RetrogeneDB ID: retro_nleu_2582

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397376.1:963233..963768(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UCHL1
• Ensembl ID: ENSNLEG00000017176
• Aliases: None
• Description: ubiquitin carboxyl-terminal esterase L1 (ubiquitin thiolesterase) [Source:HGNC Symbol;Acc:12513]

Sequence

>retro_nleu_2582
TGCCAGCAGCTGCCTGCTGTTTGTATTAGATCCCCACGCCAGAACTTCAGGAAAAAGTTGATTGAAGAACTGAAGAGACA
AGAGGTAGTCCTAAAGGGTACCTCATGAAGCAGAGCATTGGGAACTTCTGTCACACAATTAGACTTATATGAGCAGTGGC
CAATAATCAAGACAAACCAAAAATCTGAGGCAGGTCAATCCTAAAATATTTTATTTCTGACGTGGAGAAAAATATCACTC
GAAGACAGCACAAATCCTTTGAAAAGAATAAGGCCTTTCAGGCAGTTTATGATGCTATCACACAGCAAGGCCAGTGTCCG
GTACATGACAAACGAATTTTTGTTTTATTCTGTTTAGCAACGTGGATGGCCACCTCTCTGAACTTGGTGGATGAGTGCCT
TTCCCAGTGAACTATGGTGCCAGTTCAGAGGACTCACTGCTGCAGGATTATAGCGATTAGGCTGCCAAGGTCTGTAGAAA
ATTTACCGAGGAGGAAGGAGAGAAAGGCAGCCTCTCTGCTGTAACCCTCTCCAAG

Alignment

ORF - retro_nleu_2582 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.56 %
• Parental protein coverage: 78.48 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  CALLLLFPLTAQHENFRKKQIEELKGQEV-SPKVYFMKQTIGNSCGTIGLIHAVANNQDKLGFEDGSVLK
          C..L..........NFRKK.IEELK.QEV.SPK.Y.MKQ.IGN.C.TI.LI.AVANNQDK......S.LK
Retrocopy CQQLPAVCIRSPRQNFRKKLIEELKRQEV<SPKGYLMKQSIGNFCHTIRLI*AVANNQDKPKI*GRSILK

Parental  QFLSETEKMSPEDRAKCFEKNEAIQAAHDAVAQEGQCRVDDK-VNFHFILFNNVDGHLYELDGRMPFPVN
          .F.S..EK.......K.FEKN.A.QA..DA..Q.GQC.V.DK..NF.FILF.NVDGHL.EL.G..PFPVN
Retrocopy YFISDVEKNITRRQHKSFEKNKAFQAVYDAITQQGQCPVHDK<TNFCFILFSNVDGHLSELGG*VPFPVN

Parental  HGASSEDTLLKD----AAKVCREFTEREQGEVRFSAVALCK
          .GASSED.LL.D....AAKVCR.FTE.E......SAV.L.K
Retrocopy YGASSEDSLLQDYSD*AAKVCRKFTEEEGEKGSLSAVTLSK

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_2582 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 11 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019346	1 retrocopy	retro_cjac_365,
Erinaceus europaeus	ENSEEUG00000002185	3 retrocopies	retro_eeur_150, retro_eeur_573, retro_eeur_598,
Echinops telfairi	ENSETEG00000012347	1 retrocopy	retro_etel_44,
Homo sapiens	ENSG00000154277	2 retrocopies	retro_hsap_781, retro_hsap_782,
Gorilla gorilla	ENSGGOG00000008809	1 retrocopy	retro_ggor_648,
Macropus eugenii	ENSMEUG00000013774	1 retrocopy	retro_meug_8,
Myotis lucifugus	ENSMLUG00000010138	2 retrocopies	retro_mluc_1216, retro_mluc_2113,
Nomascus leucogenys	ENSNLEG00000017176	2 retrocopies	retro_nleu_2582 , retro_nleu_2583,
Oryctolagus cuniculus	ENSOCUG00000001353	1 retrocopy	retro_ocun_309,
Pan troglodytes	ENSPTRG00000016009	2 retrocopies	retro_ptro_3028, retro_ptro_3029,
Tarsius syrichta	ENSTSYG00000008305	1 retrocopy	retro_tsyr_1191,