPVFLKKGDEVQCEIEELGVIINKVV
          .PGV.VFRKPPVFLKKGDEVQCEIEELGVII.KVV
Retrocopy SPGVSVFRKPPVFLKKGDEVQCEIEELGVIISKVV

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_903 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	ENSCJAG00000018863	1 retrocopy	retro_cjac_3222,
Homo sapiens	ENSG00000144199	1 retrocopy	retro_hsap_1025,
Gorilla gorilla	ENSGGOG00000016246	1 retrocopy	retro_ggor_810,
Macaca mulatta	ENSMMUG00000012859	1 retrocopy	retro_mmul_818,
Nomascus leucogenys	ENSNLEG00000000008	1 retrocopy	retro_nleu_903 ,
Pongo abelii	ENSPPYG00000012057	1 retrocopy	retro_pabe_860,
Pan troglodytes	ENSPTRG00000012214	1 retrocopy	retro_ptro_700,