RetrogeneDB ID: retro_nleu_1990

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397321.1:5495611..5496126(+)
• Located in intron of: ENSNLEG00000002210

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMA1
• Ensembl ID: ENSNLEG00000017705
• Aliases: None
• Description: proteasome (prosome, macropain) subunit, alpha type, 1 [Source:HGNC Symbol;Acc:9530]

Sequence

>retro_nleu_1990
TTTGGAAACCAGTATGACAATGATATCATTGTCTGGAGCAGGATTCATCAAACTGAATATGCAATGGAAGCTGTTAAACA
AGGTTCAGCCACAGTTGGTCTGAAATCAAAAATCCATGCAGTATTGGTTGCATTGAAAAGGGCACCATTGGAGCTTGCAG
CTTATCAGAAAAAAATTATCCATGTTGACAACCATATTGGTATCTCAATTGCAGGGCTTACTGATGATGGTAGACTGTTA
TGTAATTTTATGTGCCAGAAGTGTTTTGATTCCAGATTTGTATCTGATAGACTACTTCCTGTGTCTTCTCTTGTATCTCT
AATTGGAAGCAAGACCCAAATATCAACACAACAATATAGCTGGAGACCATATGGTGTTAGGCTACTTATTGGTGGTTATA
ATGATATGGGCCTCACATTTTCCAAACCTGGTCATCTGCTGACTATTTTGACTACAGAGCTATGTCCACTGGGGCCCATT
CTCAGTCAGCTCGTACTTACTTGGAGAGACATGTC

Alignment

ORF - retro_nleu_1990 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.11 %
• Parental protein coverage: 63.87 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FRNQYDNDVTVWSPQGRIHQIEYAMEAVKQGSATVGLKSKTHAVLVALKRAQSELAAHQKKILHVDNHIG
          F.NQYDND..VWS...RIHQ.EYAMEAVKQGSATVGLKSK.HAVLVALKRA..ELAA.QKKI.HVDNHIG
Retrocopy FGNQYDNDIIVWS---RIHQTEYAMEAVKQGSATVGLKSKIHAVLVALKRAPLELAAYQKKIIHVDNHIG

Parental  ISIAGLTADARLLCNFMRQECLDSRFVFDRPLPVSRLVSLIGSKTQIPTQRYGRRPYGVGLLIAGYDDM-
          ISIAGLT.D.RLLCNFM.Q.C.DSRFV.DR.LPVS.LVSLIGSKTQI.TQ.Y..RPYGV.LLI.GY.DM.
Retrocopy ISIAGLTDDGRLLCNFMCQKCFDSRFVSDRLLPVSSLVSLIGSKTQISTQQYSWRPYGVRLLIGGYNDM<

Parental  GPHIFQTCPSANYFDCRAMSIGARSQSARTYLERHM
          GPHIFQT..SA.YFD.RAMS.GA.SQSARTYLERH.
Retrocopy GPHIFQTWSSADYFDYRAMSTGAHSQSARTYLERHV

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_1990 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 18 parental genes, and 40 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002440	2 retrocopies	retro_amel_1733, retro_amel_1903,
Choloepus hoffmanni	ENSCHOG00000005395	11 retrocopies	retro_chof_155, retro_chof_1844, retro_chof_1991, retro_chof_2376, retro_chof_2626, retro_chof_267, retro_chof_2712, retro_chof_459, retro_chof_519, retro_chof_719, retro_chof_77,
Equus caballus	ENSECAG00000024086	1 retrocopy	retro_ecab_1078,
Felis catus	ENSFCAG00000011381	1 retrocopy	retro_fcat_972,
Homo sapiens	ENSG00000129084	1 retrocopy	retro_hsap_4720,
Gorilla gorilla	ENSGGOG00000001416	1 retrocopy	retro_ggor_2933,
Macropus eugenii	ENSMEUG00000011112	1 retrocopy	retro_meug_71,
Myotis lucifugus	ENSMLUG00000009251	4 retrocopies	retro_mluc_2444, retro_mluc_2445, retro_mluc_2463, retro_mluc_2515,
Macaca mulatta	ENSMMUG00000016446	1 retrocopy	retro_mmul_2509,
Mustela putorius furo	ENSMPUG00000013199	4 retrocopies	retro_mputfur_1243, retro_mputfur_224, retro_mputfur_338, retro_mputfur_825,
Mus musculus	ENSMUSG00000030751	1 retrocopy	retro_mmus_831,
Nomascus leucogenys	ENSNLEG00000017705	1 retrocopy	retro_nleu_1990 ,
Ochotona princeps	ENSOPRG00000013677	1 retrocopy	retro_opri_370,
Pan troglodytes	ENSPTRG00000003385	1 retrocopy	retro_ptro_3137,
Sarcophilus harrisii	ENSSHAG00000015626	1 retrocopy	retro_shar_217,
Ictidomys tridecemlineatus	ENSSTOG00000006270	2 retrocopies	retro_itri_1470, retro_itri_987,
Tupaia belangeri	ENSTBEG00000012037	3 retrocopies	retro_tbel_2629, retro_tbel_323, retro_tbel_982,
Vicugna pacos	ENSVPAG00000008820	3 retrocopies	retro_vpac_344, retro_vpac_648, retro_vpac_82,