RetrogeneDB ID: retro_nleu_2025

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397323.1:3299591..3300907(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TAF4B
• Ensembl ID: ENSNLEG00000006545
• Aliases: None
• Description: TAF4b RNA polymerase II, TATA box binding protein (TBP)-associated factor, 105kDa [Source:HGNC Symbol;Acc:11538]

Sequence

>retro_nleu_2025
ACAGTTGTGTAGTCTGTTTTGCTTCAGACTTCAAAACCACTTGTGACATCTGTACCAAACACAGTGACAATGGTCTCACT
GCAACCTGAAAAGCCAGTTGTCCCTGGAACAGCAGTAACACTGTCCCTTCCAACAGTAACTTTTGAAGAATCTTCAGGTG
CAGCTATTTGTCTTCCATCTGTGAAACTTTTTGTTACATCTACTGGGACCACATCTGACAAGCCTGTTATTGGCACTCCA
ATTCAAATCAAACTTGCCCAGCCGGGCCCTGTCCTTTCACAACCAGCTGGGATTCCATAGGCAGTTAAAGTCAAGCAACT
AGTAGTTCAGCAGGCTTCAGGAGGCAATGAAAAACGGGTGGCCACACTTACACATTCCTCAGCATTGACCATTCAGAAAT
CTGGATAGAAGACGATGCCAGTGAACACCATAATACCTACCAGTCAGTTTCTTCCATCTTCCATTCTAAAGCAAGTTACT
CTGCCTGGAAATAAAATTCTGTCGCTTCAAGCATCTTCTACTCAAAAAAATAAAATAAAAGAGAATGGAACAATATGCTT
CAGGGATGAAGATGACATCAATGATGTGACTTCTATGGCAGGGGTCAACCTTAATGAAGAAAATGCCTGTATCTTAGCAA
CAAACTCTGAATTGGTTGGCACACTCATTCAGTCATGTAAGATGAACGATTTCTTTTTATTGGAGCTCTACAAAAGAGAA
TTTTAGACATTGGTAAAAAGCATGACATTACAGAACTTAACTCTGATGCTGTGAACTTGATCACCCATGCAACCCAGGAA
CAATTATGAGGCCTTCTAGAAAAACTGACTGCAATTGCTCAGCATTGAATGACTACTTACAAGGCAAGTGAAAATTACAT
CCTGTATAGTGATACCAGGTCACACCTCAAATTTCTTGAAAAGCTGGATCAATTGGAGAAGCAGAGAAAGGATTTAAAAG
AAAGAGAAATGTTACTTAAGGCAGCCAGGAGTCATTCTAATAAAGAAGTTCCAGACCAGCAGAGATTAAAGCAGAAAGCC
AATGAGTTACAGCAACTGGAACTTGAACAGATACAGCATAGAGATGCTAATCTCACAGCTCTTGCAGCTATTCGACCAAG
GAAGAAGAGACCACTAGAACTTGGAAGTGAGGGCTTAAAAGACAACCTTCTTGCTTCTGGGACATCCAGCCTGACAGTCA
GCAAACAGTTGCTTCGTCCAAAAATCACAAGAATCTGCCTCAGGGACTTGATATTTTGTATGGAACAGGAACAGGAGATG
AAATATTCTCGAGCTCTATACCTGGCCCTTCTGAAG

Alignment

ORF - retro_nleu_2025 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.91 %
• Parental protein coverage: 50.93 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TTAGTVLLQTSKPLVTSVANTVTTVSLQPEKPVVSGTAVTLSLPAVTFGETSGAAVCLPSVKPVVTSAGT
          T....VLLQTSKPLVTSV.NTVT.VSLQPEKPVV.GTAVTLSLP.VTF.E.SGAA.CLPSVK..VTS.GT
Retrocopy TVV*SVLLQTSKPLVTSVPNTVTMVSLQPEKPVVPGTAVTLSLPTVTFEESSGAAICLPSVKLFVTSTGT

Parental  TSDKPVIGTPIQIKLAQPGPVLSQPAGIPQAVQVKQLVVQQPSGGNEKQVTTISHSSALTIQKCGQKTMS
          TSDKPVIGTPIQIKLAQPGPVLSQPAGIP.AV.VKQLVVQQ.SGGNEK.V.T..HSSALTIQK.G.KTM.
Retrocopy TSDKPVIGTPIQIKLAQPGPVLSQPAGIP*AVKVKQLVVQQASGGNEKRVATLTHSSALTIQKSG*KTMP

Parental  VNTVIPTSQFPPASILKQITLPGNKILSLQASPTQKNKIKENGTSCFRDEDDINDVTSMAGVNLNEENAC
          VNT.IPTSQF.P.SILKQ.TLPGNKILSLQAS.T......ENGT.CFRDEDDINDVTSMAGVNLNEENAC
Retrocopy VNTIIPTSQFLPSSILKQVTLPGNKILSLQASSTXXXXXXENGTICFRDEDDINDVTSMAGVNLNEENAC

Parental  ILATNSELVGTLIQSCK-DEPFLFIGALQKRILDIGKKHDITELNSDAVNLISQATQERLRGLLEKLTTI
          ILATNSELVGTLIQSCK.DE.FLFIGALQKRILDIGKKHDITELNSDAVNLI..ATQE.L.GLLEKLT.I
Retrocopy ILATNSELVGTLIQSCK<DERFLFIGALQKRILDIGKKHDITELNSDAVNLITHATQEQL*GLLEKLTAI

Parental  AQHRMTTYKASENYILCSDTRSQLKFLEKLDQLEKQRKDLEEREMLLKAAKSRSNKEDPEQLRLKQKAKE
          AQH.MTTYKASENYIL.SDTRS.LKFLEKLDQLEKQRKDL.EREMLLKAA.S.SNKE.P.Q.RLKQKA.E
Retrocopy AQH*MTTYKASENYILYSDTRSHLKFLEKLDQLEKQRKDLKEREMLLKAARSHSNKEVPDQQRLKQKANE

Parental  LQQLELAQIQHRDANLTALAAIGPRKKRPLESGIEGLKDNLLASGTSSLTATKQLHRPRITRICLRDLIF
          LQQLEL.QIQHRDANLTALAAI.PRKKRPLE.G.EGLKDNLLASGTSSLT..KQL.RP.ITRICLRDLIF
Retrocopy LQQLELEQIQHRDANLTALAAIRPRKKRPLELGSEGLKDNLLASGTSSLTVSKQLLRPKITRICLRDLIF

Parental  CMEQEREMKYSRALYLALLK
          CMEQE.EMKYSRALYLALLK
Retrocopy CMEQEQEMKYSRALYLALLK

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_2025 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Nomascus leucogenys	ENSNLEG00000006545	1 retrocopy	retro_nleu_2025 ,