RetrogeneDB ID: retro_nleu_1201

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397284.1:13740316..13741067(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CS
• Ensembl ID: ENSNLEG00000017514
• Aliases: None
• Description: Citrate synthase [Source:UniProtKB/TrEMBL;Acc:G1S6X1]

Sequence

>retro_nleu_1201
GATGAGGGTGTCCGTTTCCGAGGCTTCGGTATCCCTGAATACCAAAAACTGCTACCCAAGGCTAAGGGTGGGGAAGAACC
CCTACCCAGGGGCTTATTTCGGCTGCTGGTAACTGGACAGATCCCAAGAGAGGAACAGGTGTCTTGGCTCTCAAGAGAGT
GGGCAAAGAGGGCAGCTCTACCTTCCCATGTGGTCACCATGCTGGACAACTTTCCCACCAATCCACACCCGTGTCTGAGC
TCAGTGCAGCCTGGCAGCCCTAAACAACTTTGCCTGAGCATATCCAGAGGGTGCCAGTCAAACCAAGTACTGGGAGTTGA
TTTATGAAGACCATGCGTATCTAATCACAAAGCTACCTTGTATTGCAGAAAAGGTCTACCGAAATATCTGTGGAGAGGGC
AGTGGTATTGGGGCCACTGACTCTGAGCTGGACCGGTCCCACAGTTTCACCAACATGTTAGGCTATACTGATGCTCAGTT
CACTGAGCTCATGCACCTGTAGCTCACCATCCACAGTGACCATGAGCACAGCAATATAAGTGCTCATACCAGCCATTTGG
TGGGCAGTGCTCTTTCAGACCCTTCCCTGTCCTTTGCAGCAGCCATGAACGGGCTGGCAGGTCCTCTACATGGACTGGCA
AATCAGGAAGTGCTTGTCTGGCTAACACAACTACAGAAGGAAGTTGGCAAATATGTGTCAGATGAGAAGTTACGAGACTA
CATTCAACTCGAGATGGGTTGTTCCAGGTTA

Alignment

ORF - retro_nleu_1201 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.52 %
• Parental protein coverage: 57.21 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DMGIRFRGFSIPECQKLLPKAKGGEEPLPEGLFWLLVTGHIPTEEQVSWLSKEWAKRAALPSHVVTMLDN
          D.G.RFRGF.IPE.QKLLPKAKGGEEPLP.GLF.LLVTG.IP.EEQVSWLS.EWAKRAALPSHVVTMLDN
Retrocopy DEGVRFRGFGIPEYQKLLPKAKGGEEPLPRGLFRLLVTGQIPREEQVSWLSREWAKRAALPSHVVTMLDN

Parental  FPTNLHP-MSQLSAA-VTALNSESNFARAYAQGISRTKYWELIYEDSMDLIAKLPCVAAKIYRNLYREGS
          FPTN.HP..S.LSAA...ALN...NFA.AY..G.S.TKYWELIYED...LI.KLPC.A.K.YRN...EGS
Retrocopy FPTNPHP<VSELSAA<LAALN---NFA*AYPEGASQTKYWELIYEDHAYLITKLPCIAEKVYRNICGEGS

Parental  SIGAIDSNLDWSHNFTNMLGYTDHQFTELMRLYLTIHSDHEGGNVSAHTSHLVGSALSDPYLSFAAAMNG
          .IGA.DS.LD.SH.FTNMLGYTD.QFTELM.L.LTIHSDHE..N.SAHTSHLVGSALSDP.LSFAAAMNG
Retrocopy GIGATDSELDRSHSFTNMLGYTDAQFTELMHL*LTIHSDHEHSNISAHTSHLVGSALSDPSLSFAAAMNG

Parental  LAGPLHGLANQEVLVWLTQLQKEVGKDVSDEKLRDYIWNTLNSGRV
          LAGPLHGLANQEVLVWLTQLQKEVGK.VSDEKLRDYI.......R.
Retrocopy LAGPLHGLANQEVLVWLTQLQKEVGKYVSDEKLRDYIQLEMGCSRL

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_1201 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 21 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004371	1 retrocopy	retro_btau_386,
Canis familiaris	ENSCAFG00000000115	1 retrocopy	retro_cfam_765,
Choloepus hoffmanni	ENSCHOG00000000397	1 retrocopy	retro_chof_1803,
Callithrix jacchus	ENSCJAG00000011275	1 retrocopy	retro_cjac_2031,
Dasypus novemcinctus	ENSDNOG00000010907	2 retrocopies	retro_dnov_205, retro_dnov_468,
Echinops telfairi	ENSETEG00000012035	1 retrocopy	retro_etel_584,
Homo sapiens	ENSG00000062485	2 retrocopies	retro_hsap_1972, retro_hsap_3621,
Gorilla gorilla	ENSGGOG00000009096	2 retrocopies	retro_ggor_1432, retro_ggor_2445,
Macropus eugenii	ENSMEUG00000005657	2 retrocopies	retro_meug_1078, retro_meug_1304,
Microcebus murinus	ENSMICG00000017659	2 retrocopies	retro_mmur_1322, retro_mmur_394,
Macaca mulatta	ENSMMUG00000002483	2 retrocopies	retro_mmul_1502, retro_mmul_1840,
Mus musculus	ENSMUSG00000005683	1 retrocopy	retro_mmus_258,
Nomascus leucogenys	ENSNLEG00000017514	2 retrocopies	retro_nleu_1201 , retro_nleu_809,
Oryctolagus cuniculus	ENSOCUG00000007216	1 retrocopy	retro_ocun_1183,
Pongo abelii	ENSPPYG00000004654	1 retrocopy	retro_pabe_2972,
Rattus norvegicus	ENSRNOG00000023520	1 retrocopy	retro_rnor_2518,
Sorex araneus	ENSSARG00000010093	2 retrocopies	retro_sara_360, retro_sara_628,
Sus scrofa	ENSSSCG00000021091	1 retrocopy	retro_sscr_321,
Sus scrofa	ENSSSCG00000022858	1 retrocopy	retro_sscr_322,
Tupaia belangeri	ENSTBEG00000006425	1 retrocopy	retro_tbel_4652,
Tarsius syrichta	ENSTSYG00000004483	1 retrocopy	retro_tsyr_1659,