RetrogeneDB ID: retro_nleu_823

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397274.1:6133554..6134228(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C9ORF78
• Ensembl ID: ENSNLEG00000017658
• Aliases: None
• Description: None

Sequence

>retro_nleu_823
ATGCTGGTCACCAGGAAGACTTTCTGTTGGCACTGGGATGAATGAGAGTCAGAGGAAGATGAAGATGATGCAGAGGAGGT
TCAATTAAAACTGGAATAGACCAGAGAAGTACATAATATAAGGAAGAGATTCAACGAGTGCTGTGGCCCTGCTGTTGGGA
AAGAAGTTACAAGAAAAGACCACTCAAATCCCTTTCAGATGAAGACAGGTGATGTGGATATGAAGAAACTGAAGGAAAAG
AGCAAAGATAAAATCAGTATAGAGGAAGACTTTCACTTGGGGACATCATTTTCTGCAGAAACAAACTGAAGGGATGAGGA
TGCAGACATGATGAAGTACACTGAGACAGAGCTAAAGAAGAGGAAAGGGATCGTGGAACATGAGGAACAGAAAGTCAAGC
CAAGGAATGCAGAGGATTGTCTTTATGAACTTCCAGAAAACATCCACATTTCCTCAGCAAAGAAGAACAAGAAGATGTTT
TCCAACCAGATGCTGAGTGGCATTTCTGAGTTGGACCTTGGCATCAATGCTAGATAAAAACTATCATTTCTTCAGAGGAT
GCCAAGGTCCATCTGCTGGCAGAGTAGCAGAATAAGAAAAAAGACAGTAAGCTATCCTTCATGCCTACCAACATGGCTGT
GAATTGTGTCTTTACTACCCAACAGAGACATGAT

Alignment

ORF - retro_nleu_823 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.39 %
• Parental protein coverage: 79.58 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MPVVRKIFRRRRGDSESEEDEQDSEEVRLKLEETREVQNLRKRPNGVSAVALLVGEKV-QEETTLVDDPF
          M.V.RK.F.......ESEEDE.D.EEV.LKLE.TREV.N.RKR.N.....A..VG..V.QE.TT....PF
Retrocopy MLVTRKTFCWHWDE*ESEEDEDDAEEVQLKLE*TREVHNIRKRFNECCGPA--VGKEV>QEKTTQI--PF

Parental  -QMKTGGMVDMKKLKERGKDKISEEEDLHLGTSFSAETNRRDEDADMMKYIETELKKRKGIVEHEEQKVK
          .QMKTG..VDMKKLKE..KDKIS.EED.HLGTSFSAETN.RDEDADMMKY.ETELKKRKGIVEHEEQKVK
Retrocopy <QMKTGD-VDMKKLKEKSKDKISIEEDFHLGTSFSAETN*RDEDADMMKYTETELKKRKGIVEHEEQKVK

Parental  PKNAEDCLYELPENIRVSSAKKTEEMLSNQMLSGIPEVDLGIDAK-IKNIISTEDAKARLLAEQQNKKKD
          P.NAEDCLYELPENI..SSAKK...M.SNQMLSGI.E.DLGI.A..IK.IIS.EDAK..LLAE.QNKKKD
Retrocopy PRNAEDCLYELPENIHISSAKKNKKMFSNQMLSGISELDLGINAR<IKTIISSEDAKVHLLAE*QNKKKD

Parental  SETSFVPTNMAVNYVQHNRFYHE
          S..SF.PTNMAVN.V......H.
Retrocopy SKLSFMPTNMAVNCVFTTQQRHD

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_823 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 14 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000019979	1 retrocopy	retro_cfam_116,
Choloepus hoffmanni	ENSCHOG00000013895	3 retrocopies	retro_chof_1103, retro_chof_1747, retro_chof_978,
Callithrix jacchus	ENSCJAG00000020318	3 retrocopies	retro_cjac_1757, retro_cjac_2299, retro_cjac_2778,
Dasypus novemcinctus	ENSDNOG00000019214	1 retrocopy	retro_dnov_1540,
Homo sapiens	ENSG00000136819	3 retrocopies	retro_hsap_2872, retro_hsap_2913, retro_hsap_320,
Gorilla gorilla	ENSGGOG00000013358	1 retrocopy	retro_ggor_1990,
Macropus eugenii	ENSMEUG00000010524	3 retrocopies	retro_meug_1046, retro_meug_1241, retro_meug_508,
Macaca mulatta	ENSMMUG00000003795	2 retrocopies	retro_mmul_1460, retro_mmul_1870,
Monodelphis domestica	ENSMODG00000006832	1 retrocopy	retro_mdom_518,
Nomascus leucogenys	ENSNLEG00000017658	3 retrocopies	retro_nleu_1763, retro_nleu_614, retro_nleu_823 ,
Otolemur garnettii	ENSOGAG00000009770	1 retrocopy	retro_ogar_1015,
Pongo abelii	ENSPPYG00000019685	1 retrocopy	retro_pabe_2426,
Pan troglodytes	ENSPTRG00000021465	3 retrocopies	retro_ptro_1943, retro_ptro_1969, retro_ptro_258,
Sarcophilus harrisii	ENSSHAG00000012313	1 retrocopy	retro_shar_746,