RetrogeneDB ID: retro_nleu_2947

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397501.1:979629..980093(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMB7
• Ensembl ID: ENSNLEG00000017268
• Aliases: None
• Description: Proteasome subunit beta type [Source:UniProtKB/TrEMBL;Acc:G1S646]

Sequence

>retro_nleu_2947
TCCAACTTGGAGCGCCACTCCATCTCTAGTGGCCATCTTCCTGAGTTGTCATGGCCAACCAGATGCTGAAGCAAATGCTT
TTAAAGTATCAAGGTTACATTGGTGCAGCCCTAGTTTTAAGGAGATTGGGAGTTTTTACCGGGCCTCACCTCTACAGCAT
CTATCCTCATGAATCAACTGATAACTAGCCTCATCACCATGGATCCTCAGCAGCAAATGCTGTATTTGAAGATATTCTAG
GCCAGATATGGGGGAAGGGGAAGCAAAGGAGATGGTAAGTGAAGCCACTGCAGCTGGCTTCTTCAACACCCTGAGCTCTG
GAAGCCACACTGATCTCAGCATTATAGGCAAGAGCAAGGTAGATTTTCTTGGCCCATTCACAGTGCCCAAAAAGAAGGGG
ACAAGATTGGCCAGGTACAGGTGTGAGAAAAGGGACCACTGCAGTCCTCACGAAAGAAGCCACT

Alignment

ORF - retro_nleu_2947 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.7 %
• Parental protein coverage: 56.68 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SNLELHSLSTGRLPR-VVTANRMLKQMLFRYQGYIGAALVLGGVDV-TGPHLYSIYPHGSTDKLPYVTMG
          SNLE.HS.S.G.LP..VV.AN.MLKQML..YQGYIGAALVL....V.TGPHLYSIYPH.STD..P.....
Retrocopy SNLERHSISSGHLPE<VVMANQMLKQMLLKYQGYIGAALVLRRLGVFTGPHLYSIYPHESTDN*PH---H

Parental  SGSLAAMAVFEDKF-RPDMEEEEAKKLVSEAIAAGIFNDLGSGSNIDLCVISKNKLDFLRPYTVPNKKGT
          .GS.AA.AVFED...RPDM.E.EAK..VSEA.AAG.FN.L.SGS..DL..I.K.K.DFL.P.TVP.KKGT
Retrocopy HGSSAANAVFEDIL<RPDMGEGEAKEMVSEATAAGFFNTLSSGSHTDLSIIGKSKVDFLGPFTVPKKKGT

Parental  RLGRYRCE-KGTTAVLTEKIT
          RL.RYRCE.KGTTAVLT...T
Retrocopy RLARYRCE>KGTTAVLTKEAT

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_2947 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 12 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003067	2 retrocopies	retro_btau_1722, retro_btau_983,
Echinops telfairi	ENSETEG00000005432	2 retrocopies	retro_etel_2093, retro_etel_231,
Homo sapiens	ENSG00000136930	1 retrocopy	retro_hsap_1303,
Gorilla gorilla	ENSGGOG00000012164	1 retrocopy	retro_ggor_1019,
Nomascus leucogenys	ENSNLEG00000017268	1 retrocopy	retro_nleu_2947 ,
Otolemur garnettii	ENSOGAG00000003513	1 retrocopy	retro_ogar_2828,
Pongo abelii	ENSPPYG00000019596	1 retrocopy	retro_pabe_1092,
Pan troglodytes	ENSPTRG00000021354	1 retrocopy	retro_ptro_893,
Pteropus vampyrus	ENSPVAG00000000204	2 retrocopies	retro_pvam_1271, retro_pvam_866,
Rattus norvegicus	ENSRNOG00000011732	3 retrocopies	retro_rnor_1581, retro_rnor_1582, retro_rnor_2469,
Sorex araneus	ENSSARG00000009395	1 retrocopy	retro_sara_532,
Tupaia belangeri	ENSTBEG00000009196	2 retrocopies	retro_tbel_2889, retro_tbel_751,